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chemaxon.alchemist.configbuilder Namespace
ConfigBuilderPanel Class
ConfigBuilderPanel Members
ConfigBuilderPanel Constructor
ConfigBuilderPanel Constructor (Object)
ConfigBuilderPanel Constructor (String)
ConfigBuilderPanel Constructor (Object, Object)
ConfigBuilderPanel Constructor (String, Object)
ConfigBuilderPanel Constructor (Object, , )
ConfigBuilderPanel Constructor (String, , )
ConfigBuilderPanel Constructor (Object, Object, , )
ConfigBuilderPanel Constructor (String, Object, , )
ConfigBuilderPanel Fields
PROPERTY_KEY_CONFIGURATION_VALID Field
PROPERTY_KEY_ELEMENT_LIST Field
PROPERTY_KEY_ELEMENT_ORDER Field
ConfigBuilderPanel Methods
__<clinit> Method
addConfigElement Method
addElementPropertyChangeListener Method
addElementPropertyChangeListener Method ()
addElementPropertyChangeListener Method (String, )
clear Method
getConfiguration Method
getDefaultHelpText Method
getLicenseSupport Method
getOpenFileAction Method
getProfile Method
getSaveFileAction Method
getTags Method
isFileSupportEnabled Method
isIgnoreMissingLicense Method
isValidConfiguration Method
readConfiguration Method
readConfiguration Method (Object)
readConfiguration Method (Object, String[])
refreshLicenses Method
removeConfigElement Method
removeConfigElement Method (ConfigElement)
removeConfigElement Method (String)
removeConfigElements Method
removeElementPropertyChangeListener Method
removeElementPropertyChangeListener Method ()
removeElementPropertyChangeListener Method (String, )
setDefaultHelpText Method
setDefaultTag Method
setFileSupportEnabled Method
setIgnoreMissingLicense Method
setLicenseSupport Method
setOpenFileAction Method
setProfile Method
setSaveFileAction Method
updateProfile Method
writeConfiguration Method
ConfigBuilderPanelFactory Class
ConfigBuilderPanelFactory Members
ConfigBuilderPanelFactory Constructor
ConfigBuilderPanelFactory Fields
DEFAULT_STANDARDIZER_ELEMENT_CONFIGURATION_PATH Field
DEFAULT_STRUCTURECHECKER_ELEMENT_CONFIGURATION_PATH Field
ConfigBuilderPanelFactory Methods
createStandardizerPanel Method
createStandardizerPanel Method
createStandardizerPanel Method (Boolean)
createStandardizerPanel Method (Object)
createStandardizerPanel Method (String)
createStandardizerPanel Method (String[])
createStandardizerPanel Method (Object, Boolean)
createStandardizerPanel Method (String, Boolean)
createStandardizerPanel Method (String, Object)
createStandardizerPanel Method (String[], Boolean)
createStandardizerPanel Method (String[], Object)
createStandardizerPanel Method (String, Object, Boolean)
createStandardizerPanel Method (String[], Object, Boolean)
createStructureCheckerPanel Method
createStructureCheckerPanel Method
createStructureCheckerPanel Method (Boolean)
createStructureCheckerPanel Method (Object)
createStructureCheckerPanel Method (String)
createStructureCheckerPanel Method (String[])
createStructureCheckerPanel Method (Object, Boolean)
createStructureCheckerPanel Method (String, Boolean)
createStructureCheckerPanel Method (String, Object)
createStructureCheckerPanel Method (String[], Boolean)
createStructureCheckerPanel Method (String[], Object)
createStructureCheckerPanel Method (String, Object, Boolean)
createStructureCheckerPanel Method (String[], Object, Boolean)
ConfigElement Class
ConfigElement Members
ConfigElement Constructor
ConfigElement Constructor
ConfigElement Constructor (String)
ConfigElement Constructor (String, String)
ConfigElement Constructor (String, String, )
ConfigElement Constructor (String, String, , String)
ConfigElement Constructor (String, String, , String, String)
ConfigElement Constructor (String, String, , , String, String)
ConfigElement Fields
FLAVOR Field
PROPERTY_KEY_DEFAULTICON Field
PROPERTY_KEY_DISABLEDICON Field
PROPERTY_KEY_EDITABLE Field
PROPERTY_KEY_HELPTEXT Field
PROPERTY_KEY_ICON Field
PROPERTY_KEY_ID Field
PROPERTY_KEY_NAME Field
PROPERTY_KEY_TOOLTIP Field
PROPERTY_KEY_VALID Field
ConfigElement Methods
__<clinit> Method
<bridge>clone Method
addGroup Method
addPropertyChangeListener Method
addPropertyChangeListener Method ()
addPropertyChangeListener Method (String, )
addTag Method
clone Method
cloneElement Method
getDefaultIcon Method
getDisabledIcon Method
getGroups Method
getHelpText Method
getIcon Method
getId Method
getLicenseName Method
getName Method
getPropertyChangeSupport Method
getTags Method
getTooltip Method
getTransferData Method
getTransferDataFlavors Method
hasGroup Method
hasGroups Method
hasTag Method
hasTags Method
Implicit Operator
isDataFlavorSupported Method
isDefault Method
isEditable Method
isLicensed Method
isValid Method
removePropertyChangeListener Method
removePropertyChangeListener Method ()
removePropertyChangeListener Method (String, )
setDefaultIcon Method
setDisabledIcon Method
setEditable Method
setHelpText Method
setId Method
setLicensed Method
setLicenseName Method
setName Method
setPropertyChangeSupport Method
setTooltip Method
store Method
ConfigElementEditor Interface
ConfigElementEditor Members
ConfigElementEditor Methods
getEditorComponent Method
getEditorValue Method
ConfigElementFactory Class
ConfigElementFactory Members
ConfigElementFactory Constructor
ConfigElementFactory Constructor (Object)
ConfigElementFactory Constructor (String)
ConfigElementFactory Constructor (Object, Object)
ConfigElementFactory Constructor (String, Object)
ConfigElementFactory Methods
create Method
create Method ()
create Method (Object)
create Method (String)
chemaxon.alchemist.markushview Namespace
CompactMarkushViewer Class
CompactMarkushViewer Members
CompactMarkushViewer Constructor
CompactMarkushViewer Methods
__<clinit> Method
getMarkushViewer Method
setMolecule Method
setMolecule Method (Molecule)
setMolecule Method ()
chemaxon.calculations Namespace
ElementalAnalyser Class
ElementalAnalyser Members
ElementalAnalyser Constructor
ElementalAnalyser Methods
atomCount Method
atomCount Method
atomCount Method (Int32)
atomCount Method (Int32, Int32)
composition Method
dotDisconnectedFormula Method
dotDisconnectedIsotopeFormula Method
dotDisconnectedIsotopeFormula Method
dotDisconnectedIsotopeFormula Method (Boolean)
exactMass Method
exactMassPrecision Method
formula Method
formula Method
formula Method (Int32)
getSmolecule Method
isotopeComposition Method
isotopeComposition Method (Int32)
isotopeComposition Method (Int32, Boolean)
isotopeFormula Method
isotopeFormula Method
isotopeFormula Method (Boolean)
mass Method
massPrecision Method
setMolecule Method
setMolecule Method (MoleculeGraph)
setMolecule Method (Smolecule)
setMolecule Method (String)
TopologyAnalyser Class
TopologyAnalyser Members
TopologyAnalyser Constructor
TopologyAnalyser Methods
aliphaticAtomCount Method
aliphaticBondCount Method
aliphaticRingCount Method
aliphaticRingCount Method
aliphaticRingCount Method (Int32)
aliphaticRings Method
aliphaticRings Method
aliphaticRings Method (Int32)
aromaticAtomCount Method
aromaticBondCount Method
aromaticRingCount Method
aromaticRingCount Method
aromaticRingCount Method (Int32)
aromaticRings Method
aromaticRings Method
aromaticRings Method (Int32)
asymmetricAtomCount Method
asymmetricAtoms Method
atomCount Method
balabanIndex Method
bondCount Method
bondType Method
carboaliphaticRingCount Method
carboaromaticRingCount Method
carboRingCount Method
carboRingCount Method
carboRingCount Method (Int32)
carboRings Method
carboRings Method
carboRings Method (Int32)
chainAtomCount Method
chainBondCount Method
chiralCenterCount Method
chiralCenters Method
cyclomaticNumber Method
distanceCount Method
distanceDegree Method
eccentricity Method
fragmentCount Method
fusedAliphaticRingCount Method
fusedAliphaticRingCount Method
fusedAliphaticRingCount Method (Int32)
fusedAliphaticRings Method
fusedAliphaticRings Method
fusedAliphaticRings Method (Int32)
fusedAromaticRingCount Method
fusedAromaticRingCount Method
fusedAromaticRingCount Method (Int32)
fusedAromaticRings Method
fusedAromaticRings Method
fusedAromaticRings Method (Int32)
fusedRingCount Method
getMolecule Method
graphInvariant Method
hararyIndex Method
heteroaliphaticRingCount Method
heteroaliphaticRingCount Method
heteroaliphaticRingCount Method (Int32)
heteroaliphaticRings Method
heteroaliphaticRings Method
heteroaliphaticRings Method (Int32)
heteroaromaticRingCount Method
heteroaromaticRingCount Method
heteroaromaticRingCount Method (Int32)
heteroaromaticRings Method
heteroaromaticRings Method
heteroaromaticRings Method (Int32)
heteroRingCount Method
heteroRingCount Method
heteroRingCount Method (Int32)
heteroRings Method
heteroRings Method
heteroRings Method (Int32)
hyperWienerIndex Method
isAliphaticAtom Method
isAromaticAtom Method
isAsymmetricAtom Method
isBarredAtom Method
isChainAtom Method
isChainBond Method
isChiral Method
isChiralCenter Method
isConnected Method
isConnected Method
isConnected Method (Int32, Int32)
isHinderedBiarylBridgeBond Method
isLicensed Method
isRingAtom Method
isRingBond Method
isRotatableBond Method
largestRing Method
largestRingSize Method
largestRingSizeOfAtom Method
largestRingSystem Method
largestRingSystemSize Method
plattIndex Method
randicIndex Method
ringAtomCount Method
ringBondCount Method
ringCount Method
ringCount Method
ringCount Method (Int32)
ringCountOfAtom Method
rings Method
rings Method
rings Method (Int32)
ringSystemCount Method
ringSystemCount Method
ringSystemCount Method (Int32)
ringSystems Method
ringSystems Method
ringSystems Method (Int32)
rotatableBondCount Method
setLicenseEnvironment Method
setMolecule Method
setMolecule Method (MoleculeGraph)
setMolecule Method (MoleculeGraph, Int32)
shortestPath Method
smallestRing Method
smallestRingSize Method
smallestRingSizeOfAtom Method
smallestRingSystem Method
smallestRingSystemSize Method
stereo Method
stereo Method (Int32)
stereo Method (Int32, Int32)
stereoDoubleBondCount Method
stericEffectIndex Method
szegedIndex Method
wienerIndex Method
wienerPolarity Method
chemaxon.calculations.clean Namespace
Cleaner Class
Cleaner Members
Cleaner Constructor
Cleaner Methods
clean Method
clean Method (MoleculeGraph, Int32, String)
clean Method (MoleculeGraph, Int32, String, Object)
partialClean Method
partialClean Method (Molecule, Molecule[], String)
partialClean Method (MoleculeGraph, MoleculeGraph, Int32[], String)
partialClean Method (MoleculeGraph, Int32, Int32[], String)
chemaxon.calculations.hydrogenize Namespace
Hydrogenize Class
Hydrogenize Members
Hydrogenize Constructor
Hydrogenize Methods
addHAtoms Method
addHAtoms Method (MoleculeGraph)
addHAtoms Method (MoleculeGraph, MolAtom[])
addHAtoms Method (MoleculeGraph, MolAtom[], Int32)
addLonePairs Method
removeHAtoms Method
removeHAtoms Method (MoleculeGraph)
removeHAtoms Method (MoleculeGraph, Int32)
removeHAtoms Method (MoleculeGraph, MolAtom[], Int32)
removeHAtoms Method (MoleculeGraph, MolAtom[], Int32, Boolean)
removeLonePairs Method
chemaxon.calculations.nmr Namespace
NMRCalculator Class
NMRCalculator Members
NMRCalculator Constructor
NMRCalculator Constructor
NMRCalculator Constructor (Object)
NMRCalculator Methods
calculate Method
getFormatter Method
getFrequency Method
getNucleus Method
getProgress Method
getUnit Method
isCoupled Method
isLicensed Method
setCoupled Method
setFrequency Method
setLicenseEnvironment Method
setLogger Method
setMolecule Method
setNucleus Method
setUnit Method
chemaxon.calculations.stereo Namespace
Stereochemistry Class
Stereochemistry Members
Stereochemistry Constructor
Stereochemistry Fields
EVEN Field
ODD Field
Stereochemistry Methods
asymmetricAtomCount Method
asymmetricAtoms Method
chiralCenterCount Method
chiralCenters Method
getEnantiomer Method
getMolecule Method
graphInvariant Method
isAsymmetricAtom Method
isChiral Method
isChiralCenter Method
setMolecule Method
stereo Method
stereo Method (Int32)
stereo Method (Int32, Int32)
stereoDoubleBondCount Method
chemaxon.checkers Namespace
AbbreviatedGroupChecker Class
AbbreviatedGroupChecker Members
AbbreviatedGroupChecker Constructor
AbbreviatedGroupChecker Constructor
AbbreviatedGroupChecker Constructor ()
AbbreviatedGroupChecker Fields
PROPERTY_KEY_CONTRACTED Field
PROPERTY_KEY_EXPANDED Field
PROPERTY_KEY_SEARCH_CONTRACTED Field
PROPERTY_KEY_SEARCH_EXPANDED Field
AbbreviatedGroupChecker Methods
equals Method
hashCode Method
isSearchContracted Method
isSearchExpanded Method
setSearchContracted Method
setSearchExpanded Method
AbstractStructureChecker Class
AbstractStructureChecker Members
AbstractStructureChecker Constructor
AbstractStructureChecker Methods
<bridge>clone Method
addPropertyChangeListener Method
addPropertyChangeListener Method ()
addPropertyChangeListener Method (String, )
check Method
clone Method
cloneItem Method
equals Method
getDescription Method
getDescriptor Method
getEditorClassName Method
getErrorCode Method
getErrorType Method
getHelpText Method
getIcon Method
getLocalMenuName Method
getName Method
hashCode Method
Implicit Operator
isAvailable Method
isLicensed Method
isValid Method
propertyChange Method
removePropertyChangeListener Method
removePropertyChangeListener Method ()
removePropertyChangeListener Method (String, )
setDescription Method
setHelpText Method
setIcon Method
setLicenseEnvironment Method
setLocalMenuName Method
setMoreErrorMessage Method
setName Method
setNoErrorMessage Method
setOneErrorMessage Method
toString Method
AliasChecker Class
AliasChecker Members
AliasChecker Constructor
AromaticityErrorChecker Class
AromaticityErrorChecker Members
AromaticityErrorChecker Constructor
AromaticityErrorChecker Constructor
AromaticityErrorChecker Constructor ()
AromaticityErrorChecker Fields
PROPERTY_KEY_AROM_TYPE Field
PROPERTY_KEY_TYPE Field
AromaticityErrorChecker Methods
equals Method
getAromType Method
getType Method
hashCode Method
setType Method
AtomChecker Class
AtomChecker Members
AtomChecker Constructor
AtomMapChecker Class
AtomMapChecker Members
AtomMapChecker Constructor
AtomQueryPropertyChecker Class
AtomQueryPropertyChecker Members
AtomQueryPropertyChecker Constructor
AtomQueryPropertyChecker Constructor
AtomQueryPropertyChecker Constructor ()
AtomQueryPropertyChecker Fields
PROPERTY_KEY_AROMATCITY Field
PROPERTY_KEY_AROMATICITY_CHECKING Field
PROPERTY_KEY_CONNECTION_COUNT Field
PROPERTY_KEY_CONNECTION_COUNT_CHECKING Field
PROPERTY_KEY_EXPLICIT_CONNECTION_COUNT Field
PROPERTY_KEY_EXPLICIT_CONNECTION_COUNT_CHECKING Field
PROPERTY_KEY_HYDROGEN_COUNT Field
PROPERTY_KEY_HYDROGEN_COUNT_CHECKING Field
PROPERTY_KEY_IMPLICIT_HYDROGEN_COUNT Field
PROPERTY_KEY_IMPLICIT_HYDROGEN_COUNT_CHECKING Field
PROPERTY_KEY_RING_BOND_COUNT Field
PROPERTY_KEY_RING_BOND_COUNT_CHECKING Field
PROPERTY_KEY_RING_COUNT Field
PROPERTY_KEY_RING_COUNT_CHECKING Field
PROPERTY_KEY_SMALLEST_RING_SIZE Field
PROPERTY_KEY_SMALLEST_RING_SIZE_CHECKING Field
PROPERTY_KEY_SUBSTITUTION_COUNT Field
PROPERTY_KEY_SUBSTITUTION_COUNT_CHECKING Field
PROPERTY_KEY_UNSATURATION Field
PROPERTY_KEY_UNSATURATION_CHECKING Field
AtomQueryPropertyChecker Methods
equals Method
hashCode Method
isAromaticityChecking Method
isConnectionCountChecking Method
isExplicitConnectionCountChecking Method
isHydrogenCountChecking Method
isImplicitHydrogenCountChecking Method
isRingBondCountChecking Method
isRingCountChecking Method
isSmallestRingSizeChecking Method
isSubstitutionCountChecking Method
isUnsaturationChecking Method
setAromaticityChecking Method
setConnectionCountChecking Method
setExplicitConnectionCountChecking Method
setHydrogenCountChecking Method
setImplicitHydrogenCountChecking Method
setRingBondCountChecking Method
setRingCountChecking Method
setSmallestRingSizeChecking Method
setSubstitutionCountChecking Method
setUnsaturationChecking Method
toString Method
AtomValueChecker Class
AtomValueChecker Members
AtomValueChecker Constructor
AttachedDataChecker Class
AttachedDataChecker Members
AttachedDataChecker Constructor
BondAngleChecker Class
BondAngleChecker Members
BondAngleChecker Constructor
BondAngleChecker Constructor
BondAngleChecker Constructor (Double)
BondAngleChecker Methods
__<clinit> Method
getRingIndex Method
BondChecker Class
BondChecker Members
BondChecker Constructor
BondLengthChecker Class
BondLengthChecker Members
BondLengthChecker Constructor
BondLengthChecker Constructor
BondLengthChecker Constructor ()
BondLengthChecker Fields
PROPERTY_KEY_DETECT_TOO_LONG_BONDS Field
PROPERTY_KEY_DETECT_TOO_SHORT_BONDS Field
PROPERTY_KEY_LONG Field
PROPERTY_KEY_SHORT Field
BondLengthChecker Methods
isDetectTooLongBonds Method
isDetectTooShortBonds Method
setDetectTooLongBonds Method
setDetectTooShortBonds Method
ComponentChecker Class
ComponentChecker Members
ComponentChecker Constructor
CoordinationSystemErrorChecker Class
CoordinationSystemErrorChecker Members
CoordinationSystemErrorChecker Constructor
CrossedDoubleBondChecker Class
CrossedDoubleBondChecker Members
CrossedDoubleBondChecker Constructor
DoubleBondStereoErrorChecker Class
DoubleBondStereoErrorChecker Members
DoubleBondStereoErrorChecker Constructor
ExternalStructureChecker Class
ExternalStructureChecker Members
ExternalStructureChecker Constructor
ExternalStructureChecker Methods
getErrorCode Method
IsotopeChecker Class
IsotopeChecker Members
IsotopeChecker Constructor
MetalloceneErrorChecker Class
MetalloceneErrorChecker Members
MetalloceneErrorChecker Constructor
MetalloceneErrorChecker Methods
__<clinit> Method
MissingAtomMapChecker Class
MissingAtomMapChecker Members
MissingAtomMapChecker Constructor
MoleculeChargeChecker Class
MoleculeChargeChecker Members
MoleculeChargeChecker Constructor
MultiCenterChecker Class
MultiCenterChecker Members
MultiCenterChecker Constructor
OverlappingAtomsChecker Class
OverlappingAtomsChecker Members
OverlappingAtomsChecker Constructor
OverlappingBondsChecker Class
OverlappingBondsChecker Members
OverlappingBondsChecker Constructor
PseudoAtomChecker Class
PseudoAtomChecker Members
PseudoAtomChecker Constructor
QueryAtomChecker Class
QueryAtomChecker Members
QueryAtomChecker Constructor
QueryBondChecker Class
QueryBondChecker Members
QueryBondChecker Constructor
RadicalChecker Class
RadicalChecker Members
RadicalChecker Constructor
RatomChecker Class
RatomChecker Members
RatomChecker Constructor
RatomChecker Constructor
RatomChecker Constructor ()
RatomChecker Fields
PROPERTY_KEY_SEARCH_ALL Field
PROPERTY_KEY_SEARCH_DISCONNECTED Field
PROPERTY_KEY_SEARCH_GENERIC Field
PROPERTY_KEY_SEARCH_LINKER Field
PROPERTY_KEY_SEARCH_NESTED Field
RatomChecker Methods
isSearchAll Method
isSearchDisconnected Method
isSearchGeneric Method
isSearchLinker Method
isSearchNested Method
setSearchAll Method
setSearchDisconnected Method
setSearchGeneric Method
setSearchLinker Method
setSearchNested Method
ReactionChecker Class
ReactionChecker Members
ReactionChecker Constructor
ReactionMapErrorChecker Class
ReactionMapErrorChecker Members
ReactionMapErrorChecker Constructor
RgroupAttachmentErrorChecker Class
RgroupAttachmentErrorChecker Members
RgroupAttachmentErrorChecker Constructor
RgroupReferenceErrorChecker Class
RgroupReferenceErrorChecker Members
RgroupReferenceErrorChecker Constructor
RgroupReferenceErrorChecker Constructor
RgroupReferenceErrorChecker Constructor ()
RgroupReferenceErrorChecker Fields
PROPERTY_KEY_SEARCH_MISSING_RATOM Field
PROPERTY_KEY_SEARCH_MISSING_RGROUP Field
PROPERTY_KEY_SEARCH_SELF_REFERENCE Field
RgroupReferenceErrorChecker Methods
isSearchMissingRatom Method
isSearchMissingRgroup Method
isSearchSelfReference Method
setSearchMissingRatom Method
setSearchMissingRgroup Method
setSearchSelfReference Method
RingStrainErrorChecker Class
RingStrainErrorChecker Members
RingStrainErrorChecker Constructor
RingStrainErrorChecker Constructor
RingStrainErrorChecker Constructor ()
RingStrainErrorChecker Fields
PROPERTY_KEY_DETECT_CUMULATED_DOUBLE_BONDS Field
PROPERTY_KEY_DETECT_TRANS_DOUBLE_BONDS Field
PROPERTY_KEY_DETECT_TRIPLE_BONDS Field
RingStrainErrorChecker Methods
isDetectCumulatedDoubleBonds Method
isDetectTransDoubleBonds Method
isDetectTripleBonds Method
setDetectCumulatedDoubleBonds Method
setDetectTransDoubleBonds Method
setDetectTripleBonds Method
StructureChecker Interface
StructureChecker Members
StructureChecker Fields
PROPERTY_KEY_VALID Field
StructureChecker Methods
addPropertyChangeListener Method
addPropertyChangeListener Method ()
addPropertyChangeListener Method (String, )
check Method
cloneItem Method
getDescription Method
getDescriptor Method
getEditorClassName Method
getErrorCode Method
getErrorType Method
getHelpText Method
getIcon Method
getLocalMenuName Method
getName Method
isAvailable Method
isValid Method
removePropertyChangeListener Method
removePropertyChangeListener Method ()
removePropertyChangeListener Method (String, )
setDescription Method
setHelpText Method
setIcon Method
setLocalMenuName Method
setMoreErrorMessage Method
setName Method
setNoErrorMessage Method
setOneErrorMessage Method
StructureChecker.__Fields Class
StructureChecker.__Fields Members
StructureChecker.__Fields Fields
PROPERTY_KEY_VALID Field
StructureCheckerErrorType Class
StructureCheckerErrorType Members
StructureCheckerErrorType Fields
ABBREVIATED_GROUP Field
ABBREVIATED_GROUP_WITH_ONLY_CONTRACTED Field
ABBREVIATED_GROUP_WITH_ONLY_EXPANDED Field
ALIAS Field
ALIAS_ATOM Field
ALIAS_GROUP Field
ALIAS_NONE Field
AROMATICITY Field
ATOM_MAP Field
ATOM_QUERY_PROPERTY Field
ATOM_TYPE Field
ATOM_VALUE Field
ATTACHED_DATA Field
BOND_ANGLE Field
BOND_LENGTH Field
COVALENT_COUNTER_ION Field
CROSSED_DOUBLE_BOND Field
DOODLE Field
EMPTY Field
EXPLICIT_H Field
EXPLICIT_LONE_PAIR Field
EXTERNAL Field
INVALID_CHIRAL_FLAG Field
INVALID_COORD_SYSTEM Field
INVALID_REACTION_MAP Field
INVALID_RGROUP Field
INVALID_STEREO Field
INVALID_WEDGE Field
ISOTOPE Field
METALLOCENE Field
METALLOCENE_AMBIGUOUS Field
MISSING_ATOM_MAP Field
MOLECULE_CHARGE Field
MULTI_CENTER Field
MULTI_COMPONENT Field
NO_ERROR Field
OVERLAPPING_ATOMS Field
OVERLAPPING_BONDS Field
PSEUDO Field
PSEUDO_NO_GROUP Field
QUERY_ATOM Field
QUERY_BOND Field
RACEMATE Field
RADICAL Field
RARE_ELEMENT Field
RATOM Field
RGROUP_ATTACHMENT_COUNT_ERROR Field
RGROUP_ATTACHMENT_ERROR Field
RGROUP_ORPHAN_ATTACHMENT_ERROR Field
RGROUP_REFERENCE_ERROR Field
SMALL_RING Field
SOLVENT Field
SOLVENT_AMBIGOUS Field
STAR Field
STEREO_CARE_BOX Field
SUBSTRUCTURE Field
SUBSTRUCTURE_NOFIX Field
THREE_DIM Field
UNBALANCED_REACTION Field
VALENCE Field
VALENCE_PROPERTY Field
WIGGLY Field
StructureCheckerErrorType Methods
__<clinit> Method
valueOf Method
values Method
StructureCheckerErrorType.__Enum Enumeration
ThreeDimensionChecker Class
ThreeDimensionChecker Members
ThreeDimensionChecker Constructor
UnbalancedReactionChecker Class
UnbalancedReactionChecker Members
UnbalancedReactionChecker Constructor
ValenceErrorChecker Class
ValenceErrorChecker Members
ValenceErrorChecker Constructor
ValencePropertyChecker Class
ValencePropertyChecker Members
ValencePropertyChecker Constructor
ValencePropertyChecker Constructor
ValencePropertyChecker Constructor ()
ValencePropertyChecker Fields
PROPERTY_KEY_DEFAULT_VALENCE Field
PROPERTY_KEY_NON_DEFAULT_VALENCE Field
PROPERTY_KEY_SEARCH_DEFAULT_VALENCE Field
PROPERTY_KEY_SEARCH_NON_DEFAULT_VALENCE Field
ValencePropertyChecker Methods
equals Method
hashCode Method
isSearchDefaultValence Method
isSearchNonDefaultValence Method
setSearchDefaultValence Method
setSearchNonDefaultValence Method
WedgeErrorChecker Class
WedgeErrorChecker Members
WedgeErrorChecker Constructor
WigglyDoubleBondChecker Class
WigglyDoubleBondChecker Members
WigglyDoubleBondChecker Constructor
chemaxon.checkers.result Namespace
AromaticityCheckerResult Class
AromaticityCheckerResult Members
AromaticityCheckerResult Constructor
AromaticityCheckerResult Methods
equals Method
getAromataType Method
hashCode Method
DefaultStructureCheckerResult Class
DefaultStructureCheckerResult Members
DefaultStructureCheckerResult Constructor
DefaultStructureCheckerResult Constructor (StructureChecker, , , StructureCheckerErrorType, Molecule, String, String, String, String, )
DefaultStructureCheckerResult Constructor (StructureChecker, , , Molecule)
DefaultStructureCheckerResult Methods
convert Method
equals Method
getAtoms Method
getBonds Method
getDescription Method
getErrorType Method
getHelpText Method
getIcon Method
getLocalMenuName Method
getMolecule Method
getName Method
getSource Method
hashCode Method
setAtoms Method
setBonds Method
setMolecule Method
toString Method
ExplicitHydrogenResult Class
ExplicitHydrogenResult Members
ExplicitHydrogenResult Constructor
ExplicitHydrogenResult Methods
equals Method
getImplicitizeFlag Method
hashCode Method
ExternalStructureCheckerResult Interface
ExternalStructureCheckerResult Members
ExternalStructureCheckerResult Methods
getErrorCode Method
SgroupCheckerResult Class
SgroupCheckerResult Members
SgroupCheckerResult Constructor
SgroupCheckerResult Methods
convert Method
equals Method
getSgroups Method
hashCode Method
setSrgoups Method
StructureCheckerResult Interface
StructureCheckerResult Members
StructureCheckerResult Methods
convert Method
getAtoms Method
getBonds Method
getDescription Method
getErrorType Method
getHelpText Method
getIcon Method
getLocalMenuName Method
getMolecule Method
getName Method
getSource Method
setAtoms Method
setBonds Method
setMolecule Method
chemaxon.checkers.runner Namespace
AdvancedCheckerRunner Class
AdvancedCheckerRunner Members
AdvancedCheckerRunner Constructor
AdvancedCheckerRunner Methods
check Method
checkAndWait Method
fix Method
getLogger Method
setLogger Method
setMolecule Method
BasicCheckerRunner Class
BasicCheckerRunner Members
BasicCheckerRunner Constructor
BasicCheckerRunner Constructor (ConfigurationReader)
BasicCheckerRunner Constructor ()
BasicCheckerRunner Methods
addPropertyChangeListener Method
addPropertyChangeListener Method ()
addPropertyChangeListener Method (String, )
cancel Method
check Method
checkAndWait Method
fix Method
fix Method
fix Method (StructureCheckerResult)
getCurrent Method
getCurrentCheckerName Method
getFixers Method
getProgessLength Method
getResultList Method
isChecking Method
setConfigurationReader Method
setMolecule Method
CheckerRunner Interface
CheckerRunner Members
CheckerRunner Methods
addPropertyChangeListener Method
addPropertyChangeListener Method ()
addPropertyChangeListener Method (String, )
cancel Method
check Method
checkAndWait Method
fix Method
fix Method
fix Method (StructureCheckerResult)
getCurrent Method
getCurrentCheckerName Method
getFixers Method
getProgessLength Method
getResultList Method
isChecking Method
setConfigurationReader Method
setMolecule Method
CheckerRunnerImpl Class
CheckerRunnerImpl Members
CheckerRunnerImpl Constructor
CheckerRunnerImpl Methods
addPropertyChangeListener Method
addPropertyChangeListener Method ()
addPropertyChangeListener Method (String, )
cancel Method
check Method
checkAndWait Method
fix Method
fix Method
fix Method (StructureCheckerResult)
getCurrent Method
getCurrentCheckerName Method
getFixers Method
getProgessLength Method
getResultList Method
isChecking Method
setConfigurationReader Method
setMolecule Method
SketchCheckerRunner Class
SketchCheckerRunner Members
SketchCheckerRunner Constructor
SketchCheckerRunner Methods
getFixers Method
setMolecule Method
chemaxon.checkers.runner.configuration.reader Namespace
ConfigurationReader Interface
ConfigurationReader Members
ConfigurationReader Constructor
ConfigurationReader Fields
DEFAULT_CHECKERS_CONFIG_PATH Field
USER_CHECKERS_CONFIG_PATH Field
ConfigurationReader Methods
__<clinit> Method
getCheckerList Method
getErrorTypeDefaultFixerMap Method
ConfigurationReader.__Fields Class
ConfigurationReader.__Fields Members
ConfigurationReader.__Fields Fields
DEFAULT_CHECKERS_CONFIG_PATH Field
USER_CHECKERS_CONFIG_PATH Field
XMLBasedConfigurationReader Class
XMLBasedConfigurationReader Members
XMLBasedConfigurationReader Constructor
XMLBasedConfigurationReader Fields
DEFAULT_CONFIGURATION_SCHEMA Field
XMLBasedConfigurationReader Methods
getCheckerList Method
getErrorTypeDefaultFixerMap Method
chemaxon.clustering Namespace
Common Class
Common Members
Common Constructor
Common Methods
getDimensions Method
getElapsedTime Method
getFpSize Method
getIdGeneration Method
getStartTime Method
getStatStream Method
getWeights Method
isOnlyStat Method
isStatNeeded Method
setDimensions Method
setFpSize Method
setIdGeneration Method
setOnlyStat Method
setOutput Method
setOutput Method ()
setOutput Method ()
setOutput Method (String)
setOutput Method (, String)
setStatNeeded Method
setStatStream Method
setWeights Method
Compare Class
Compare Members
Compare Constructor
Compare Methods
__<clinit> Method
getMaxSimilar Method
getThreshold Method
isDifferentIdsOnly Method
isOnlyDissimilarListed Method
isOrderSimilarObjects Method
isSimilarListed Method
main Method
run Method
setDifferentIdsOnly Method
setInput1 Method
setInput1 Method ()
setInput1 Method ()
setInput1 Method (String)
setInput1 Method (ConnectionHandler, String)
setInput2 Method
setInput2 Method ()
setInput2 Method ()
setInput2 Method (String)
setInput2 Method (ConnectionHandler, String)
setMaxSimilar Method
setOnlyDissimilarListed Method
setOrderSimilarObjects Method
setSimilarListed Method
setThreshold Method
JarvisPatrick Class
JarvisPatrick Members
JarvisPatrick Constructor
JarvisPatrick Methods
__<clinit> Method
getMinCommonRatio Method
isCentralShown Method
isSingletonNegative Method
main Method
run Method
setCentralShown Method
setMinCommonRatio Method
setSingletonNegative Method
LibraryMCS Class
LibraryMCS Members
LibraryMCS Constructor
LibraryMCS Fields
ATOM_COUNT_UPPER_BOUND Field
DEFAULT_ALLOWED_LEVEL_COUNT Field
DEFAULT_ATOM_TYPE_MATCH Field
DEFAULT_BOND_TYPE_MATCH Field
DEFAULT_CHARGE_MATCH Field
DEFAULT_KEEP_RINGS Field
DEFAULT_MCS_MODE Field
DEFAULT_MIN_MCS_SIZE Field
DEFAULT_REQUIRED_CLUSTER_COUNT Field
MAX_LEVEL_COUNT Field
TERMINATION_CANCEL Field
TERMINATION_CLUSTER_COUNT Field
TERMINATION_ERROR Field
TERMINATION_LEVEL_COUNT Field
TERMINATION_MCS_SIZE_LIMIT Field
TERMINATION_SAME_PARAMETERS Field
TERMINATION_STEP_NOT_ALLOWED Field
TERMINATION_UNKNOWN Field
LibraryMCS Methods
__<clinit> Method
addMolecule Method
getClusterEnumerator Method
getClusterEnumerator Method (Boolean)
getClusterEnumerator Method (Boolean, Boolean)
getInputStructureCount Method
getLevelCount Method
getStopCause Method
getStopCauseExplanation Method
getTopLevelClusterCount Method
getTotalClusterCount Method
isLicensed Method
main Method
reset Method
search Method
setAllowedLevelCount Method
setAtomCountUpperBound Method
setAtomTypeMatch Method
setBondTypeMatch Method
setChargeMatch Method
setDissimCutoff Method
setFastSearch Method
setKeepRings Method
setLicenseEnvironment Method
setMCSMode Method
setMCSSimilarityThreshold Method
setMinimalSimilarityMeasurement Method
setMinimumMCSSize Method
setMode Method
setRequiredClusterCount Method
step Method
LibraryMCS.ClusterEnumerator Class
LibraryMCS.ClusterEnumerator Members
LibraryMCS.ClusterEnumerator Methods
hasNext Method
next Method
NearestNeighbors Class
NearestNeighbors Members
NearestNeighbors Constructor
NearestNeighbors Methods
__<clinit> Method
getThreshold Method
main Method
run Method
setInput Method
setInput Method ()
setInput Method ()
setInput Method (String)
setInput Method (ConnectionHandler, String)
setThreshold Method
Ward Class
Ward Members
Ward Constructor
Ward Fields
ONLY_CLUSTERING Field
ONLY_RNN Field
RNN_AND_CLUSTERING Field
Ward Methods
__<clinit> Method
getCentralShown Method
getClusterCount Method
getMode Method
isSingletonNegative Method
main Method
run Method
setCentralShown Method
setClusterCount Method
setInput Method
setInput Method ()
setInput Method ()
setInput Method (String)
setInput Method (ConnectionHandler, String)
setKelleyStats Method
setKelleyStats Method ()
setKelleyStats Method ()
setKelleyStats Method (String)
setMode Method
setSingletonNegative Method
chemaxon.descriptors Namespace
BCUT Class
BCUT Members
BCUT Constructor
BCUT Constructor
BCUT Constructor (BCUT)
BCUT Constructor (BCUTParameters)
BCUT Constructor (String)
BCUT Methods
__<clinit> Method
clear Method
clone Method
fromData Method
fromFloatArray Method
fromString Method
generate Method
getDefaultDissimilarityMetricThresholds Method
getDissimilarity Method
getDissimilarity Method (MolecularDescriptor)
getDissimilarity Method (MolecularDescriptor, Int32)
getDissimilarityMetrics Method
getEuclidean Method
getHighestEigenvalue Method
getLowestEigenvalue Method
getName Method
getParametersClassName Method
getShortName Method
getWeightedEuclidean Method
isLicensed Method
setLicenseEnvironment Method
setParameters Method
setParameters Method (MDParameters)
setParameters Method (String)
toData Method
toDecimalString Method
toFloatArray Method
toString Method
BCUTGenerator Class
BCUTGenerator Members
BCUTGenerator Constructor
BCUTGenerator Methods
generate Method
BCUTParameters Class
BCUTParameters Members
BCUTParameters Constructor
BCUTParameters Constructor
BCUTParameters Constructor ()
BCUTParameters Constructor (String)
BCUTParameters Methods
fromString Method
getDefaultDocumentFrame Method
getHighestEigenvaluesCount Method
getLowestEigenvaluesCount Method
getType Method
toString Method
CDParameters Class
CDParameters Members
CDParameters Constructor
CDParameters Constructor
CDParameters Constructor ()
CDParameters Constructor (Int32)
CDParameters Constructor (String)
CDParameters Fields
BINARY_DESCRIPTOR Field
FLOAT_DESCRIPTOR Field
INTEGER_DESCRIPTOR Field
CDParameters Methods
__<clinit> Method
fromFile Method
fromString Method
getDefaultDocumentFrame Method
getDescrType Method
setLength Method
CFGenerator Class
CFGenerator Members
CFGenerator Constructor
CFGenerator Constructor
CFGenerator Constructor (Int32)
CFGenerator Constructor (Standardizer, Int32)
CFGenerator Methods
generate Method
generate Method (Molecule, MolecularDescriptor)
generate Method (Molecule, Int32[], MolecularDescriptor)
CFParameters Class
CFParameters Members
CFParameters Constructor
CFParameters Constructor
CFParameters Constructor ()
CFParameters Constructor (String)
CFParameters Fields
DEFAULT_BITS_SET Field
DEFAULT_BOND_COUNT Field
DEFAULT_LENGTH Field
CFParameters Methods
fromFile Method
fromString Method
getBitCount Method
getBondCount Method
getDefaultDocumentFrame Method
setBitCount Method
setBondCount Method
setLength Method
ChemicalFingerprint Class
ChemicalFingerprint Members
ChemicalFingerprint Constructor
ChemicalFingerprint Constructor
ChemicalFingerprint Constructor (CFParameters)
ChemicalFingerprint Constructor (ChemicalFingerprint)
ChemicalFingerprint Constructor (String)
ChemicalFingerprint Methods
__<clinit> Method
clear Method
clone Method
fromData Method
fromFloatArray Method
fromString Method
generate Method
getAsymmetricEuclidean Method
getBrightness Method
getCommonBitCount Method
getDefaultDissimilarityMetricThresholds Method
getDefaultMetricIndex Method
getDefaultThreshold Method
getDissimilarity Method
getDissimilarity Method (MolecularDescriptor)
getDissimilarity Method (MolecularDescriptor, Int32)
getDissimilarityMetrics Method
getEuclidean Method
getLowerBound Method
getName Method
getParametersClassName Method
getShortName Method
getTanimoto Method
getTversky Method
getWeightedAsymmetricEuclidean Method
getWeightedEuclidean Method
isSubSetOf Method
setParameters Method
setParameters Method (MDParameters)
setParameters Method (String)
toBinaryString Method
toData Method
toDecimalString Method
toFloatArray Method
toString Method
CustomDescriptor Class
CustomDescriptor Members
CustomDescriptor Constructor
CustomDescriptor Constructor
CustomDescriptor Constructor (CDParameters)
CustomDescriptor Constructor (CustomDescriptor)
CustomDescriptor Constructor (String)
CustomDescriptor Constructor (Int32, Int32)
CustomDescriptor Methods
__<clinit> Method
clear Method
clone Method
fromData Method
fromFloatArray Method
fromString Method
getAsymmetricEuclidean Method
getBit Method
getDefaultDissimilarityMetricThresholds Method
getDissimilarity Method
getDissimilarity Method (MolecularDescriptor)
getDissimilarity Method (MolecularDescriptor, Int32)
getDissimilarityMetrics Method
getEuclidean Method
getFloat Method
getInt Method
getName Method
getParametersClassName Method
getScaledTanimoto Method
getShortName Method
getTanimoto Method
getWeightedAsymmetricEuclidean Method
getWeightedEuclidean Method
set Method
set Method (Int32, Int32)
set Method (Int32, Int32[])
set Method (Int32, Single)
set Method (Int32, Single[])
setParameters Method
setParameters Method (CDParameters)
setParameters Method (String)
toData Method
toDecimalString Method
toFloatArray Method
toString Method
DescriptorGenerator Class
DescriptorGenerator Members
DescriptorGenerator Constructor
DescriptorGenerator Constructor (String)
DescriptorGenerator Constructor (String, String)
DescriptorGenerator Methods
__<clinit> Method
generate Method
generate Method (Molecule)
generate Method (Molecule, Int32[])
getAsBitSet Method
getAsFloatArray Method
getAsIntArray Method
getAsString Method
getDescriptorLongName Method
getDescriptorTypes Method
setParameter Method
setStandardizer Method
ECFP Class
ECFP Members
ECFP Constructor
ECFP Constructor
ECFP Constructor (ECFP)
ECFP Constructor (ECFPParameters)
ECFP Constructor (String)
ECFP Methods
__<clinit> Method
clear Method
clone Method
dropBinaryVector Method
fromData Method
fromFeatureSet Method
fromFloatArray Method
fromIdentiferSet Method
fromIntArray Method
fromString Method
generate Method
getAsymmetricEuclidean Method
getBrightness Method
getDefaultDissimilarityMetricThresholds Method
getDefaultMetricIndex Method
getDefaultThreshold Method
getDissimilarity Method
getDissimilarity Method (MolecularDescriptor)
getDissimilarity Method (MolecularDescriptor, Int32)
getDissimilarityMetrics Method
getEuclidean Method
getFeatureCount Method
getIdentiferCount Method
getName Method
getParametersClassName Method
getShortName Method
getTanimoto Method
getWeightedAsymmetricEuclidean Method
getWeightedEuclidean Method
isLicensed Method
setLicenseEnvironment Method
setParameters Method
setParameters Method (MDParameters)
setParameters Method (String)
toBinaryString Method
toBitSet Method
toData Method
toDecimalString Method
toFeatureSet Method
toFloatArray Method
toIdentiferSet Method
toIntArray Method
toString Method
ECFPFeature Class
ECFPFeature Members
ECFPFeature Methods
getBitPosition Method
getCenterAtom Method
getDiameter Method
getIdentifier Method
getSubstructure Method
ECFPFeatureLookup Class
ECFPFeatureLookup Members
ECFPFeatureLookup Constructor
ECFPFeatureLookup Constructor
ECFPFeatureLookup Constructor (ECFPParameters)
ECFPFeatureLookup Constructor (String)
ECFPFeatureLookup Methods
getBitPosition Method
getBitPosition Method (Int32)
getBitPosition Method (MolAtom, Int32)
getFeaturesFromBitPosition Method
getFeaturesFromIdentifier Method
getIdentifier Method
processMolecule Method
ECFPGenerator Class
ECFPGenerator Members
ECFPGenerator Constructor
ECFPGenerator Methods
generate Method
isLicensed Method
setLicenseEnvironment Method
ECFPParameters Class
ECFPParameters Members
ECFPParameters Constructor
ECFPParameters Constructor
ECFPParameters Constructor ()
ECFPParameters Constructor (String)
ECFPParameters Fields
DEFAULT_DIAMETER Field
DEFAULT_LENGTH Field
ECFPParameters Methods
__<clinit> Method
fromFile Method
fromString Method
getDefaultDocumentFrame Method
getDefaultStandardizerConfiguration Method
getDiameter Method
getKeepCounts Method
setDiameter Method
setKeepCounts Method
setLength Method
GenerateMD Class
GenerateMD Members
GenerateMD Constructor
GenerateMD Constructor
GenerateMD Constructor (Int32)
GenerateMD Methods
__<clinit> Method
addMDConfig Method
addMDConfig Method (String, String, )
addMDConfig Method (String, String, String)
close Method
createMDTable Method
deleteMDConfig Method
deleteMDTable Method
getASSBClusters Method
getCounter Method
getMDNames Method
getStatistics Method
init Method
main Method
run Method
setBinaryOutput Method
setConnectionHandler Method
setCreateStat Method
setDecimalOutput Method
setDescriptor Method
setDescriptor Method (String, String, MDParameters, String)
setDescriptor Method (String, String, String, String)
setDescriptor Method (Int32, String, String, MDParameters, String)
setDescriptor Method (Int32, String, String, String, String)
setDescriptors Method
setDescriptors Method (String[], String[], MDParameters[], String[])
setDescriptors Method (String[], String[], String[], String[])
setGenerateId Method
setIdTagName Method
setInput Method
setInput Method ()
setInput Method (String)
setOutputFileName Method
setSDfileInput Method
setSDfileOutput Method
setSelectStatement Method
setStructureTableName Method
setTagName Method
setTagName Method (String)
setTagName Method (Int32, String)
setTagNames Method
setUpdateOnInsert Method
setValidateDescriptor Method
step Method
updateMDTable Method
validateDescriptor Method
MDArrayReader Class
MDArrayReader Members
MDArrayReader Constructor
MDArrayReader Constructor (MDReader)
MDArrayReader Constructor (MDSet[])
MDArrayReader Methods
close Method
next Method
reset Method
size Method
MDDBReader Class
MDDBReader Members
MDDBReader Constructor
MDDBReader Constructor (ConnectionHandler, String, MDSet, String)
MDDBReader Constructor (ConnectionHandler, String, String[], String)
MDDBReader Constructor (String, ConnectionHandler, MDSet, String)
MDDBReader Constructor (String, ConnectionHandler, String[], String)
MDDBReader Constructor (String, ConnectionHandler, String[], String, Int32[], Boolean)
MDDBReader Methods
__<clinit> Method
close Method
getLastID Method
getMDSet Method
getMolecule Method
next Method
reset Method
MDDBWriter Class
MDDBWriter Members
MDDBWriter Constructor
MDDBWriter Constructor
MDDBWriter Constructor (Boolean)
MDDBWriter Methods
close Method
getConnectionHandler Method
getMDNames Method
getMDParameters Method
getStructureTable Method
put Method
put Method (Molecule, Int32)
put Method (String, Int32)
setConnectionHandler Method
setMDNames Method
setStructureTable Method
setUpdateMode Method
MDFileReader Class
MDFileReader Members
MDFileReader Constructor
MDFileReader Constructor (String)
MDFileReader Constructor (String[])
MDFileReader Constructor (, MDSet)
MDFileReader Constructor (String, MDSet)
MDFileReader Methods
close Method
getMolecule Method
next Method
reset Method
setKeepOriginalMolecule Method
MDFileWriter Class
MDFileWriter Members
MDFileWriter Constructor
MDFileWriter Constructor (Int32)
MDFileWriter Constructor (String, Int32)
MDFileWriter Constructor (String, String, MDParameters)
MDFileWriter Constructor (String, String, String)
MDFileWriter Constructor (String[], String[], MDParameters[])
MDFileWriter Constructor (String[], String[], String[])
MDFileWriter Constructor (String, String[], String[], MDParameters[])
MDFileWriter Constructor (String, String[], String[], String[])
MDFileWriter Methods
close Method
getMDParameters Method
getMDSet Method
put Method
put Method (MDSet)
put Method (Molecule, Int32)
put Method (Molecule, String)
setBinaryOutputFormat Method
setComponent Method
setComponent Method (Int32, String, String, MDParameters)
setComponent Method (Int32, String, String, String)
setDecimalOutputFormat Method
setPrintId Method
MDGenerator Class
MDGenerator Members
MDGenerator Constructor
MDGenerator Methods
generate Method
getAverageNonZeroRatio Method
getBrightestMolId Method
getDarkestMolId Method
getDensityCounts Method
getFrequencyCounts Method
getMaximumBitRatio Method
getMinimumBitRatio Method
getMoleculeCount Method
setCreateStatistics Method
MDGeneratorException Class
MDGeneratorException Members
MDGeneratorException Constructor
MDGeneratorException Constructor
MDGeneratorException Constructor (Exception)
MDGeneratorException Constructor (String)
MDGeneratorException Constructor (String, Exception)
MDHitEvaluator Class
MDHitEvaluator Members
MDHitEvaluator Constructor
MDHitEvaluator Fields
evaluatorFunctions Field
MDHitEvaluator Methods
calcDissimilarity Method
calcMetricDistribution Method
calcMetricDistribution Method (Int32, Int32, Single, Single, Int32, Single[])
calcMetricDistribution Method (Int32, Int32, Single, Single, Int32, Single[], MDReader, MDReader)
evaluateByAll Method
evaluateByAll Method (Int32)
evaluateByAll Method (Int32, Int32)
evaluateByDescriptor Method
evaluateByDescriptor Method (Int32, Int32)
evaluateByDescriptor Method (Int32, Int32, Int32)
evaluateByMetric Method
evaluateByMetric Method (Int32, Int32, Int32)
evaluateByMetric Method (Int32, Int32, Single)
evaluateByMetric Method (Int32, Int32, Int32, Int32)
evaluateByMetric Method (Int32, Int32, Int32, MDReader, MDReader)
evaluateByMetric Method (Int32, Int32, Single, MDReader, MDReader)
evaluateByMetric Method (Int32, Int32, Int32, Int32, MDReader, MDReader)
getCurrentEvaluatorFunction Method
getEvaluatorFunctionIndex Method
getEvaluatorFunctionName Method
getInsertedDissimilars Method
getNextDissimilarHit Method
getNextSimilarHit Method
getNumberOfDissimilarHits Method
getNumberOfDissimilars Method
getNumberOfSimilarHits Method
getNumberOfSimilars Method
getSelectivityAsymmetryFactor Method
getThreshold Method
resetDissimilarHits Method
resetSimilarHits Method
screen Method
screen Method (Int32, Int32, Single)
screen Method (Int32, Int32, Single, MDReader, MDReader)
setCurrentEvaluatorFunction Method
setSelectivityAsymmetryFactor Method
MDHypothesisCreator Class
MDHypothesisCreator Members
MDHypothesisCreator Constructor
MDHypothesisCreator Fields
defaultTypeName Field
typeNames Field
MDHypothesisCreator Methods
__<clinit> Method
create Method
main Method
MDHypothesisGenerator Interface
MDHypothesisGenerator Members
MDHypothesisGenerator Methods
add Method
generate Method
getTypeName Method
MDMetricOptimizer Class
MDMetricOptimizer Members
MDMetricOptimizer Constructor
MDMetricOptimizer Fields
maxErrorInF Field
maxErrorInX Field
nrOfIterations Field
percentage Field
MDMetricOptimizer Methods
optimizeParameters Method
MDParameters Class
MDParameters Members
MDParameters Fields
DEFAULT_ASYMMETRY_FACTOR Field
DEFAULT_OUTPUT_PRECISION Field
DEFAULT_SCALE_FACTOR Field
DEFAULT_WEIGHT Field
MDParameters Methods
addParameters Method
addParameters Method ()
addParameters Method (String)
addParametrizedMetric Method
fromFile Method
fromString Method
getAsymmetryFactor Method
getCellSize Method
getCurrentMetricIndex Method
getData Method
getDecForm Method
getDefaultDocumentFrame Method
getDefaultStandardizerConfiguration Method
getDescriptorTypeName Method
getInternalMetricIndex Method
getInternalSize Method
getLength Method
getMetricIndex Method
getMetricName Method
getMetricName Method
getMetricName Method (Int32)
getNumberOfMetrics Method
getNumberOfWeights Method
getScaleFactor Method
getScalingHypothesis Method
getScreeningConfigurationString Method
getThreshold Method
getThreshold Method
getThreshold Method (Int32)
getTverskyAlpha Method
getTverskyBeta Method
getWeights Method
isAsymmetric Method
isCellwiseWeights Method
isNormalized Method
isScaled Method
isStandardizationMandatory Method
isWeighted Method
setAsymmetryFactor Method
setCellSize Method
setCellwiseWeights Method
setCreateStatistics Method
setCurrentParametrizedMetric Method
setLength Method
setNormalized Method
setOutputPrecision Method
setParameters Method
setParameters Method ()
setParameters Method (String)
setScaleFactor Method
setScalingHypothesis Method
setThreshold Method
setWeights Method
standardize Method
toString Method
MDParametersException Class
MDParametersException Members
MDParametersException Constructor
MDParametersException Constructor
MDParametersException Constructor (String)
MDParametersException Constructor (String, Exception)
MDReader Class
MDReader Members
MDReader Methods
close Method
getCloneResult Method
getMDSet Method
getMolecule Method
next Method
reset Method
setCloneResult Method
setFirstId Method
setGenerateId Method
setIdTagName Method
setTakeTag Method
MDReaderException Class
MDReaderException Members
MDReaderException Constructor
MDReaderException Constructor
MDReaderException Constructor (String)
MDReaderException Constructor (String, Exception)
MDSet Class
MDSet Members
MDSet Constructor
MDSet Constructor
MDSet Constructor (MDSet)
MDSet Constructor (Int32)
MDSet Constructor (Int32, Int32)
MDSet Fields
dissim Field
MDSet Methods
addDescriptor Method
clone Method
generate Method
getDescriptor Method
getDissimilarity Method
getId Method
getLowerBound Method
getNaturalId Method
getParameters Method
getUserData Method
getUserData Method
getUserData Method (Int32)
newInstance Method
newInstance Method (String[])
newInstance Method (String[], [])
newInstance Method (String[], String[])
setDescriptor Method
setDescriptors Method
setId Method
setNaturalId Method
setParameters Method
setSize Method
setSize Method (Int32)
setSize Method (Int32, Int32)
setUserData Method
setUserData Method (Single[])
setUserData Method (Int32, Single)
size Method
MDSetParameters Class
MDSetParameters Members
MDSetParameters Constructor
MDSetParameters Constructor
MDSetParameters Constructor (Int32)
MDSetParameters Constructor (Int32, Int32)
MDSetParameters Constructor (Single[], Int32[])
MDSetParameters Constructor (Single[], Single[], Int32[])
MDSetParameters Methods
getMetricIndex Method
getUserDataWeight Method
getWeight Method
setMetricIndex Method
setMetricIndices Method
setSize Method
setSize Method (Int32)
setSize Method (Int32, Int32)
setUserDataWeight Method
setUserDataWeights Method
setWeight Method
setWeights Method
size Method
MDSimilarity Class
MDSimilarity Members
MDSimilarity Constructor
MDSimilarity Methods
addQueries Method
addQueries Method (MDReader)
addQueries Method (MDSet[])
addQuery Method
addResultWriter Method
compare Method
compare Method (MDReader)
compare Method (MDSet)
compare Method (Int32, Int32, MDSet)
getDissimilarityCoeff Method
getDissimilarityCoeffs Method
getDissimilarityCoeffs Method (Int32)
getDissimilarityCoeffs Method (Int32, Int32)
getNrOfQueries Method
getNrOfUsedMetrics Method
getQuery Method
isComponentWise Method
isLicensed Method
isPassWithAllDescriptors Method
isPassWithAllMetrics Method
isPassWithOneDescriptor Method
isPassWithOneMetric Method
isUsedMetric Method
passWithAllDescriptors Method
passWithAllMetrics Method
passWithOneDescriptor Method
passWithOneMetric Method
setComponentWise Method
setLicenseEnvironment Method
setThreshold Method
threshold Method
useMetric Method
useMetric Method (Int32, Int32)
useMetric Method (Int32, Int32, Single)
MDSimilarityResultWriter Class
MDSimilarityResultWriter Members
MDSimilarityResultWriter Constructor
MDSimilarityResultWriter Methods
close Method
getQueryName Method
open Method
setMolecule Method
setQueryName Method
setVerboseFrequency Method
setVerbosity Method
write Method
writesMolecules Method
MDWriter Class
MDWriter Members
MDWriter Methods
close Method
getMDParameters Method
put Method
MDWriterException Class
MDWriterException Members
MDWriterException Constructor
MDWriterException Constructor
MDWriterException Constructor (String)
MDWriterException Constructor (String, Exception)
Metrics Class
Metrics Members
Metrics Constructor
Metrics Methods
__<clinit> Method
asymmetricEuclidean Method
asymmetricEuclidean Method (Int32[], Int32[], Double)
asymmetricEuclidean Method (Single[], Single[], Double)
asymmetricNormalizedEuclidean Method
asymmetricNormalizedEuclidean Method (Int32[], Int32[], Double)
asymmetricNormalizedEuclidean Method (Single[], Single[], Double)
asymmetricTanimoto Method
asymmetricTanimoto Method (Int32[], Int32[], Single)
asymmetricTanimoto Method (Single[], Single[], Single)
binaryAsymmetricEuclidean Method
binaryAsymmetricNormalizedEuclidean Method
binaryAsymmetricNormalizedEuclidean Method (Int32[], Int32[], Single)
binaryAsymmetricNormalizedEuclidean Method (Int32[], Int32, Int32[], Int32, Single)
binaryAsymmetricTanimoto Method
binaryAsymmetricTanimoto Method (Int32[], Int32[], Single)
binaryAsymmetricTanimoto Method (Int32[], Int32, Int32[], Int32, Single)
binaryEuclidean Method
binaryNormalizedEuclidean Method
binaryNormalizedEuclidean Method (Int32[], Int32[])
binaryNormalizedEuclidean Method (Int32[], Int32, Int32[], Int32)
binaryTanimoto Method
binaryTanimoto Method (Int32[], Int32[])
binaryTanimoto Method (Int32[], Int32, Int32[], Int32)
binaryTversky Method
binaryWeightedAsymmetricEuclidean Method
binaryWeightedAsymmetricNormalizedEuclidean Method
binaryWeightedAsymmetricNormalizedEuclidean Method (Int32[], Int32[], Single[], Single)
binaryWeightedAsymmetricNormalizedEuclidean Method (Int32[], Int32, Int32[], Int32, Single[], Single)
binaryWeightedEuclidean Method
binaryWeightedNormalizedEuclidean Method
binaryWeightedNormalizedEuclidean Method (Int32[], Int32[], Single[])
binaryWeightedNormalizedEuclidean Method (Int32[], Int32, Int32[], Int32, Int32[])
calcBitCount Method
calcBitCount Method (Int32)
calcBitCount Method (Int32[])
euclidean Method
euclidean Method (Int32[], Int32[])
euclidean Method (Single[], Single[])
normalizedEuclidean Method
normalizedEuclidean Method (Int32[], Int32[])
normalizedEuclidean Method (Single[], Single[])
scaledAsymmetricTanimoto Method
scaledAsymmetricTanimoto Method (Int32[], Int32[], Single[], Single, Single)
scaledAsymmetricTanimoto Method (Single[], Single[], Single[], Single, Single)
scaledTanimoto Method
scaledTanimoto Method (Int32[], Int32[], Single[], Single)
scaledTanimoto Method (Single[], Single[], Single[], Single)
tanimoto Method
tanimoto Method (Int32[], Int32[])
tanimoto Method (Single[], Single[])
tversky Method
tversky Method (Int32[], Single, Int32[], Single)
tversky Method (Single[], Single, Single[], Single)
weightedAsymmetricEuclidean Method
weightedAsymmetricEuclidean Method (Int32[], Int32[], Single[], Single)
weightedAsymmetricEuclidean Method (Single[], Single[], Single[], Single)
weightedAsymmetricNormalizedEuclidean Method
weightedAsymmetricNormalizedEuclidean Method (Int32[], Int32[], Single[], Single)
weightedAsymmetricNormalizedEuclidean Method (Single[], Single[], Single[], Single)
weightedEuclidean Method
weightedEuclidean Method (Int32[], Int32[], Single[])
weightedEuclidean Method (Single[], Single[], Single[])
weightedNormalizedEuclidean Method
weightedNormalizedEuclidean Method (Int32[], Int32[], Single[])
weightedNormalizedEuclidean Method (Single[], Single[], Single[])
MetricsType Class
MetricsType Members
MetricsType Fields
DEFAULT Field
DICE Field
EUCLIDEAN Field
NORMALIZED_EUCLIDEAN Field
SEPARATOR Field
SUBSTRUCTURE Field
SUPERSTRUCTURE Field
TANIMOTO Field
TVERSKY Field
MetricsType Methods
__<clinit> Method
getSimpleParamString Method
valueOf Method
values Method
MetricsType.__Enum Enumeration
MolecularDescriptor Class
MolecularDescriptor Members
MolecularDescriptor Constructor
MolecularDescriptor Constructor
MolecularDescriptor Constructor (MDParameters)
MolecularDescriptor Constructor (MolecularDescriptor)
MolecularDescriptor Methods
<bridge>clone Method
clone Method
fromData Method
fromFloatArray Method
fromString Method
generate Method
generate Method (Molecule)
generate Method (String)
getAtomSetColors Method
getAtomSetIndexes Method
getAtomSetNames Method
getDefaultDissimilarityMetricThresholds Method
getDefaultMetricIndex Method
getDefaultThreshold Method
getDissimilarity Method
getDissimilarity Method (MolecularDescriptor)
getDissimilarity Method (MolecularDescriptor, Int32)
getDissimilarityMetricIndex Method
getDissimilarityMetrics Method
getLowerBound Method
getMetricIndex Method
getMetricName Method
getMetricName Method
getMetricName Method (Int32)
getName Method
getNumberOfMetrics Method
getNumberOfWeights Method
getParameters Method
getParametersClassName Method
getShortName Method
getThreshold Method
getThreshold Method
getThreshold Method (Int32)
Implicit Operator
main Method
needsConfig Method
newInstance Method
newInstance Method (String)
newInstance Method (String, String)
newInstanceFromXML Method
setParameters Method
setParameters Method (MDParameters)
setParameters Method (String)
setScreeningConfiguration Method
toBinaryString Method
toData Method
toDecimalString Method
toFloatArray Method
toString Method
MolecularDescriptorGenerator Interface
MolecularDescriptorGenerator Members
MolecularDescriptorGenerator Methods
generate Method
PFGenerator Class
PFGenerator Members
PFGenerator Constructor
PFGenerator Methods
generate Method
getPMap Method
getPMAPTagName Method
setPMAPTagName Method
setUsePMAP Method
PFParameters Class
PFParameters Members
PFParameters Constructor
PFParameters Constructor
PFParameters Constructor ()
PFParameters Constructor (String)
PFParameters Fields
asymmetricXYZSum Field
DEFAULT_FUZZINESS_FACTOR Field
DEFAULT_FUZZY_CUTOFF Field
DEFAULT_FUZZY_LOWER_BOUND Field
DEFAULT_RESOLUTION Field
DEFAULT_XML_CONFIG Field
xyz Field
PFParameters Methods
fromFile Method
fromString Method
getAtomSetColors Method
getAtomSetIndexes Method
getAtomSetNames Method
getCustomFuzzyIncrements Method
getDefaultDocumentFrame Method
getDefaultStandardizerConfiguration Method
getFuzzyExponents Method
getFuzzyLowerBound Method
getFuzzySmoothingFactor Method
getGaussianFuzzyIncrements Method
getIgnoreRotatableBonds Method
getMaxDist Method
getMinDist Method
getNDists Method
getNumberOfFeatures Method
getPSymbols Method
getResolution Method
getSymbol Method
getSymbolIndex Method
isFuzzyFingerprint Method
isGaussianSmoothing Method
isSymmetricalFuzzy Method
setCurrentParametrizedMetric Method
setFuzzinessFactor Method
setFuzzyCutOff Method
setFuzzyLowerBound Method
setFuzzySmoothingFactor Method
setIgnoreRotatableBonds Method
setParameters Method
setParameters Method ()
setParameters Method (String)
setPMAPTagName Method
setSymmetricalFuzzy Method
setUsePMAP Method
setWeights Method
toString Method
tripletIndex Method
PharmacophoreFingerprint Class
PharmacophoreFingerprint Members
PharmacophoreFingerprint Constructor
PharmacophoreFingerprint Constructor
PharmacophoreFingerprint Constructor (PFParameters)
PharmacophoreFingerprint Constructor (PharmacophoreFingerprint)
PharmacophoreFingerprint Constructor (String)
PharmacophoreFingerprint Methods
__<clinit> Method
clear Method
clone Method
fromData Method
fromFloatArray Method
fromString Method
generate Method
get Method
get Method (Int32)
get Method (Int32, Int32, Int32)
get Method (Int32, Int32, Single)
getAsymmetricEuclidean Method
getAsymmetricFBPA Method
getAtomSetColors Method
getAtomSetIndexes Method
getAtomSetNames Method
getDefaultDissimilarityMetricThresholds Method
getDissimilarity Method
getDissimilarity Method (MolecularDescriptor)
getDissimilarity Method (MolecularDescriptor, Int32)
getDissimilarityMetrics Method
getEuclidean Method
getLowerBound Method
getMaxDist Method
getMinDist Method
getName Method
getNumberOfFeatures Method
getParametersClassName Method
getResolution Method
getScaledTanimoto Method
getShortName Method
getSymbol Method
getSymmetricFBPA Method
getTanimoto Method
getTversky Method
getWeightedAsymmetricEuclidean Method
getWeightedEuclidean Method
inc Method
inc Method (Int32)
inc Method (Int32, Int32, Int32)
inc Method (Int32, Int32, Int32, Int32)
inc Method (Int32, Int32, Int32, Single[])
index Method
isLicensed Method
isSubsetOf Method
put Method
put Method (Int32, Int32)
put Method (Int32, Single)
setLicenseEnvironment Method
setParameters Method
setParameters Method (MDParameters)
setParameters Method (String)
toData Method
toDecimalString Method
toFloatArray Method
toHistogramString Method
toString Method
toString Method
toString Method (String, Boolean)
ReactionFingerprint Class
ReactionFingerprint Members
ReactionFingerprint Constructor
ReactionFingerprint Constructor
ReactionFingerprint Constructor (ReactionFingerprint)
ReactionFingerprint Constructor (RFParameters)
ReactionFingerprint Constructor (String)
ReactionFingerprint Methods
__<clinit> Method
clear Method
clone Method
fromData Method
fromFloatArray Method
fromString Method
generate Method
getBrightness Method
getChemicalHashedFingerprint Method
getCoarseReactionTanimoto Method
getCommonBitCount Method
getDefaultDissimilarityMetricThresholds Method
getDefaultMetricIndex Method
getDefaultThreshold Method
getDissimilarity Method
getDissimilarity Method (MolecularDescriptor)
getDissimilarity Method (MolecularDescriptor, Int32)
getDissimilarityMetrics Method
getDissimilarityMetricsParamDefault Method
getDissimilarityMetricsParamHelp Method
getDissimilarityMetricsParamNames Method
getDissimilarityMetricsParamNum Method
getDissimilarityMetricsParamRanges Method
getLowerBound Method
getMediumReactionTanimoto Method
getName Method
getParametersClassName Method
getProductTanimoto Method
getReactantTanimoto Method
getShortName Method
getStrictReactionTanimoto Method
isReactionMappingIncomplete Method
isSubSetOf Method
main Method
setParameters Method
setParameters Method (MDParameters)
setParameters Method (String)
toBinaryString Method
toData Method
toDecimalString Method
toFloatArray Method
toString Method
RFGenerator Class
RFGenerator Members
RFGenerator Constructor
RFGenerator Methods
generate Method
RFParameters Class
RFParameters Members
RFParameters Constructor
RFParameters Constructor
RFParameters Constructor ()
RFParameters Constructor (String)
RFParameters Fields
DEFAULT_BITS_SET Field
DEFAULT_BOND_COUNT Field
DEFAULT_LENGTH Field
RFParameters Methods
fromFile Method
fromString Method
getBitCount Method
getBondCount Method
getDefaultDocumentFrame Method
setBitCount Method
setBondCount Method
setLength Method
ScalarDescriptor Class
ScalarDescriptor Members
ScalarDescriptor Constructor
ScalarDescriptor Constructor
ScalarDescriptor Constructor (ScalarDescriptor)
ScalarDescriptor Constructor (SDParameters)
ScalarDescriptor Constructor (String)
ScalarDescriptor Methods
__<clinit> Method
<bridge>clone Method
clear Method
clone Method
fromData Method
fromFloatArray Method
fromString Method
generate Method
getDefaultDissimilarityMetricThresholds Method
getDefaultThreshold Method
getDissimilarity Method
getDissimilarity Method (MolecularDescriptor)
getDissimilarity Method (MolecularDescriptor, Int32)
getDissimilarityMetrics Method
getLowerBound Method
getName Method
getParametersClassName Method
getShortName Method
set Method
setParameters Method
setParameters Method (MDParameters)
setParameters Method (String)
toData Method
toDecimalString Method
toFloatArray Method
toString Method
SDParameters Class
SDParameters Members
SDParameters Constructor
SDParameters Constructor
SDParameters Constructor ()
SDParameters Constructor (String)
SDParameters Methods
fromFile Method
fromString Method
getNumberOfMetrics Method
getType Method
setLength Method
ShapeDescriptor Class
ShapeDescriptor Members
ShapeDescriptor Constructor
ShapeDescriptor Constructor
ShapeDescriptor Constructor (ShapeDescriptor)
ShapeDescriptor Constructor (ShapeParameters)
ShapeDescriptor Constructor (String)
ShapeDescriptor Methods
clear Method
clone Method
fromData Method
fromFloatArray Method
fromString Method
generate Method
getAlignmenMolecule Method
getDefaultDissimilarityMetricThresholds Method
getDefaultThreshold Method
getDissimilarity Method
getDissimilarity Method (MolecularDescriptor)
getDissimilarity Method (MolecularDescriptor, Int32)
getDissimilarityMetrics Method
getHistogramSimilarity Method
getName Method
getParametersClassName Method
getShapeSimilarity Method
getShortName Method
isLicensed Method
setAlignmentMolecule Method
setLicenseEnvironment Method
setParameters Method
toBinaryString Method
toData Method
toDecimalString Method
toFloatArray Method
toString Method
ShapeGenerator Class
ShapeGenerator Members
ShapeGenerator Constructor
ShapeGenerator Methods
generate Method
setColoring Method
setFlexible Method
setFlexibleRingRotatableBondCount Method
setFlexibleRingSize Method
ShapeParameters Class
ShapeParameters Members
ShapeParameters Constructor
ShapeParameters Constructor
ShapeParameters Constructor ()
ShapeParameters Constructor (String)
ShapeParameters Methods
fromFile Method
fromString Method
getDefaultDocumentFrame Method
getDefaultStandardizerConfiguration Method
setFlexible Method
SimilarityCalculator Class
SimilarityCalculator Members
SimilarityCalculator Constructor
SimilarityCalculator Methods
getDissimilarity Method
getSimilarity Method
setQueryFingerprint Method
SimilarityCalculatorFactory Class
SimilarityCalculatorFactory Members
SimilarityCalculatorFactory Fields
SEPARATOR Field
SimilarityCalculatorFactory Methods
__<clinit> Method
create Method
create Method (String)
create Method (String, Int32, Int32)
getNumberFormat Method
parse Method
SimilarityCalculatorFactory.Representation Class
SimilarityCalculatorFactory.Representation Members
SimilarityCalculatorFactory.Representation Fields
ALIGNMENT Field
FLOAT_ARRAY Field
INTEGER_ARRAY Field
INTEGER_ARRAY_BIT_REPR Field
SCALAR Field
SimilarityCalculatorFactory.Representation Methods
__<clinit> Method
valueOf Method
values Method
SimilarityCalculatorFactory.Representation.__Enum Enumeration
chemaxon.descriptors.scalars Namespace
HAcc Class
HAcc Members
HAcc Constructor
HAcc Constructor
HAcc Constructor (ScalarDescriptor)
HAcc Constructor (HBParameters)
HAcc Constructor (String)
HAcc Methods
__<clinit> Method
clone Method
generate Method
getName Method
getParametersClassName Method
getShortName Method
setParameters Method
HBParameters Class
HBParameters Members
HBParameters Constructor
HBParameters Constructor
HBParameters Constructor ()
HBParameters Constructor (String)
HBParameters Fields
DEFAULT_PH Field
HBParameters Methods
toString Method
HDon Class
HDon Members
HDon Constructor
HDon Constructor
HDon Constructor (ScalarDescriptor)
HDon Constructor (HBParameters)
HDon Constructor (String)
HDon Methods
__<clinit> Method
<bridge>clone Method
clone Method
generate Method
getName Method
getParametersClassName Method
getShortName Method
setParameters Method
Heavy Class
Heavy Members
Heavy Constructor
Heavy Constructor
Heavy Constructor (ScalarDescriptor)
Heavy Constructor (SDParameters)
Heavy Constructor (String)
Heavy Methods
__<clinit> Method
<bridge>clone Method
clone Method
generate Method
getName Method
getParametersClassName Method
getShortName Method
needsConfig Method
setParameters Method
LDParameters Class
LDParameters Members
LDParameters Constructor
LDParameters Constructor
LDParameters Constructor ()
LDParameters Constructor (String)
LDParameters Fields
DEFAULT_LOWER_BOUND Field
DEFAULT_PH Field
DEFAULT_STEP_SIZE Field
DEFAULT_UPPER_BOUND Field
LDParameters Methods
toString Method
LogD Class
LogD Members
LogD Constructor
LogD Constructor
LogD Constructor (ScalarDescriptor)
LogD Constructor (LDParameters)
LogD Constructor (String)
LogD Methods
__<clinit> Method
<bridge>clone Method
clone Method
generate Method
getName Method
getParametersClassName Method
getShortName Method
setParameters Method
LogP Class
LogP Members
LogP Constructor
LogP Constructor
LogP Constructor (ScalarDescriptor)
LogP Constructor (SDParameters)
LogP Constructor (String)
LogP Methods
__<clinit> Method
<bridge>clone Method
clone Method
generate Method
getName Method
getParametersClassName Method
getShortName Method
needsConfig Method
setParameters Method
Mass Class
Mass Members
Mass Constructor
Mass Constructor
Mass Constructor (ScalarDescriptor)
Mass Constructor (SDParameters)
Mass Constructor (String)
Mass Methods
__<clinit> Method
<bridge>clone Method
clone Method
generate Method
getName Method
getParametersClassName Method
getShortName Method
needsConfig Method
setParameters Method
TPSA Class
TPSA Members
TPSA Constructor
TPSA Constructor
TPSA Constructor (ScalarDescriptor)
TPSA Constructor (SDParameters)
TPSA Constructor (String)
TPSA Methods
__<clinit> Method
<bridge>clone Method
clone Method
generate Method
getName Method
getParametersClassName Method
getShortName Method
needsConfig Method
setParameters Method
chemaxon.fixers Namespace
AbsoluteStereoFixer Class
AbsoluteStereoFixer Members
AbsoluteStereoFixer Constructor
AbsoluteStereoFixer Methods
fix Method
AbstractStructureFixer Class
AbstractStructureFixer Members
AbstractStructureFixer Constructor
AbstractStructureFixer Methods
fix Method
getDescription Method
getDescriptor Method
getName Method
setDescription Method
setName Method
CleanFixer Class
CleanFixer Members
CleanFixer Constructor
CleanFixer Methods
fix Method
ContractGroupFixer Class
ContractGroupFixer Members
ContractGroupFixer Constructor
ContractGroupFixer Methods
fix Method
ConvertAliasToGroupFixer Class
ConvertAliasToGroupFixer Members
ConvertAliasToGroupFixer Constructor
ConvertAliasToGroupFixer Methods
fix Method
ConvertPseudoToGroupFixer Class
ConvertPseudoToGroupFixer Members
ConvertPseudoToGroupFixer Constructor
ConvertPseudoToGroupFixer Methods
fix Method
ConvertToAtomFixer Class
ConvertToAtomFixer Members
ConvertToAtomFixer Constructor
ConvertToAtomFixer Methods
fix Method
ConvertToCarbonFixer Class
ConvertToCarbonFixer Members
ConvertToCarbonFixer Constructor
ConvertToCarbonFixer Methods
fix Method
CrossedDoubleBondFixer Class
CrossedDoubleBondFixer Members
CrossedDoubleBondFixer Constructor
CrossedDoubleBondFixer Methods
fix Method
ExpandGroupFixer Class
ExpandGroupFixer Members
ExpandGroupFixer Constructor
ExpandGroupFixer Methods
fix Method
Fixes Interface
Fixes Members
Fixes Methods
value Method
FixesAttribute Class
FixesAttribute Members
FixesAttribute Constructor
FixesAttribute Constructor (StructureCheckerErrorType.__Enum[])
FixesAttribute Constructor (Object[])
FixesExternal Interface
FixesExternal Members
FixesExternal Methods
value Method
FixesExternalAttribute Class
FixesExternalAttribute Members
FixesExternalAttribute Constructor
FixesExternalAttribute Constructor (Object[])
FixesExternalAttribute Constructor (String[])
IsotopeFixer Class
IsotopeFixer Members
IsotopeFixer Constructor
IsotopeFixer Methods
fix Method
MapMoleculeFixer Class
MapMoleculeFixer Members
MapMoleculeFixer Constructor
MapMoleculeFixer Methods
fix Method
MapReactionFixer Class
MapReactionFixer Members
MapReactionFixer Constructor
MapReactionFixer Methods
fix Method
MetalloceneFixer Class
MetalloceneFixer Members
MetalloceneFixer Constructor
MetalloceneFixer Methods
fix Method
PartialCleanFixer Class
PartialCleanFixer Members
PartialCleanFixer Constructor
PartialCleanFixer Methods
fix Method
RearomatizeFixer Class
RearomatizeFixer Members
RearomatizeFixer Constructor
RearomatizeFixer Methods
fix Method
RemoveAtomFixer Class
RemoveAtomFixer Members
RemoveAtomFixer Constructor
RemoveAtomFixer Methods
fix Method
RemoveAtomMapFixer Class
RemoveAtomMapFixer Members
RemoveAtomMapFixer Constructor
RemoveAtomMapFixer Methods
fix Method
RemoveAtomValueFixer Class
RemoveAtomValueFixer Members
RemoveAtomValueFixer Constructor
RemoveAtomValueFixer Methods
fix Method
RemoveAttachedDataFixer Class
RemoveAttachedDataFixer Members
RemoveAttachedDataFixer Constructor
RemoveAttachedDataFixer Methods
fix Method
RemoveBondFixer Class
RemoveBondFixer Members
RemoveBondFixer Constructor
RemoveBondFixer Methods
fix Method
RemoveRadicalFixer Class
RemoveRadicalFixer Members
RemoveRadicalFixer Constructor
RemoveRadicalFixer Methods
fix Method
StructureFixer Interface
StructureFixer Members
StructureFixer Methods
fix Method
getDescription Method
getDescriptor Method
getName Method
setDescription Method
setName Method
UngroupFixer Class
UngroupFixer Members
UngroupFixer Constructor
UngroupFixer Methods
fix Method
ValenceFixer Class
ValenceFixer Members
ValenceFixer Constructor
ValenceFixer Methods
fix Method
WigglyDoubleBondFixer Class
WigglyDoubleBondFixer Members
WigglyDoubleBondFixer Constructor
WigglyDoubleBondFixer Methods
fix Method
chemaxon.formats Namespace
MdlCompressor Class
MdlCompressor Members
MdlCompressor Constructor
MdlCompressor Fields
COMPRESS Field
DECOMPRESS Field
SDF Field
TEXTMODE Field
MdlCompressor Methods
__<clinit> Method
convert Method
convert Method
convert Method (Byte[], Int32)
convert Method (String, Int32)
main Method
MFileFormat Class
MFileFormat Members
MFileFormat Constructor
MFileFormat Fields
ABBREVGROUP Field
AWT_IMAGE Field
BASE64 Field
CDX Field
CDXML Field
CHIME Field
CML Field
CSMDL_IN Field
CSMOL_OUT Field
CSRDF Field
CSRXN_OUT Field
CSSDF_OUT Field
CXSMARTS Field
CXSMILES Field
D2S Field
DNA Field
EMF Field
F_ARCHIVE Field
F_BINARY Field
F_COORDS Field
F_EXPORT Field
F_GRAPHICS Field
F_IMAGE Field
F_IMPORT Field
F_MIXED Field
F_MOLECULE Field
F_MULTIPLE_RECORDS_LEGAL Field
F_MULTIPLE_RECORDS_POSSIBLE Field
F_OBJECT Field
F_REACTION Field
F_RECOGNIZER Field
F_SINGLE_LINE Field
F_USER_DEFINED Field
F_XML Field
GAUSSIAN_CUBE Field
GAUSSIAN_INPUT Field
GAUSSIAN_INPUTZ Field
GAUSSIAN_OUTPUT Field
GZIP Field
INCHI Field
INCHIKEY Field
JPEG Field
JTF Field
MOL Field
MOL_V3_OUT Field
MOL2 Field
MRV Field
MSBMP Field
NAME Field
OSRA Field
PDB Field
PDF Field
PEPTIDE_IN Field
PEPTIDE1_OUT Field
PEPTIDE3_OUT Field
PNG Field
POVRAY Field
PPM Field
RDF Field
RNA Field
RXN Field
RXN_V3_OUT Field
SDF Field
SMARTS Field
SMILES Field
SVG Field
SYBYLMOL Field
VMN Field
XYZ Field
MFileFormat Methods
__<clinit> Method
createExportModule Method
createImportModule Method
createRecognizer Method
createRecordReader Method
getAssociatedNonQueryFormat Method
getAssociatedQueryFormat Method
getDescription Method
getExtensions Method
getFlags Method
getMIMEType Method
getName Method
getNames Method
getPriority Method
isFlagSet Method
matches Method
toString Method
MFileFormatUtil Class
MFileFormatUtil Members
MFileFormatUtil Constructor
MFileFormatUtil Fields
MOLMOVIE Field
MULTISET Field
NOMOLMOVIE Field
MFileFormatUtil Methods
__<clinit> Method
canBeAbbrevgroup Method
canBeJTF Method
canBePDBRecord Method
convertToSmilingFormat Method
convertToSmilingFormat Method (Molecule)
convertToSmilingFormat Method (MProp)
createExportModule Method
createRecordReader Method
createRecordReader Method (, String)
createRecordReader Method (, String, String, String)
findFormats Method
getEncodingFromOptions Method
getFileExtensionLC Method
getFileExtensionLC Method ()
getFileExtensionLC Method (String)
getFormat Method
getJTFFields Method
getKnownExtension Method
getMolfileExtensions Method
getMolfileFormats Method
getMostLikelyMolFormat Method
getUnguessableFormat Method
guessPeptideFormat Method
isCubeLine Method
isOutputCleanable Method
isSubFormatOf Method
isURLOrFileName Method
preprocessFormatAndOptions Method
recognizeOneLineFormat Method
registerFormat Method
splitFileAndOptions Method
splitFormatAndOptions Method
testEncoding Method
MolConverter Class
MolConverter Members
MolConverter Constructor
MolConverter Constructor (MolConverter.Builder)
MolConverter Constructor (MolConverter.Options)
MolConverter Constructor (, , String, Boolean)
MolConverter Constructor (, String, String, Boolean)
MolConverter Constructor (, , String, Boolean)
MolConverter Constructor (, String, String, Boolean)
MolConverter Constructor (, , , String, Boolean)
MolConverter Constructor (, , String, String, Boolean)
MolConverter Constructor (, , , String, Boolean, String[])
MolConverter Constructor (, , , String, Boolean, String[], String)
MolConverter Methods
__<clinit> Method
close Method
close Method
close Method (Int32)
convert Method
createMolConverter Method
main Method
mainWithoutExit Method
otell Method
setIgnoreError Method
setThreadCount Method
MolConverter.Builder Class
MolConverter.Builder Members
MolConverter.Builder Constructor
MolConverter.Builder Methods
addInput Method
addInput Method (, String)
addInput Method (, String)
addInput Method (String, String)
build Method
clean Method
clean Method (Int32)
clean Method (Int32, String)
clear Method
getInputCount Method
setEncodings Method
setFields Method
setOutput Method
setOutput Method (, String)
setOutput Method (, String)
setOutput Method (String, String)
setOutputFlags Method
MolConverter.Options Class
MolConverter.Options Members
MolConverter.Options Constructor
MolConverter.Options Methods
addInput Method
addInput Method (, String)
addInput Method (, String)
addInput Method (String, String)
build Method
clean Method
clean Method (Int32)
clean Method (Int32, String)
clear Method
getInputCount Method
setEncodings Method
setFields Method
setOutput Method
setOutput Method (, String)
setOutput Method (, String)
setOutput Method (String, String)
setOutputFlags Method
MolExporter Class
MolExporter Members
MolExporter Constructor
MolExporter Constructor (, String)
MolExporter Constructor (String, String)
MolExporter Constructor (, String, String)
MolExporter Constructor (, String, Boolean, String[])
MolExporter Constructor (, String, Boolean, String[], String)
MolExporter Constructor (String, String, Int32, String[], String)
MolExporter Fields
C_CLOSE_STREAM Field
C_FLUSH_STREAM Field
FILTER_DIM0 Field
MULTIPLE Field
TEXT Field
MolExporter Methods
__<clinit> Method
close Method
close Method
close Method (Int32)
convertToString Method
exportToBinFormat Method
exportToBinFormat Method (MDocument, String)
exportToBinFormat Method (Molecule, String)
exportToFormat Method
exportToFormat Method (MDocument, String)
exportToFormat Method (Molecule, String)
exportToObject Method
exportToObject Method (MDocument, String)
exportToObject Method (Molecule, String)
exportToObject Method (Molecule[], String, MolExportModule)
flush Method
getFormat Method
isCleanable Method
setClean Method
setClean Method (Int32, String)
setClean Method (Int32, String, MolFilter)
setErrorProcessor Method
setThreadCount Method
write Method
MolFormatException Class
MolFormatException Members
MolFormatException Constructor
MolFormatException Constructor
MolFormatException Constructor (Exception)
MolFormatException Constructor (String)
MolFormatException Constructor (String, Exception)
MolFormatException Methods
getFinalCause Method
getLineNumberInFile Method
getLineNumberInRecord Method
setLineNumberInFile Method
setLineNumberInRecord Method
MolImporter Class
MolImporter Members
MolImporter Constructor
MolImporter Constructor
MolImporter Constructor ()
MolImporter Constructor (String)
MolImporter Constructor (, String)
MolImporter Constructor (, String)
MolImporter Constructor (, String, String)
MolImporter Constructor (String, Object, String)
MolImporter Constructor (, String, String, String)
MolImporter Fields
F_MOLMOVIE Field
MolImporter Methods
close Method
createMol Method
estimateNumRecords Method
getFile Method
getFileName Method
getFormat Method
getGlobalProperties Method
getGrabbedMoleculeString Method
getLineCount Method
getMolImportModule Method
getOptionFlags Method
getOptions Method
getQueryMode Method
getRecordCount Method
getRecordCountMax Method
importDoc Method
importDoc Method (Byte[])
importDoc Method (Byte[], String, String)
importMol Method
importMol Method (Byte[])
importMol Method (String)
importMol Method (Byte[], Molecule)
importMol Method (String, Molecule)
importMol Method (String, String)
importMol Method (Byte[], String, String)
importMol Method (String, String, String)
importMol Method (Byte[], String, String, Molecule)
importMol Method (String, String, String, Molecule)
isEndReached Method
isGrabbingEnabled Method
isMolMovie Method
isMultiSet Method
isRewindable Method
nextDoc Method
parseMRV Method
read Method
read Method
read Method (Molecule)
readDoc Method
readMol Method
readRecordAsText Method
seekRecord Method
setFileName Method
setGrabbingEnabled Method
setOptionFlags Method
setOptions Method
setQueryMode Method
setThreadCount Method
skipRecord Method
skipToNext Method
tell Method
MolInputStream Class
MolInputStream Members
MolInputStream Constructor
MolInputStream Constructor ()
MolInputStream Constructor (, String)
MolInputStream Constructor (, String, String)
MolInputStream Constructor (, String, String, String)
MolInputStream Methods
__<clinit> Method
getFormat Method
getPath Method
setFormat Method
chemaxon.formats.recognizer Namespace
AbbrevGroupRecognizer Class
AbbrevGroupRecognizer Members
AbbrevGroupRecognizer Constructor
AbbrevGroupRecognizer Fields
CAN_BE Field
NO Field
SURE Field
AbbrevGroupRecognizer Methods
needsMore Method
testLine Method
tryToRecognize Method
Base64Recognizer Class
Base64Recognizer Members
Base64Recognizer Constructor
Base64Recognizer Methods
canBeBase64 Method
canBeBase64Line Method
needsMore Method
tryToRecognize Method
ChimeRecognizer Class
ChimeRecognizer Members
ChimeRecognizer Constructor
ChimeRecognizer Methods
__<clinit> Method
canBeChime Method
needsMore Method
tryToRecognize Method
JTFRecognizer Class
JTFRecognizer Members
JTFRecognizer Constructor
JTFRecognizer Methods
canBeJTFHeader Method
needsMore Method
tryToRecognize Method
PDBRecognizer Class
PDBRecognizer Members
PDBRecognizer Constructor
PDBRecognizer Fields
CAN_BE Field
NO Field
SURE Field
PDBRecognizer Methods
__<clinit> Method
needsMore Method
testLine Method
testRecord Method
tryToRecognize Method
PeptideRecognizer Class
PeptideRecognizer Members
PeptideRecognizer Constructor
PeptideRecognizer Methods
canBe1LetterPeptide Method
canBe3LetterPeptide Method
guessPeptideFormat Method
needsMore Method
tryToRecognize Method
Recognizer Class
Recognizer Members
Recognizer Constructor
Recognizer Methods
getLastProcessedLineNum Method
getPriority Method
isLastLine Method
needsMore Method
tryToRecognize Method
SMILESRecognizer Class
SMILESRecognizer Members
SMILESRecognizer Constructor
SMILESRecognizer Methods
__<clinit> Method
canBeSMARTS Method
canBeSMILES Method
isComment Method
isCxSMILESLine Method
needsMore Method
tryToRecognize Method
chemaxon.fragmenter Namespace
CutBondReviser Class
CutBondReviser Members
CutBondReviser Constructor
CutBondReviser Methods
clear Method
create Method
revise Method
set Method
ExhaustiveFragmenter Class
ExhaustiveFragmenter Members
ExhaustiveFragmenter Constructor
ExhaustiveFragmenter Constructor ()
ExhaustiveFragmenter Constructor ()
ExhaustiveFragmenter Constructor (String)
ExhaustiveFragmenter Constructor (RxnMolecule[], Standardizer)
ExhaustiveFragmenter Constructor (RxnMolecule[], Standardizer, CutBondReviser)
ExhaustiveFragmenter Methods
__<clinit> Method
create Method
setExtensive Method
setMaxSetCount Method
Fragmenter Class
Fragmenter Members
Fragmenter Constructor
Fragmenter Constructor
Fragmenter Constructor (RxnMolecule[])
Fragmenter Constructor (RxnMolecule[], Standardizer)
Fragmenter Constructor (RxnMolecule[], Standardizer, CutBondReviser)
Fragmenter Fields
ATTACH_AL_AR Field
ATTACH_ANY_ATOM Field
ATTACH_NONE Field
Fragmenter Methods
__<clinit> Method
collect Method
collect Method (String, String, String, String, String[])
collect Method (String, String, String, String, String[], Boolean)
create Method
find Method
fragment Method
getCutBond Method
getData Method
isCutBond Method
isLicensed Method
main Method
setAttachmentPointType Method
setCountTag Method
setDataInLabel Method
setFragmentSetsTag Method
setLicenseEnvironment Method
setMaxFragmentCount Method
MoleculeFragmenter Class
MoleculeFragmenter Members
MoleculeFragmenter Constructor
MoleculeFragmenter Methods
__<clinit> Method
calculateFragments Method
calculateFragments Method
calculateFragments Method (Molecule)
calculateFragmentsArray Method
isCleaveAliphaticRingBonds Method
isCleaveAromaticBonds Method
isExplicitizedOutput Method
isLicensed Method
main Method
setCleaveAliphaticRingBonds Method
setCleaveAromaticBonds Method
setExplicitizedOutput Method
setLicenseEnvironment Method
setMaxBondCount Method
setMolecule Method
Recap Class
Recap Members
Recap Constructor
Recap Constructor
Recap Constructor (Molecule[], Int32, Int32, Boolean)
Recap Methods
clear Method
revise Method
set Method
setCutRingCHetero Method
setMaxCutCount Method
setMinAtomCount Method
setNotlist Method
chemaxon.jchem.db Namespace
CacheRegistrationUtil Class
CacheRegistrationUtil Members
CacheRegistrationUtil Constructor
CacheRegistrationUtil Fields
CACHE_REGISTRATION_SENSITIVITY_EXCEPTION Field
CACHE_REGISTRATION_SENSITIVITY_LOG Field
CACHE_REGISTRATION_SENSITIVITY_NONE Field
PROP_CACHE_REGISTRATION_SENSITIVITY Field
CacheRegistrationUtil Methods
__<clinit> Method
getCacheID Method
getRegisteredCacheIDs Method
isCacheIDRegistered Method
isPermanent Method
registerCache Method
registerPermanentCache Method
resetCacheID Method
setPermanentCacheID Method
unRegisterCache Method
unRegisterCache Method
unRegisterCache Method (String)
DatabaseConstants Class
DatabaseConstants Members
DatabaseConstants Constructor
DatabaseConstants Fields
ACCESS Field
ACCESS_DRIVER Field
ACCESS_URL_EXAMPLE Field
ACCESS_URL_TEMPLATE Field
COMPOSITE Field
COMPOSITE_DRIVER Field
COMPOSITE_URL_EXAMPLE Field
COMPOSITE_URL_TEMPLATE Field
DB2 Field
DB2_DRIVER Field
DB2_URL_EXAMPLE Field
DB2_URL_TEMPLATE Field
DBMS_DRIVERS Field
DBMS_NAMES Field
DBMS_URL_EXAMPLES Field
DBMS_URL_TEMPLATES Field
DERBY Field
DERBY_DRIVER Field
DERBY_URL_EXAMPLE Field
DERBY_URL_TEMPLATE Field
HSQLDB Field
HSQLDB_DRIVER Field
HSQLDB_URL_EXAMPLE Field
HSQLDB_URL_TEMPLATE Field
INTERBASE Field
INTERBASE_DRIVER Field
INTERBASE_URL_EXAMPLE Field
INTERBASE_URL_TEMPLATE Field
MSSQL Field
MSSQL_DRIVER Field
MSSQL_URL_EXAMPLE Field
MSSQL_URL_TEMPLATE Field
MSSQL2005 Field
MSSQL2005_DRIVER Field
MSSQL2005_URL_EXAMPLE Field
MSSQL2005_URL_TEMPLATE Field
MYSQL Field
MYSQL_DRIVER Field
MYSQL_URL_EXAMPLE Field
MYSQL_URL_TEMPLATE Field
ORACLE Field
ORACLE_DRIVER Field
ORACLE_URL_EXAMPLE Field
ORACLE_URL_TEMPLATE Field
POSGRESQL_DRIVER Field
POSGRESQL_URL_EXAMPLE Field
POSGRESQL_URL_TEMPLATE Field
POSTGRESQL Field
DatabaseConstants Methods
__<clinit> Method
getDefaultDerbySettings Method
DatabaseProperties Class
DatabaseProperties Members
DatabaseProperties Constructor
DatabaseProperties Constructor (ConnectionHandler)
DatabaseProperties Constructor (ConnectionHandler, Boolean)
DatabaseProperties Fields
DEFAULT_PROPERTY_TABLE Field
MD_PROPERTY_PREFIX Field
NAME_COLUMN Field
PROP_READONLY_DATABASE_NAME Field
VALUE_COLUMN Field
VALUE_COLUMN_EXT Field
DatabaseProperties Methods
__<clinit> Method
addProperty Method
close Method
createPropertyTable Method
createPropertyTable Method (ConnectionHandler)
createPropertyTable Method (ConnectionHandler, Int32)
deleteChemTermForColumn Method
deleteMDTableProperty Method
deleteProperty Method
deleteTableProperties Method
deleteTableProperty Method
getAllProperties Method
getCacheRegistrationTableName Method
getCacheRegistrationTableName Method
getCacheRegistrationTableName Method (ConnectionHandler)
getChemTermColumns Method
getChemTermForColumn Method
getFingerprintParams Method
getIntProperty Method
getMDConfigs Method
getMDTableProperty Method
getMolecularDescriptors Method
getProperty Method
getStructureTableNames Method
getTableIntProperty Method
getTableProperties Method
getTableProperty Method
getTableType Method
incrementProperty Method
isChemTermColumnDefined Method
isDatabaseReadonly Method
isDuplicateFilteringOption Method
isGenericTautomerProtectsChirality Method
isMolecularDescriptorDefined Method
isSetSwitchOffAllProtectionsForTDF Method
isTautomerDuplicateFilteringEnabled Method
isUsePreparedStatement Method
propertyTableExists Method
setAbsoluteStereoOption Method
setCacheRegistrationTableName Method
setChemTermForColumn Method
setDuplicateFilteringOption Method
setMDTableProperty Method
setProperty Method
setStandardizerConfigOption Method
setTableProperty Method
setTautomerDuplicateFilteringOption Method
setUsePreparedStatement Method
updateProperty Method
DatabaseSearchException Class
DatabaseSearchException Members
DatabaseSearchException Constructor
DatabaseSearchException Constructor
DatabaseSearchException Constructor (Exception)
DatabaseSearchException Constructor (String)
DatabaseSearchException Constructor (String, Exception)
Exporter Class
Exporter Members
Exporter Constructor
Exporter Methods
__<clinit> Method
getConditions Method
getConnectionHandler Method
getDelimiter Method
getEol Method
getFieldList Method
getFormat Method
getIDList Method
getOutputFieldConversion Method
getOutputFieldNames Method
getOutputStream Method
getQuotation Method
getTableName Method
isDefaults Method
isJtfWithStructure Method
setConditions Method
setConnectionHandler Method
setDefaults Method
setDelimiter Method
setEol Method
setFieldList Method
setFormat Method
setIDList Method
setJtfWithStructure Method
setOutputFieldConversion Method
setOutputFieldNames Method
setOutputStream Method
setQuotation Method
setSelectStatement Method
setTableName Method
writeAll Method
writeNext Method
Importer Class
Importer Members
Importer Constructor
Importer Methods
__<clinit> Method
cancel Method
getConnectionHandler Method
getConnections Method
getDuplicateIDs Method
getDuplicates Method
getEmptyStructures Method
getEmptyStructuresAllowed Method
getErrorCause Method
getErrorMessage Method
getFieldConnections Method
getFieldNames Method
getFieldNames Method
getFieldNames Method (, Int32)
getImportedIDs Method
getImportedNumber Method
getInput Method
getLinesToCheck Method
getNameFieldInDB Method
getNote Method
getProgress Method
getProgressWriter Method
getSetChiralFlag Method
getSkip Method
getStructCount Method
getTableName Method
importMols Method
init Method
isDuplicateImportAllowed Method
isFinished Method
isHaltOnError Method
run Method
setConnectionHandler Method
setConnections Method
setDuplicateImportAllowed Method
setDuplicateImportAllowed Method (Boolean)
setDuplicateImportAllowed Method (Int32)
setEmptyStructuresAllowed Method
setFieldConnections Method
setHaltOnError Method
setInfoStream Method
setInput Method
setInput Method ()
setInput Method ()
setInput Method (String)
setLinesToCheck Method
setNameFieldInDB Method
setOutputOptions Method
setProgressWriter Method
setSetChiralFlag Method
setSkip Method
setStoreDuplicates Method
setStoreImportedIDs Method
setTableName Method
skip Method
JChemSearch Class
JChemSearch Members
JChemSearch Constructor
JChemSearch Constructor
JChemSearch Constructor (Object)
JChemSearch Constructor (String, String)
JChemSearch Constructor (String, String, Object)
JChemSearch Fields
APPEND_TO_RESULT_TABLE Field
CREATE_OR_REPLACE_RESULT_TABLE Field
NO_ORDERING Field
NO_RESULT_TABLE Field
ORDERING_BY_FILTER_ID_LIST Field
ORDERING_BY_ID Field
ORDERING_BY_ID_OR_SIMILARITY Field
RUN_MODE_ASYNCH_COMPLETE Field
RUN_MODE_ASYNCH_PROGRESSIVE Field
RUN_MODE_SYNCH_COMPLETE Field
JChemSearch Methods
__<clinit> Method
cleanResults Method
clearCache Method
createJCSObserver Method
getAvailableNewHits Method
getCachedTables Method
getCacheError Method
getCacheLoadTime Method
getCacheSize Method
getCacheSizeEstimate Method
getConnection Method
getConnectionHandler Method
getCurrentId Method
getDissimilarity Method
getDissimilarity Method
getDissimilarity Method (Int32)
getDissimilarityMetrics Method
getEnumerationCount Method
getException Method
getFirstHitTime Method
getHitsAsHitDisplayTool Method
getHitsAsMolecules Method
getHitsAsRgDecomp Method
getNextHit Method
getNumberOfProcessingThreads Method
getOrder Method
getProgressMessage Method
getQueryStructure Method
getResult Method
getResultCount Method
getResults Method
getResultTable Method
getResultTableMode Method
getRunMode Method
getScreenedCount Method
getScreenedCountTotal Method
getScreenedCountUnique Method
getScreenedResults Method
getScreeningTime Method
getSearchOptions Method
getSearchTime Method
getStructureTable Method
getTimeout Method
hasMoreHits Method
Implicit Operator
isInfoToStdError Method
isLicensed Method
isMaxResultCountReached Method
isMaxTimeReached Method
isRunning Method
isTargetMarkush Method
run Method
setCacheExpirationTime Method
setConnectionHandler Method
setFilterIDList Method
setFilterIDNotList Method
setInfoToStdError Method
setLicenseEnvironment Method
setMaxCacheSize Method
setMinNonCachedMemory Method
setNumberOfProcessingThreads Method
setOrder Method
setQueryFingerprint Method
setQueryStructure Method
setQueryStructure Method (Molecule)
setQueryStructure Method (String)
setRegCode Method
setResultTable Method
setResultTableMode Method
setRunMode Method
setRunning Method
setSearchOptions Method
setStructureTable Method
setThreadPriority Method
setTimeout Method
waitUntilSearchComplete Method
JChemSearch.DissimilarityMetrics Class
JChemSearch.DissimilarityMetrics Members
JChemSearch.DissimilarityMetrics Constructor
JChemSearch.DissimilarityMetrics Fields
defaultDissimilarityMetricThresholds Field
defaultMetricIndex Field
metricNames Field
name Field
numOfParam Field
paramDefault Field
paramHelp Field
paramNames Field
paramRanges Field
MaxSearchFrequencyExceededException Class
MaxSearchFrequencyExceededException Members
MaxSearchFrequencyExceededException Constructor
MaxSearchFrequencyExceededException Constructor
MaxSearchFrequencyExceededException Constructor (String)
MDTableHandler Class
MDTableHandler Members
MDTableHandler Constructor
MDTableHandler Constructor (ConnectionHandler, String)
MDTableHandler Constructor (ConnectionHandler, String, Boolean)
MDTableHandler Fields
MD_PROPERTY_COMMENT Field
MD_PROPERTY_CONF_PREFIX Field
MD_PROPERTY_SETTINGS Field
MD_PROPERTY_TYPE Field
MD_PROPERTY_UPDATE Field
MDTableHandler Methods
createMD Method
createMDSet Method
createMDTable Method
createMDTable Method (String, String, String, String)
createMDTable Method (String, String, String, String, Boolean)
deleteMDConfig Method
deleteMDTable Method
getMDComment Method
getMDConfig Method
getMDConfigs Method
getMDSettings Method
getMDTableName Method
getMDTables Method
getMDType Method
getMDUpdateOnInsert Method
getMolecularDescriptors Method
incRegenerateDescriptorTable Method
isMDTableValid Method
isMDTableValidByAllIDs Method
setMDConfig Method
PropertyNotSetException Class
PropertyNotSetException Members
PropertyNotSetException Constructor
PropertyNotSetException Constructor
PropertyNotSetException Constructor (String)
RecalculationException Class
RecalculationException Members
RecalculationException Constructor
RecalculationException Constructor
RecalculationException Constructor (String)
RegenerationChecker Class
RegenerationChecker Members
RegenerationChecker Constructor
RegenerationChecker Fields
ATTR_ID Field
ATTR_OPERATION Field
OPER_EQUALS Field
OPER_NOT_EQUALS Field
TAG_CONDITION Field
TAG_CT Field
TAG_FULL Field
TAG_MD Field
TAG_NOCT Field
TAG_PROPERTY Field
TAG_PROPERTY_NAME Field
TAG_PROPERTY_VALUE Field
TAG_TABLE_VERSION Field
RegenerationChecker Methods
__<clinit> Method
deduceTableVersion Method
deduceTableVersion Method (String, DatabaseProperties)
deduceTableVersion Method (String, DatabaseProperties, Int32)
getColumnsToRegenerate Method
getRegenerationTypeForTable Method
getTablesToRegenerate Method
getTablesToRegenerate Method (ConnectionHandler, Int32)
getTablesToRegenerate Method (ConnectionHandler, Int32, ProgressWriter)
getXml Method
isRegenerationNeeded Method
isRegenerationNeeded Method (String, DatabaseProperties)
isRegenerationNeeded Method (String, DatabaseProperties, Int32)
isRegenerationNeeded Method (String, DatabaseProperties, , Int32)
isRegenerationNeededExact Method
RegenerationConstants Class
RegenerationConstants Members
RegenerationConstants Constructor
RegenerationConstants Fields
EXCLUDED_CD_FIELDS Field
GROUP_TYPE_ANY Field
REGENERATION_MODE_NORMAL Field
REGENERATION_MODE_NOT_PRECALCULATED Field
REGENERATION_MODE_PRECALCULATION Field
REGENERATION_TYPE_ANY Field
REGENERATION_TYPE_CT Field
REGENERATION_TYPE_FULL Field
REGENERATION_TYPE_MD Field
REGENERATION_TYPE_NONE Field
REGENERATION_TYPE_WITHOUT_CT Field
TABLE_VERSION_NEWER Field
TABLE_VERSION_OK Field
TABLE_VERSION_OLDER Field
RegenerationConstants Methods
__<clinit> Method
StructureTableOptions Class
StructureTableOptions Members
StructureTableOptions Constructor
StructureTableOptions Fields
absoluteStereo Field
cartridgeIndexTable Field
chemTermColsConfig Field
duplicateFiltering Field
extraColumnDefinitions Field
fp_numberOfEdges Field
fp_numberOfInts Field
fp_numberOfOnes Field
mysqlTableType Field
name Field
standardizerConfig Field
structuralKeyConfig Field
structureColumnType Field
tableType Field
tautomerDuplicateChecking Field
tautomerSwitchOffAllProtections Field
TableStatistics Class
TableStatistics Members
TableStatistics Constructor
TableStatistics Constructor
TableStatistics Constructor (Boolean)
TableStatistics Methods
collectStatisitcs Method
getPrintableStats Method
TableTypeConstants Interface
TableTypeConstants Members
TableTypeConstants Constructor
TableTypeConstants Fields
FP_DEFAULT_BITS_PER_PATTERN Field
FP_DEFAULT_LENGTH_IN_INTS Field
FP_DEFAULT_PATTERN_LENGTH Field
MYSQL_DEFAULT_TABLE_TYPE Field
MYSQL_FORCE_INNO_DB Field
MYSQL_FORCE_MYISAM Field
TABLE_TYPE_ANY_STRUCTURES Field
TABLE_TYPE_DEFAULT Field
TABLE_TYPE_EXPLANATIONS Field
TABLE_TYPE_IS_NOT_SUPPORTED Field
TABLE_TYPE_MARKUSH_LIBRARIES Field
TABLE_TYPE_MOLECULES Field
TABLE_TYPE_NAMES Field
TABLE_TYPE_QUERY_STRUCTURES Field
TABLE_TYPE_REACTIONS Field
TableTypeConstants Methods
__<clinit> Method
TableTypeConstants.__Fields Class
TableTypeConstants.__Fields Members
TableTypeConstants.__Fields Fields
FP_DEFAULT_BITS_PER_PATTERN Field
FP_DEFAULT_LENGTH_IN_INTS Field
FP_DEFAULT_PATTERN_LENGTH Field
MYSQL_DEFAULT_TABLE_TYPE Field
MYSQL_FORCE_INNO_DB Field
MYSQL_FORCE_MYISAM Field
TABLE_TYPE_ANY_STRUCTURES Field
TABLE_TYPE_DEFAULT Field
TABLE_TYPE_EXPLANATIONS Field
TABLE_TYPE_IS_NOT_SUPPORTED Field
TABLE_TYPE_MARKUSH_LIBRARIES Field
TABLE_TYPE_MOLECULES Field
TABLE_TYPE_NAMES Field
TABLE_TYPE_QUERY_STRUCTURES Field
TABLE_TYPE_REACTIONS Field
TransferException Class
TransferException Members
TransferException Constructor
TransferException Constructor
TransferException Constructor (String)
TransferException Constructor (String, Exception)
UpdateHandler Class
UpdateHandler Members
UpdateHandler Constructor
UpdateHandler Constructor
UpdateHandler Constructor (ConnectionHandler, Int32, String, String)
UpdateHandler Constructor (ConnectionHandler, Int32, String, String, String, String)
UpdateHandler Fields
DUPLICATE_FILTERING_OFF Field
DUPLICATE_FILTERING_ON Field
DUPLICATE_FILTERING_TABLE_OPTION Field
INSERT Field
INSERT_WITH_ID Field
QUERY_TABLE_ENUMERATION_LIMIT Field
UPDATE Field
UpdateHandler Methods
__<clinit> Method
checkChemTermColValue Method
close Method
createRowData Method
createRowData Method (Byte[])
createRowData Method (String)
createStructureTable Method
deleteRow Method
deleteRow Method (ConnectionHandler, String, Int32)
deleteRow Method (ConnectionHandler, String, Int32, Boolean)
deleteRows Method
deleteRows Method (ConnectionHandler, String, String)
deleteRows Method (ConnectionHandler, String, String, Boolean)
dropStructureTable Method
execute Method
execute Method
execute Method (Boolean)
getMolecule Method
getPrecalculatedRowNumber Method
getPreferredTableType Method
getSetChiralFlag Method
getStructureNameField Method
getStructureTables Method
init Method
isInsertable Method
isLoggingEnabled Method
recalculateCTColumns Method
recalculateCTColumns Method (ConnectionHandler, String, String[], ProgressWriter)
recalculateCTColumns Method (ConnectionHandler, String, String[], ProgressWriter, Int32)
recalculateMDTables Method
recalculateTable Method
recalculateTable Method (ConnectionHandler, String, Boolean, String, , , ProgressWriter)
recalculateTable Method (ConnectionHandler, String, Boolean, String, , , ProgressWriter, Int32)
recalculateWithoutCTColumns Method
recalculateWithoutCTColumns Method (ConnectionHandler, String, Boolean, String, , ProgressWriter)
recalculateWithoutCTColumns Method (ConnectionHandler, String, Boolean, String, , ProgressWriter, Int32)
saveUpdateLogs Method
setChemTermCalc Method
setDuplicateFiltering Method
setDuplicateFiltering Method (Boolean)
setDuplicateFiltering Method (Int32)
setEmptyStructuresAllowed Method
setID Method
setIgnoreChemicalTermsExceptions Method
setLoggingEnabled Method
setRowData Method
setROWID Method
setSetChiralFlag Method
setStandardizationEnabled Method
setStructure Method
setStructure Method (Byte[])
setStructure Method (String)
setStructureNameField Method
setValueForAdditionalColumn Method
setValueForAdditionalColumn Method (Int32, Object)
setValueForAdditionalColumn Method (Int32, Object, Int32)
UpdateHandler.RowData Class
UpdateHandler.RowData Members
UpdateHandler.RowData Constructor
UpdateHandler.RowData Fields
chemTermColValues Field
fingerprint Field
flags Field
formula Field
genericTautomer Field
hashCode Field
isMarkush Field
molecule Field
molName Field
F:chemaxon.jchem.db.UpdateHandler.RowData.molRecord/chemaxon.jchem.file.MolRecord
molString Field
molWeight Field
noRingInfoInFP Field
reactionMappingIncomplete Field
smiles Field
sortableFormula Field
UpdateHandler.RowData Methods
getMarkushData Method
UpdateHandlerException Class
UpdateHandlerException Members
UpdateHandlerException Constructor
UpdateHandlerException Constructor
UpdateHandlerException Constructor (Exception)
UpdateHandlerException Constructor (String)
UpdateHandlerException Constructor (String, Exception)
Updater Class
Updater Members
Updater Constructor
Updater Constructor (ConnectionHandler)
Updater Constructor (ConnectionHandler, )
Updater Methods
__<clinit> Method
getNextUpdateInfo Method
getNextUpdateInfo Method
getNextUpdateInfo Method (ProgressWriter)
isUpdateNeededForTable Method
performCurrentUpdate Method
performCurrentUpdate Method
performCurrentUpdate Method (ProgressWriter)
Updater.UpdateInfo Class
Updater.UpdateInfo Members
Updater.UpdateInfo Constructor
Updater.UpdateInfo Fields
entityList Field
isOperationRequired Field
isProgressMonitoringSupported Field
isRegeneration Field
isStructuralChange Field
message Field
processingMessage Field
regenerationType Field
Updater.UpdateInfo Methods
Implicit Operator
chemaxon.jchem.file Namespace
ProgressWriter Class
ProgressWriter Members
ProgressWriter Constructor
ProgressWriter Fields
ERROR Field
INFO Field
WARNING Field
ProgressWriter Methods
addLogger Method
calcExpTime Method
close Method
getExpTimeString Method
getMaximum Method
getMinimum Method
getNote Method
getProgress Method
getRemainingDays Method
getRemainingHours Method
getRemainingMinutes Method
getRemainingSeconds Method
getText Method
isCanceled Method
log Method
reset Method
setCanceled Method
setMaximum Method
setMinimum Method
setNote Method
setProgress Method
setText Method
ProgressWriter.Logger Interface
ProgressWriter.Logger Members
ProgressWriter.Logger Methods
addMessage Method
chemaxon.jchem.version Namespace
VersionInfo Class
VersionInfo Members
VersionInfo Constructor
VersionInfo Fields
JCHEM_MAIN_VERSION Field
JCHEM_REVISION_NUMBER Field
JCHEM_TABLE_VERSION Field
JCHEM_VERSION Field
VersionInfo Methods
__<clinit> Method
getInternalVersionId Method
main Method
chemaxon.jep Namespace
ChemContext Class
ChemContext Members
ChemContext Constructor
ChemContext Methods
callback Method
clear Method
getContextFunctionNames Method
Implicit Operator
ChemJEP Class
ChemJEP Members
ChemJEP Constructor
ChemJEP Constructor
ChemJEP Constructor ()
ChemJEP Fields
FALSE Field
TRUE Field
UNDECIDED Field
ChemJEP Methods
__<clinit> Method
addFunction Method
callback Method
compile Method
evaluate Method
evaluate_boolean Method
evaluate_booleans Method
evaluate_double Method
evaluate_doubles Method
getLogicalValue Method
isUndecided Method
Evaluator Class
Evaluator Members
Evaluator Constructor
Evaluator Constructor
Evaluator Constructor (Standardizer)
Evaluator Constructor ()
Evaluator Constructor (String)
Evaluator Constructor (, Standardizer)
Evaluator Constructor (String, Standardizer)
Evaluator Constructor (, Standardizer, MolImporter, String)
Evaluator Constructor (String, Standardizer, MolImporter, String)
Evaluator Fields
CONFIG_DIR Field
DEFAULT_TAG_NAME Field
EVALUATOR_DEFAULTS_FILE Field
EVALUATOR_NAMED_MOLS_FILE Field
EVALUATOR_SCRIPT_FILE Field
Evaluator Methods
__<clinit> Method
compile Method
compile Method (String)
compile Method (String, )
compile Method (String, , Object)
getFunctionalGroupDisplayMolTable Method
getFunctionData Method
getFunctionData Method
getFunctionData Method (Boolean)
getFunctionParameterData Method
getPluginIDs Method
getSymbolTable Method
Implicit Operator
main Method
runScript Method
setFingerprintGenerator Method
setLicenseEnvironment Method
setVerbose Method
toString Method
toString Method (Object)
toString Method (Object, )
toString Method (Object, Int32)
FingerprintGenerator Interface
FingerprintGenerator Members
FingerprintGenerator Methods
getFingerprint Method
MolCondition Interface
MolCondition Members
MolCondition Methods
check Method
setParameters Method
Standardizer Interface
Standardizer Members
Standardizer Methods
standardize Method
chemaxon.jep.context Namespace
AtomContext Class
AtomContext Members
AtomContext Constructor
AtomContext Fields
CFNS Field
AtomContext Methods
__<clinit> Method
callback Method
clear Method
getAtom Method
getContextFunctionNames Method
setAtom Method
MolContext Class
MolContext Members
MolContext Constructor
MolContext Constructor
MolContext Constructor (Molecule)
MolContext Fields
CFNS Field
MolContext Methods
__<clinit> Method
callback Method
clear Method
getContextFunctionNames Method
getFingerprint Method
getMolecule Method
setFingerprint Method
setMolecule Method
ReactionContext Class
ReactionContext Members
ReactionContext Constructor
ReactionContext Constructor
ReactionContext Constructor (Boolean)
ReactionContext Fields
CFNS Field
ReactionContext Methods
__<clinit> Method
callback Method
clear Method
getContextFunctionNames Method
isEmpty Method
setProductAtomsByMap Method
setProducts Method
setReactantAtomsByMap Method
setReactants Method
SearchContext Class
SearchContext Members
SearchContext Constructor
SearchContext Fields
CFNS Field
SearchContext Methods
__<clinit> Method
callback Method
clear Method
getContextFunctionNames Method
getQuery Method
getQueryFingerprint Method
getTarget Method
getTargetFingerprint Method
setHit Method
setQuery Method
setQueryFingerprint Method
setTarget Method
setTargetFingerprint Method
chemaxon.license Namespace
LicenseManager Class
LicenseManager Members
LicenseManager Constructor
LicenseManager Fields
ALIGNMENT Field
CALCULATIONS_PACK Field
CARTRIDGE Field
CHARGE_PLUGIN_GROUP Field
CONFORMATION_PLUGIN_GROUP Field
DOCUMENT_TO_STRUCTURE Field
ECFP_FCFP Field
FRAGMENTER Field
GEOMETRY_PLUGIN_GROUP Field
HBDA_PLUGIN Field
HUCKEL_ANALYSIS_PLUGIN Field
INSTANT_JCHEM Field
INSTANT_JCHEM_VIZ Field
ISOMERS_PLUGIN_GROUP Field
IUPAC_NAMING_PLUGIN Field
JCHEM Field
JCHEM_FOR_EXCEL Field
JKLUSTOR Field
MARKUSH_ENUM_PLUGIN Field
MARKUSH_SEARCH Field
MARVIN_APPLETS Field
MARVIN_BEANS Field
MCES Field
METABOLIZER Field
MOLECULAR_DESCRIPTORS Field
NAME_TO_STRUCTURE Field
PARTITIONING_PLUGIN_GROUP Field
PREDICTOR_PLUGIN Field
PROTONATION_PLUGIN_GROUP Field
REACTOR Field
REFRACTIVITY_PLUGIN Field
REGISTRATION_SYSTEM Field
SCREEN Field
SCREEN3D Field
SHAREPOINT Field
STANDARDIZER Field
STRUCTURAL_FRAMEWORKS_PLUGIN Field
STRUCTURE_CHECKER Field
STRUCTURE_TO_NAME Field
WEB_SERVICES_SERVER Field
LicenseManager Methods
createLicenseManagerPanel Method
getLicenseExceptionMessage Method
getLicenseExceptionPanel Method
getLicenseExceptionPanel Method (Object)
getLicenseExceptionPanel Method (String)
getPluginList Method
getProductList Method
isLicensed Method
refresh Method
setLicense Method
setLicenseFile Method
chemaxon.marvin Namespace
MolPrinter Class
MolPrinter Members
MolPrinter Constructor
MolPrinter Constructor
MolPrinter Constructor (MDocument)
MolPrinter Constructor (MoleculeGraph)
MolPrinter Methods
getAtomSize Method
M:chemaxon.marvin.MolPrinter.getAtomSize
getBackgroundColor Method
getBallRadius Method
getBondSpacing Method
getBondWidth Method
getBoundingRectangle Method
getCarbonVisibility Method
getChiralitySupport Method
getColorScheme Method
getCoordinateBondStyle Method
getCoordinateBondStyleAtMulticenter Method
getDisplayQuality Method
getDispopts Method
getDispoptsExt Method
getDownWedge Method
getImplicitH Method
getLigandOrderVisibility Method
getRendering Method
getScale Method
getStickThickness Method
getWireThickness Method
isAtomMappingVisible Method
isAtomNumbersVisible Method
isAtomPropertiesVisible Method
isAtomSymbolsVisible Method
isBondLengthVisible Method
isExplicitHVisible Method
isEZLabelsVisible Method
isEzVisible Method
isGraphInvariantVisible Method
isLigandErrorVisible Method
isLonePairsAutoCalculated Method
isLonePairsVisible Method
isRLogicVisible Method
isSetColoringEnabled Method
isTransparent Method
isValenceErrorvisible Method
isValencePropertyVisible Method
maxScale Method
maxScale Method ()
maxScale Method ()
molToScreenCoords Method
paint Method
paint Method (, )
paint Method (, )
paint Method (, )
setAtomMappingVisible Method
setAtomNumbersVisible Method
setAtomPropertiesVisible Method
setAtomSize Method
M:chemaxon.marvin.MolPrinter.setAtomSize(System.Double)
setAtomSymbolsVisible Method
setBackgroundColor Method
setBallRadius Method
setBondLengthVisible Method
setBondSpacing Method
setBondWidth Method
setCarbonVisibility Method
setChiralitySupport Method
setColorScheme Method
setCoordinateBondStyle Method
setCoordinateBondStyleAtMulticenter Method
setDisplayQuality Method
setDispopts Method
setDispopts Method (Int32)
setDispopts Method (Int32, Int32)
setDispoptsExt Method
setDispoptsExt Method (Int32)
setDispoptsExt Method (Int32, Int32)
setDoc Method
setDownWedge Method
setExplicitH Method
setExplicitHVisible Method
setEZLabelsVisible Method
setEzVisible Method
setGraphInvariantVisible Method
setImplicitH Method
setLigandErrorVisible Method
setLigandOrderVisibility Method
setLonePairsAutoCalculated Method
setLonePairsVisible Method
setMol Method
setMol Method (Molecule)
setMol Method (String)
setMolTemplate Method
setRendering Method
setRLogicVisible Method
setScale Method
setSetColoringEnabled Method
setStickThickness Method
setTransparent Method
setValenceErrorVisible Method
setValencePropertyVisible Method
setWireThickness Method
VersionInfo Class
VersionInfo Members
VersionInfo Constructor
VersionInfo Fields
IS_SUPPORTED_JAVA Field
MARVIN_MAJOR_VERSION Field
MARVIN_VERSION Field
VersionInfo Methods
__<clinit> Method
buildDate Method
main Method
chemaxon.marvin.alignment Namespace
AlignmentAccuracyMode Class
AlignmentAccuracyMode Members
AlignmentAccuracyMode Fields
ACCURATE Field
FAST Field
NORMAL Field
AlignmentAccuracyMode Methods
__<clinit> Method
getMode Method
valueOf Method
values Method
AlignmentAccuracyMode.__Enum Enumeration
AlignmentMolecule Class
AlignmentMolecule Members
AlignmentMolecule Methods
<bridge>clone Method
clearAssigned Method
clone Method
crdMolRefresh Method
crdSafeRefresh Method
create Method
getAtomCount Method
getColoringScheme Method
getColors Method
getMolCrd Method
getMoleculeOrig Method
getMolID Method
getNodeCount Method
getNodes Method
getRotBondCount Method
getVolume Method
Implicit Operator
initVariables Method
isAssigned Method
isEnableTranslateAndRotate Method
setAssigned Method
setEnableTranslateAndRotate Method
showSelectedNodes Method
toData Method
toString Method
updateGaussianProducts Method
AlignmentMoleculeFactory Class
AlignmentMoleculeFactory Members
AlignmentMoleculeFactory Constructor
AlignmentMoleculeFactory Methods
generate Method
generateData Method
getColor Method
getFlexibleRingRotatableBondCount Method
getFlexibleRingSize Method
getProgressBar Method
getResultMolecule Method
isAromatize Method
isCreateRingCenters Method
isDehidrogenize Method
isGenerateDistanceRanges Method
setAromatize Method
setColor Method
setDehidrogenize Method
setFlexibleRingRotatableBondCount Method
setFlexibleRingSize Method
setGenerateDistanceRanges Method
setNodeType Method
setNotSpecCase Method
setProgressBar Method
AlignmentMoleculeFactory.ProgressBarInterface Interface
AlignmentMoleculeFactory.ProgressBarInterface Members
AlignmentMoleculeFactory.ProgressBarInterface Methods
setMaximum Method
setMessage Method
setMinimum Method
setProgress Method
start Method
stop Method
AlignmentProperties Class
AlignmentProperties Members
AlignmentProperties Fields
GAUSS_44_SAME Field
GAUSS_FAST_EXTENDED_ATOMTYPE Field
GAUSS_FAST_EXTENDED_ATOMTYPE_MCS Field
GAUSS_FAST_PHARMACOPHORE Field
GAUSS_FAST_SHAPE_ONLY Field
PAIRED Field
AlignmentProperties Methods
__<clinit> Method
getColor Method
getNotSpec Method
getOrientation Method
Implicit Operator
isDistancerangeSet Method
valueOf Method
values Method
AlignmentProperties.__Enum Enumeration
AlignmentProperties.ColoringScheme Class
AlignmentProperties.ColoringScheme Members
AlignmentProperties.ColoringScheme Fields
ATOM_TYPES Field
EXTENDED_ATOMTYPES Field
PHARMACOPHORE Field
SAME Field
AlignmentProperties.ColoringScheme Methods
__<clinit> Method
Implicit Operator
valueOf Method
values Method
AlignmentProperties.ColoringScheme.__Enum Enumeration
AlignmentProperties.ColorNotSpecifiedCase Class
AlignmentProperties.ColorNotSpecifiedCase Members
AlignmentProperties.ColorNotSpecifiedCase Fields
ACCEPT_ONLY_SAME Field
DENY_IF_NOT_SPECIFIED Field
EVERY_WEIGHT_IS_ONE Field
AlignmentProperties.ColorNotSpecifiedCase Methods
__<clinit> Method
valueOf Method
values Method
AlignmentProperties.ColorNotSpecifiedCase.__Enum Enumeration
AlignmentProperties.NodeType Class
AlignmentProperties.NodeType Members
AlignmentProperties.NodeType Fields
GAUSS_VOLUME_SIMPLE_44 Field
GAUSS_VOLUME_SIMPLE_45 Field
GAUSS_VOLUME_SIMPLE_FAST Field
GAUSS_VOLUME_SIMPLE_FULL Field
MODEL_NODE Field
SIMPLE Field
AlignmentProperties.NodeType Methods
__<clinit> Method
Implicit Operator
isGaussLike Method
valueOf Method
values Method
AlignmentProperties.NodeType.__Enum Enumeration
AlignmentProperties.OrientationType Class
AlignmentProperties.OrientationType Members
AlignmentProperties.OrientationType Fields
ALIGN_AS_IS Field
MCS Field
SIMPLE Field
AlignmentProperties.OrientationType Methods
__<clinit> Method
Implicit Operator
valueOf Method
values Method
AlignmentProperties.OrientationType.__Enum Enumeration
AlignRigidEasy Class
AlignRigidEasy Members
AlignRigidEasy Constructor
AlignRigidEasy Methods
align Method
align Method
align Method (Int32[][])
convert Method
getReferenceAndRotatedFused Method
getRotatedCoordinates Method
getRotatedMolecule Method
isLicensed Method
rmsd Method
setLicenseEnvironment Method
setReference Method
setReference Method (Molecule)
setReference Method (Double[][])
setRotatable Method
setRotatable Method (Molecule)
setRotatable Method (Double[][])
AtropIsomerDetector Class
AtropIsomerDetector Members
AtropIsomerDetector Constructor
AtropIsomerDetector Methods
calculate Method
getAtropBonds Method
getPossibleRotatableBondCount Method
getRealRotatableBondCount Method
getResultMolecule Method
isLicensed Method
setBarrierLimit Method
setFlexibleRingRotatableBondCount Method
setFlexibleRingSize Method
setLicenseEnvironment Method
setMethylsRotatable Method
setNumberOfAtomsAcceptToRotate Method
setSamplingAccuracy Method
setSamplingAccuracy Method (AtropIsomerDetector.Accuracy)
setSamplingAccuracy Method (Int32)
AtropIsomerDetector.Accuracy Class
AtropIsomerDetector.Accuracy Members
AtropIsomerDetector.Accuracy Fields
ACCURATE Field
FAST Field
NORMAL Field
AtropIsomerDetector.Accuracy Methods
__<clinit> Method
getSteps Method
valueOf Method
values Method
AtropIsomerDetector.Accuracy.__Enum Enumeration
DihedralRotator Class
DihedralRotator Members
DihedralRotator Constructor
DihedralRotator Methods
rotateBy Method
rotateTo Method
PairwiseAlignment Class
PairwiseAlignment Members
PairwiseAlignment Constructor
PairwiseAlignment Constructor
PairwiseAlignment Constructor (AlignmentProperties)
PairwiseAlignment Methods
addNodeColorWeight Method
getAlignedMoleculesAsFragments Method
getAlignedQuery Method
getAlignedTarget Method
getShapeTanimoto Method
removeAllMolecules Method
setCount Method
setFlexibleRingSize Method
setLicenseEnvironment Method
setMinimumCommonSize Method
setMode Method
setProgressBar Method
setProgressMonitor Method
setQuery Method
setQuery Method (AlignmentMolecule)
setQuery Method (Molecule)
setQueryRigidForced Method
setTargetRigidForced Method
similarity Method
similarity Method (AlignmentMolecule)
similarity Method (Molecule)
PairwiseComparison Interface
PairwiseComparison Members
PairwiseComparison Methods
addNodeColorWeight Method
getAlignedMoleculesAsFragments Method
getAlignedQuery Method
getAlignedTarget Method
getShapeTanimoto Method
removeAllMolecules Method
setCount Method
setLicenseEnvironment Method
setProgressBar Method
setQuery Method
setQuery Method (AlignmentMolecule)
setQuery Method (Molecule)
setQueryRigidForced Method
setTargetRigidForced Method
similarity Method
similarity Method (AlignmentMolecule)
similarity Method (Molecule)
PairwiseSimilarity3D Class
PairwiseSimilarity3D Members
PairwiseSimilarity3D Constructor
PairwiseSimilarity3D Methods
addNodeColorWeight Method
getAlignedMoleculesAsFragments Method
getAlignedQuery Method
getAlignedTarget Method
getShapeTanimoto Method
removeAllMolecules Method
setCount Method
setLicenseEnvironment Method
setProgressBar Method
setQuery Method
setQuery Method (AlignmentMolecule)
setQuery Method (Molecule)
setQueryRigidForced Method
setTargetRigidForced Method
similarity Method
similarity Method (AlignmentMolecule)
similarity Method (Molecule)
Pharmacophore3D Class
Pharmacophore3D Members
Pharmacophore3D Constructor
Pharmacophore3D Constructor
Pharmacophore3D Constructor (Molecule)
Pharmacophore3D Fields
ACCP Field
ALIPHATIC_RINGCENTER Field
AROMATIC_ATOM Field
AROMATIC_RINGCENTER Field
DONR Field
H Field
HYDR Field
LP Field
NEG Field
POS Field
SHAPE Field
Pharmacophore3D Methods
getColors Method
getPharmacophore Method
isAcceptor Method
isAliphaticRC Method
isAromatic Method
isAromaticRC Method
isDonor Method
isH Method
isHydrophobic Method
isLP Method
isNegative Method
isPositive Method
isShape Method
labelWithShape Method
typeLabel Method
withoutType Method
RotatableBondDetector Class
RotatableBondDetector Members
RotatableBondDetector Constructor
RotatableBondDetector Methods
isRotatableBond Method
chemaxon.marvin.beans Namespace
MarvinPane Class
MarvinPane Members
MarvinPane Fields
VERSION Field
MarvinPane Methods
__<clinit> Method
addActionListener Method
addHelpMenu Method
addMenuBarChangeListener Method
addToolsMenu Method
arePopupMenusEnabled Method
beginHourglass Method
closeWindows Method
componentHidden Method
componentMoved Method
componentResized Method
componentShown Method
createMenu Method
doPaste Method
endHourglass Method
exit Method
getAtomNumbersVisible Method
getAtomSetColor Method
getAtomsize Method
getBallRadius Method
getBondSpacing Method
getBondWidth Method
getChiralitySupport Method
getCleanDim Method
getColorScheme Method
getCommonActions Method
getDebug Method
getDirectory Method
getDispopts Method
getDispQuality Method
getDownWedge Method
getExplicitH Method
getFile Method
getFormat Method
getImplicitH Method
getInvisibleSets Method
getLabels Method
getLonePairsVisible Method
getMolbg Method
getMolPanel Method
getParameter Method
getParams Method
getPopupMenusEnabled Method
getReadGlobalGUIProperties Method
getRendering Method
getResourceBundle Method
getSaveGlobalGUIProperties Method
getSetColor Method
getStickThickness Method
getTopLevelContainer Method
getUserSettings Method
getWireThickness Method
initAction Method
initButton Method
isAtomMappingVisible Method
isAtomNumbersVisible Method
isAtomSymbolsVisible Method
isBondLengthVisible Method
isExitCanceled Method
isExperimentalEnabled Method
isEzVisible Method
isGrinv Method
isGrinvVisible Method
isPrintEnabled Method
isRgroupsVisible Method
isSaveIniEnabled Method
isSetColoringEnabled Method
keyPressed Method
keyReleased Method
keyTyped Method
propertyChange Method
readExternal Method
removeActionListener Method
setAtomMappingVisible Method
setAtomNumbersVisible Method
setAtomSetColor Method
setAtomsize Method
setAtomSymbolsVisible Method
setBallRadius Method
setBondLengthVisible Method
setBondSetColor Method
setBondSpacing Method
setBondWidth Method
setChiralitySupport Method
setCleanDim Method
setColorScheme Method
setDebug Method
setDirectory Method
setDispopts Method
setDispQuality Method
setDownWedge Method
setEnabled Method
setExperimentalEnabled Method
setExplicitH Method
setEzVisible Method
setFile Method
setFormat Method
setGlobalGUIProperties Method
setGrinv Method
setGrinvVisible Method
setImplicitH Method
setInvisibleSets Method
setLabels Method
setLonePairsVisible Method
setMolbg Method
setParams Method
setPopupMenusEnabled Method
setPrintEnabled Method
setRendering Method
setRgroupsVisible Method
setSaveIniEnabled Method
setSetColor Method
setSetColoringEnabled Method
setStickThickness Method
setTopLevelContainer Method
setUserSettings Method
setWireThickness Method
showErrorDialog Method
showFileDialog Method
showFileOpenDialog Method
writeExternal Method
MarvinPaneBeanInfo Class
MarvinPaneBeanInfo Members
MarvinPaneBeanInfo Constructor
MolRenderer Class
MolRenderer Members
MolRenderer Constructor
MolRenderer Methods
__<clinit> Method
getTableCellRendererComponent Method
paintComponent Method
MSketch Class
MSketch Members
MSketch Constructor
MSketch Constructor
MSketch Constructor (MSketchPane)
MSketch Methods
getMSketchPane Method
Implicit Operator
readExternal Method
writeExternal Method
MSketchPane Class
MSketchPane Members
MSketchPane Constructor
MSketchPane Constructor
MSketchPane Constructor (UserSettings)
MSketchPane Constructor (UserSettings, Boolean)
MSketchPane Fields
SM_ATOM Field
SM_BOND Field
SM_DELETE Field
SM_FLAGS_OFF Field
SM_MASK Field
SM_SELECT Field
SM_SELECT_LASSO Field
MSketchPane Methods
__<clinit> Method
addPropertyChangeListener Method
centralizeMoleculeDisplay Method
clearHistory Method
doPaste Method
getAutoScale Method
getBoundRectSize Method
getCanvasComponent Method
getCommonActions Method
getDefaultScale Method
getDisabledGroupTypes Method
getDocument Method
getImage Method
getImage Method ()
getImage Method (Double)
getMag Method
getMergedst Method
getMol Method
getMol Method
getMol Method (String)
getMrvWithSettings Method
getObjectAtPointer Method
getPiece Method
getReactionSupport Method
getScale Method
getSelection Method
getSimpView Method
getSketchMode Method
getStickdst Method
getUndo Method
isBondDraggedAlong Method
isCloseEnabled Method
isConfirmExit Method
isLoadedMolModified Method
isReactionErrorVisible Method
isValenceErrorVisible Method
propertyChange Method
readExternal Method
redo Method
setAutoScale Method
setBondDraggedAlong Method
setCloseEnabled Method
setConfirmExit Method
setDisabledGroupTypes Method
setDocument Method
setMag Method
setMergedst Method
setMol Method
setMol Method (Molecule)
setMol Method (String)
setMol Method (Molecule, Boolean)
setMol Method (, String)
setMol Method (String, String)
setMrvWithSettings Method
setPiece Method
setReactionErrorVisible Method
setReactionSupport Method
setScale Method
setSimpView Method
setSketchMode Method
setStickdst Method
setUndo Method
setValenceErrorVisible Method
undo Method
writeExternal Method
MSketchPaneBeanInfo Class
MSketchPaneBeanInfo Members
MSketchPaneBeanInfo Constructor
MSketchPaneBeanInfo Methods
getIcon Method
getPropertyDescriptors Method
MView Class
MView Members
MView Constructor
MView Constructor
MView Constructor (MViewPane)
MView Methods
getMViewPane Method
Implicit Operator
readExternal Method
writeExternal Method
MViewEditor Class
MViewEditor Members
MViewEditor Constructor
MViewEditor Methods
getCellEditorValue Method
getEditable Method
getEditorComponent Method
getTableCellEditorComponent Method
setEditable Method
MViewPane Class
MViewPane Members
MViewPane Constructor
MViewPane Constructor
MViewPane Constructor (UserSettings)
MViewPane Fields
EDITABLE Field
SKETCHABLE Field
VIEW_ONLY Field
MViewPane Methods
__<clinit> Method
addPropertyChangeListener Method
applyRotationMatrices Method
applyRotationMatrix Method
closeSketcher Method
closeWindow Method
destroySketcher Method
doPaste Method
getAbsoluteCellIndex Method
getAbsoluteCellIndex Method ()
getAbsoluteCellIndex Method (Int32)
getAnimated Method
getAnimDelay Method
getAnimFPS Method
getAutoTabScale Method
getBestTabScale Method
getBestTabScale Method
getBestTabScale Method (Int32)
getBorderWidth Method
getC Method
getCanvasComponent Method
getCellCount Method
getCommonActions Method
getDocStorage Method
getDocument Method
getDocuments Method
getEditable Method
getFieldFont Method
getL Method
getM Method
getM Method (Int32)
getM Method (Int32, String)
getNavmode Method
getPreferredSize Method
getRecordIDBackground Method
getRecordIDForeground Method
getRotationMatrix Method
getSelectedIndex Method
getT Method
getTableSupport Method
getTabScale Method
getTabScale Method
getTabScale Method (Int32)
getTopLeftIndex Method
getVisibleButtonB Method
getVisibleButtonC Method
getVisibleCellComponent Method
getVisibleCellCount Method
getVisibleCellIndex Method
getWinScale Method
indexOfButtonB Method
indexOfButtonC Method
isAnimated Method
isAnimSync Method
isDetachable Method
isDraggable Method
isSelectable Method
isSketchWindowOpened Method
isValenceErrorVisibleInView Method
isViewWindowOpened Method
makeEditMenu Method
makeHelpMenu Method
makeRecentFileListMenu Method
makeSaveAsMenu Method
makeStructureMenu Method
makeToolsMenu Method
makeViewMenu Method
openSketcher Method
openWindow Method
print Method
readExternal Method
setActionB Method
setActionC Method
setAnimated Method
setAnimated Method (Boolean)
setAnimated Method (Int32, Boolean)
setAnimDelay Method
setAnimFPS Method
setAnimSync Method
setAtomSetSeq Method
setAutoTabScale Method
setBorderWidth Method
setC Method
setDetachable Method
setDocument Method
setDraggable Method
setEditable Method
setEnabled Method
setFieldFont Method
setL Method
setM Method
setM Method (Int32, Molecule)
setM Method (Int32, Molecule[])
setM Method (Int32, String)
setM Method (Int32, , String)
setM Method (Int32, String, String)
setNavmode Method
setPreferredSize Method
setRecordIDBackground Method
setRecordIDForeground Method
setSelectable Method
setSelectedIndex Method
setSetSeq Method
setT Method
setTabScale Method
setTopLeftIndex Method
setValenceErrorVisibleInView Method
setWinScale Method
writeExternal Method
MViewPaneBeanInfo Class
MViewPaneBeanInfo Members
MViewPaneBeanInfo Constructor
MViewPaneBeanInfo Methods
getIcon Method
getPropertyDescriptors Method
MViewParams Class
MViewParams Members
MViewParams Constructor
MViewParams Methods
addLabel Method
addLabel Method (Int32, Int32, Int32, Int32)
addLabel Method (Int32, Int32, Int32, Int32, Int32, Int32, Int32, Int32)
addMolecule Method
addMolecule Method (Int32, Int32, Int32, Int32)
addMolecule Method (Int32, Int32, Int32, Int32, Int32, Int32, Int32, Int32)
getMViewParam Method
setColumnCount Method
setHeaderCellSize Method
setLabelProperty Method
setMoleculeCellSize Method
setRowCount Method
setVisibleRows Method
MViewRenderer Class
MViewRenderer Members
MViewRenderer Constructor
MViewRenderer Methods
__<clinit> Method
getTableCellRendererComponent Method
chemaxon.marvin.calculations Namespace
AlignmentPlugin Class
AlignmentPlugin Members
AlignmentPlugin Constructor
AlignmentPlugin Fields
STEP_DEFAULT Field
AlignmentPlugin Methods
__<clinit> Method
getProductName Method
getResultMolecule Method
getResultTypes Method
getVolumeTanimoto Method
getWarningMessage Method
handlesMultiFragmentMolecules Method
run Method
setAccuracyMode Method
setMinimumCommonSize Method
setParameters Method
setProgressMonitor Method
setRingFlexibility Method
standardize Method
ChargePlugin Class
ChargePlugin Members
ChargePlugin Constructor
ChargePlugin Methods
__<clinit> Method
getAromaticRingCharge Method
getAromaticRingCharge Method (Int32)
getAromaticRingCharge Method (Int32, Int32)
getAromaticSystemCharge Method
getAromaticSystemCharge Method (Int32)
getAromaticSystemCharge Method (Int32, Int32)
getErrorMessage Method
getFormalCharge Method
getFormalCharge Method
getFormalCharge Method (Int32)
getPiCharge Method
getProductName Method
getResult Method
getResultantImplicitHCharge Method
getResultAsString Method
getResultCount Method
getResultDomain Method
getResultMolecule Method
getResultTypes Method
getSigmaCharge Method
getTotalCharge Method
getTypeString Method
handlesMultiFragmentMolecules Method
isLicensed Method
run Method
setParameters Method
setTakeResonantStructures Method
ConformerPlugin Class
ConformerPlugin Members
ConformerPlugin Constructor
ConformerPlugin Fields
OPTIMIZATION_NORMAL Field
OPTIMIZATION_STRICT Field
OPTIMIZATION_VERY_LOOSE Field
OPTIMIZATION_VERY_STRICT Field
ConformerPlugin Methods
__<clinit> Method
checkMolecule Method
getConformer Method
getConformerCount Method
getConformers Method
getEnergy Method
getEnergy Method
getEnergy Method (Int32)
getLowestEnergyConformer Method
getMMFF94OptimizedStrucutre Method
getProductName Method
getResult Method
getResultAsString Method
getResultCount Method
getResultDomain Method
getResultSource Method
getResultTypes Method
getTypeString Method
getWarningMessage Method
handlesMultiFragmentMolecules Method
hasValidConformer Method
run Method
setDiversity Method
setHyperfine Method
setLowestEnergyConformerCalculation Method
setMaxNumberOfConformers Method
setMMFF94Optimization Method
setOptimization Method
setParameters Method
setPrehydrogenize Method
setProgressMonitor Method
setTimelimit Method
standardize Method
ElementalAnalyserPlugin Class
ElementalAnalyserPlugin Members
ElementalAnalyserPlugin Constructor
ElementalAnalyserPlugin Methods
__<clinit> Method
checkMolecule Method
getAllAtomCount Method
getAtomCount Method
getAtomCount Method (Int32)
getAtomCount Method (Int32, Int32)
getComposition Method
getDotDisconnectedFormula Method
getDotDisconnectedIsotopeFormula Method
getDotDisconnectedIsotopeFormula Method
getDotDisconnectedIsotopeFormula Method (Boolean)
getErrorMessage Method
getExactMass Method
getFormula Method
getIsotopeComposition Method
getIsotopeComposition Method
getIsotopeComposition Method (Boolean)
getIsotopeFormula Method
getIsotopeFormula Method
getIsotopeFormula Method (Boolean)
getMass Method
getProductName Method
getResult Method
getResult Method (Object, Int32)
getResult Method (Object, String)
getResultAsString Method
getResultCount Method
getResultDomain Method
getResultMolecule Method
getResultTypes Method
getTypeString Method
handlesMultiFragmentMolecules Method
run Method
setMolecule Method
setParameters Method
standardize Method
EnumerationPlugin Class
EnumerationPlugin Members
EnumerationPlugin Constructor
EnumerationPlugin Methods
__<clinit> Method
GeometryPlugin Class
GeometryPlugin Members
GeometryPlugin Constructor
GeometryPlugin Methods
__<clinit> Method
checkMolecule Method
getAngle Method
getAngle Method (Int32[])
getAngle Method (Int32, Int32, Int32)
getDihedral Method
getDihedral Method (Int32[])
getDihedral Method (Int32, Int32, Int32, Int32)
getDistance Method
getDistance Method (Int32[])
getDistance Method (Int32, Int32)
getDreidingEnergy Method
getLowestEnergyConformer Method
getMaximalProjectionArea Method
getMaximalProjectionRadius Method
getMaxZ Method
getMinimalProjectionArea Method
getMinimalProjectionRadius Method
getMinZ Method
getMMFF94Energy Method
getProductName Method
getRemark Method
getResult Method
getResult Method (Object, Int32)
getResult Method (Object, String)
getResultAsString Method
getResultCount Method
getResultDomain Method
getResultMolecule Method
getResultMolecules Method
getResultTypes Method
getStericHindrance Method
getTypeString Method
getVolume Method
getWarningMessage Method
handlesMultiFragmentMolecules Method
isMultiThreadedRunEnabled Method
run Method
setCalculateEnergy Method
setCalculateForLEConformer Method
setCalculateMMFF94Energy Method
setCalculateMoleculeProjections Method
setCalculateVolume Method
setLicenseEnvironment Method
setMMFF94Optimization Method
setOptimization Method
setOptimizeProjection Method
setParameters Method
setProgressMonitor Method
standardize Method
HBDAPlugin Class
HBDAPlugin Members
HBDAPlugin Constructor
HBDAPlugin Fields
ACCEPTOR_SIGN Field
DONOR_SIGN Field
EPSILON Field
HBDAPlugin Methods
__<clinit> Method
checkMolecule Method
getAcceptorAtomCount Method
getAcceptorCount Method
getAcceptorCount Method
getAcceptorCount Method (Int32)
getDonorAtomCount Method
getDonorCount Method
getDonorCount Method
getDonorCount Method (Int32)
getErrorMessage Method
getMsAcceptorCounts Method
getMsDonorCounts Method
getpHs Method
getProductName Method
getResult Method
getResultAsRGB Method
getResultAsString Method
getResultCount Method
getResultDomain Method
getResultMolecule Method
getResultsAsRGB Method
getResultsAsString Method
getResultTypes Method
getTypeString Method
getWarningMessage Method
isLicensed Method
isNegligibleResult Method
run Method
setExcludeHalogens Method
setExcludeSulfur Method
setMsCalc Method
setParameters Method
setpHLower Method
setpHStep Method
setpHUpper Method
HuckelAnalysisPlugin Class
HuckelAnalysisPlugin Members
HuckelAnalysisPlugin Constructor
HuckelAnalysisPlugin Methods
__<clinit> Method
getChargeDensity Method
getEigenVector Method
getElectronDensity Method
getElectrophilicEnergy Method
getElectrophilicOrder Method
getErrorMessage Method
getHMOChargeDensity Method
getHMOEigenVector Method
getHMOElectronDensity Method
getHMOElectrophilicEnergy Method
getHMOElectrophilicOrder Method
getHMOHuckelOrbitalCoefficients Method
getHMONucleophilicEnergy Method
getHMONucleophilicOrder Method
getHMORealEigenValue Method
getHMOTotalPiEnergy Method
getHuckelOrbitalCoefficients Method
getNucleophilicEnergy Method
getNucleophilicOrder Method
getProductName Method
getRealEigenValue Method
getResult Method
getResultAsString Method
getResultCount Method
getResultDomain Method
getResultMolecule Method
getResultsAsRGB Method
getResultsAsString Method
getResultTypes Method
getTotalPiEnergy Method
getTypeString Method
getWarningMessage Method
isLicensed Method
run Method
setParameters Method
IonChargePlugin Class
IonChargePlugin Members
IonChargePlugin Constructor
IonChargePlugin Methods
__<clinit> Method
checkMolecule Method
getErrorMessage Method
getProductName Method
getResult Method
getResultAsString Method
getResultCount Method
getResultDomain Method
getResultTypes Method
run Method
setParameters Method
standardize Method
IsoelectricPointPlugin Class
IsoelectricPointPlugin Members
IsoelectricPointPlugin Constructor
IsoelectricPointPlugin Fields
TYPE_DISTR Field
IsoelectricPointPlugin Methods
__<clinit> Method
checkMolecule Method
getChargeDistribution Method
getErrorMessage Method
getpHs Method
getpI Method
getProductName Method
getResult Method
getResult Method (Object, Int32)
getResult Method (Object, String)
getResultAsString Method
getResultCount Method
getResultDomain Method
getResultMolecule Method
getResultTypes Method
getTypeString Method
getWarningMessage Method
run Method
setParameters Method
setpH Method
setpHLower Method
setpHStep Method
setpHUpper Method
setProgressMonitor Method
standardize Method
IUPACNamingPlugin Class
IUPACNamingPlugin Members
IUPACNamingPlugin Constructor
IUPACNamingPlugin Methods
__<clinit> Method
canRepeat Method
checkMolecule Method
getPreferredIUPACName Method
getProductName Method
getResult Method
getResultAsString Method
getResultMolecule Method
getResultTypes Method
getTraditionalName Method
getTypeString Method
handlesMultiFragmentMolecules Method
run Method
setGeneratePreferredIUPACName Method
setGenerateTraditionalIUPACName Method
setLicenseEnvironment Method
setParameters Method
standardize Method
logDPlugin Class
logDPlugin Members
logDPlugin Constructor
logDPlugin Fields
METHOD_KLOP Field
METHOD_PHYS Field
METHOD_USER_DEFINED Field
METHOD_VG Field
METHOD_WEIGHTED Field
logDPlugin Methods
__<clinit> Method
calclogD Method
checkMolecule Method
getErrorMessage Method
getlogD Method
getlogDs Method
getLogPTrainingIds Method
getpHs Method
getProductName Method
getReflogDs Method
getRefpHs Method
getResult Method
getResult Method (Object, Int32)
getResult Method (Object, String)
getResultAsString Method
getResultCount Method
getResultDomain Method
getResultTypes Method
run Method
setCloridIonConcentration Method
setConsiderTautomerization Method
setlogPMethod Method
setLogPTrainingId Method
setNaKIonConcentration Method
setParameters Method
setpH Method
setpHLower Method
setpHStep Method
setpHUpper Method
setpKaCorrectionLibrary Method
setWeightOfMethods Method
standardize Method
logPPlugin Class
logPPlugin Members
logPPlugin Constructor
logPPlugin Fields
METHOD_KLOP Field
METHOD_PHYS Field
METHOD_USER_DEFINED Field
METHOD_VG Field
METHOD_WEIGHTED Field
logPPlugin Methods
__<clinit> Method
checkMolecule Method
getAtomlogPHIncrement Method
getAtomlogPIncrement Method
getErrorMessage Method
getlogDpI Method
getlogPMicro Method
getlogPNonionic Method
getlogPTrue Method
getProductName Method
getResult Method
getResultAsString Method
getResultCount Method
getResultDomain Method
getResultMolecule Method
getResultTypes Method
getStandardError Method
getStructurallogPIncrement Method
getTrainingIds Method
getTypeString Method
getUserTypes Method
needError Method
run Method
setCloridIonConcentration Method
setConsiderTautomerization Method
setlogPMethod Method
setNaKIonConcentration Method
setParameters Method
setTakeMajorTatomericForm Method
setTraining Method
setUserTypes Method
setWeightOfMethods Method
standardize Method
MajorMicrospeciesAccessorPlugin Class
MajorMicrospeciesAccessorPlugin Members
MajorMicrospeciesAccessorPlugin Constructor
MajorMicrospeciesAccessorPlugin Methods
checkMolecule Method
getErrorMessage Method
getIonizerErrorMessage Method
getpH Method
isLicensed Method
setParameters Method
setpH Method
standardize Method
MajorMicrospeciesPlugin Class
MajorMicrospeciesPlugin Members
MajorMicrospeciesPlugin Constructor
MajorMicrospeciesPlugin Methods
__<clinit> Method
checkMolecule Method
getErrorMessage Method
getIonizerErrorMessage Method
getMajorMicrospecies Method
getMicrospecies Method
getMicrospeciesCount Method
getpH Method
getProductName Method
getResult Method
getResultAsString Method
getResultCount Method
getResultDomain Method
getResultMolecule Method
getResultTypes Method
getSortedMicrospecies Method
getSortedMsDistribution Method
run Method
setParameters Method
setpH Method
setTakeMajorTatomericForm Method
standardize Method
MarkushEnumerationPlugin Class
MarkushEnumerationPlugin Members
MarkushEnumerationPlugin Constructor
MarkushEnumerationPlugin Fields
COLORING_ALL Field
COLORING_NONE Field
COLORING_RGROUPS Field
COLORING_SCAFFOLD Field
FILTER_VALENCE Field
MarkushEnumerationPlugin Methods
__<clinit> Method
checkMolecule Method
countEnumerations Method
countEnumerationsMagnitude Method
getAlignScaffold Method
getAromatizedStructures Method
getColoring Method
getEnumCodeNeeded Method
getLibrarySizeString Method
getLimitedStructureCount Method
getNextAromatizedStructure Method
getNextStructure Method
getProductName Method
getRemark Method
getResult Method
getResult Method (Object, Int32)
getResult Method (Object, String)
getResultAsString Method
getResultCount Method
getResultDomain Method
getResultMolecule Method
getResultSource Method
getResultTypes Method
getStructureCount Method
getStructureID Method
getStructures Method
getTypeString Method
handlesMultiFragmentMolecules Method
hasMoreStructures Method
isApproximateCount Method
isHomologyEnumerated Method
isLicensed Method
isRandomEnumeration Method
run Method
setAlignScaffold Method
setColoring Method
setEnumCodeNeeded Method
setEnumerateHomology Method
setFilter Method
setLicenseEnvironment Method
setMaxStructureCount Method
setParameters Method
setRandomEnumeration Method
setStructureID Method
standardize Method
MolecularDynamicsPlugin Class
MolecularDynamicsPlugin Members
MolecularDynamicsPlugin Constructor
MolecularDynamicsPlugin Methods
__<clinit> Method
checkMolecule Method
getProductName Method
getResult Method
getResultAsString Method
getResultCount Method
getResultDomain Method
getResultSource Method
getResultTypes Method
getStructure Method
getStructureCount Method
getStructures Method
handlesMultiFragmentMolecules Method
run Method
setCenterMolecule Method
setForceField Method
setInitialTemperature Method
setIntegrator Method
setParameters Method
setProgressMonitor Method
setSamplingInterval Method
setSamplingStart Method
setStepNumber Method
setStepTime Method
standardize Method
MSAPlugin Class
MSAPlugin Members
MSAPlugin Constructor
MSAPlugin Fields
SOLVENT Field
VAN_DER_WAALS Field
MSAPlugin Methods
__<clinit> Method
checkMolecule Method
get3DMolecule Method
getASA Method
getASAHydrophobic Method
getASANegative Method
getASAPlus Method
getASAPolar Method
getAtomicSurfaceAreaIncrement Method
getErrorMessage Method
getProductName Method
getResult Method
getResultAsString Method
getResultCount Method
getResultDomain Method
getResultMolecule Method
getResultTypes Method
getSurfaceArea Method
getTypeString Method
getVDWSA Method
isLicensed Method
isMultiThreadedRunEnabled Method
run Method
setParameters Method
setSolventRadius Method
setSurfaceAreaType Method
OrbitalElectronegativityPlugin Class
OrbitalElectronegativityPlugin Members
OrbitalElectronegativityPlugin Constructor
OrbitalElectronegativityPlugin Methods
__<clinit> Method
getErrorMessage Method
getPiOEN Method
getProductName Method
getResult Method
getResultAsString Method
getResultCount Method
getResultDomain Method
getResultMolecule Method
getResultTypes Method
getSigmaOEN Method
getTypeString Method
isLicensed Method
run Method
setParameters Method
setTakeResonantStructures Method
pKaPlugin Class
pKaPlugin Members
pKaPlugin Constructor
pKaPlugin Fields
ACIDIC Field
BASIC Field
DEF_MAXIONS Field
DEF_TEMPERATURE Field
DYNAMICpKaPREFIX Field
MODEL_LARGE Field
MODEL_SMALL Field
STATICpKaPREFIX Field
TYPE_DISTR Field
pKaPlugin Methods
__<clinit> Method
checkMolecule Method
getCorrectionLibraryIds Method
getErrorMessage Method
getMacropKaValues Method
getMacropKaValues Method (Int32)
getMacropKaValues Method (Int32, Double[], Int32[])
getMacroSpeciesCharge Method
getMsCount Method
getMsDistribution Method
getMsDistributions Method
getMsMolecule Method
getpHs Method
getpKa Method
getpKa Method (Int32)
getpKa Method (Int32, Int32)
getpKaPrefixType Method
getpKaType Method
getpKaValues Method
getProductName Method
getResult Method
getResult Method (Object, Int32)
getResult Method (Object, String)
getResultAsRGB Method
getResultAsString Method
getResultCount Method
getResultDomain Method
getResultMolecule Method
getResultsAsRGB Method
getResultsAsString Method
getResultTypes Method
getSingleMsDistribution Method
getSortedValues Method
getWarningMessage Method
isNegligibleResult Method
isOverflowCalculation Method
run Method
setAcidicpKaUpperLimit Method
setBasicpKaLowerLimit Method
setCalcAlways Method
setConsiderTautomerization Method
setCorrectionLibrary Method
setMaxIons Method
setMicropKaCalc Method
setModel Method
setMsCalc Method
setParameters Method
setpH Method
setpHLower Method
setpHStep Method
setpHUpper Method
setpKaPrefixType Method
setProgressMonitor Method
setTakeMajorTatomericForm Method
setTemperature Method
standardize Method
useCorrectionLibrary Method
PolarizabilityPlugin Class
PolarizabilityPlugin Members
PolarizabilityPlugin Constructor
PolarizabilityPlugin Methods
__<clinit> Method
checkMolecule Method
getAveragePolarizabilityComponent Method
getErrorMessage Method
getHPolarizability Method
getMolPolarizability Method
getPolarizability Method
getPrincipalPolarizabilityComponents Method
getProductName Method
getResult Method
getResultAsString Method
getResultCount Method
getResultDomain Method
getResultMolecule Method
getResultTypes Method
isLicensed Method
run Method
setGeom3D Method
setParameters Method
PredictorPlugin Class
PredictorPlugin Members
PredictorPlugin Constructor
PredictorPlugin Methods
__<clinit> Method
getErrorMessage Method
getPredictedValue Method
getProductName Method
getResult Method
getResult Method (Object, Int32)
getResult Method (Object, String)
getResultAsString Method
getResultMolecule Method
getResultTypes Method
getStandardError Method
getTrainingIds Method
needError Method
run Method
setParameters Method
setTraining Method
standardize Method
RefractivityPlugin Class
RefractivityPlugin Members
RefractivityPlugin Constructor
RefractivityPlugin Methods
__<clinit> Method
checkMolecule Method
getErrorMessage Method
getProductName Method
getRefractivity Method
getRefractivityHIncrement Method
getRefractivityIncrement Method
getResult Method
getResultAsString Method
getResultCount Method
getResultDomain Method
getResultMolecule Method
getResultTypes Method
getTypeString Method
run Method
setParameters Method
standardize Method
ResonancePlugin Class
ResonancePlugin Members
ResonancePlugin Constructor
ResonancePlugin Methods
__<clinit> Method
checkMolecule Method
getErrorMessage Method
getProductName Method
getRemark Method
getResult Method
getResultAsString Method
getResultCount Method
getResultDomain Method
getResultSource Method
getResultTypes Method
getStructure Method
getStructureCount Method
getStructures Method
handlesMultiFragmentMolecules Method
isMultiThreadedRunEnabled Method
run Method
setCleanResultStructures Method
setInputMoleculeModified Method
setMaxStructureCount Method
setParameters Method
setpH Method
setProgressMonitor Method
setSymmetryFiltering Method
setTakeCanonicalForm Method
setTakeMajorContributors Method
standardize Method
StereoisomerPlugin Class
StereoisomerPlugin Members
StereoisomerPlugin Constructor
StereoisomerPlugin Fields
BOTH Field
DOUBLE_BOND Field
TETRAHEDRAL Field
StereoisomerPlugin Methods
__<clinit> Method
checkMolecule Method
chiralCenterCount Method
getProductName Method
getResult Method
getResultAsString Method
getResultCount Method
getResultDomain Method
getResultSource Method
getResultTypes Method
getStereoisomer Method
getStereoisomerCount Method
getStereoisomers Method
getTypeString Method
getWarningMessage Method
handlesMultiFragmentMolecules Method
isChiralCenter Method
isIn3D Method
run Method
setCheck3DStereo Method
setIn3D Method
setMaxNumberOfStereoisomers Method
setParameters Method
setProgressMonitor Method
setProtectDoubleBondStereo Method
setProtectTetrahedralStereo Method
setStereoisomerismType Method
standardize Method
StructuralFrameworksPlugin Class
StructuralFrameworksPlugin Members
StructuralFrameworksPlugin Constructor
StructuralFrameworksPlugin Methods
__<clinit> Method
canRepeat Method
checkMolecule Method
getProductName Method
getResult Method
getResult Method
getResult Method (Object, Int32)
getResultAsString Method
getResultCount Method
getResultDomain Method
getResultMolecule Method
getResultTypes Method
getTypeString Method
handlesMultiFragmentMolecules Method
run Method
setDehydrogenize Method
setFormat Method
setHydrogenize Method
setKeepSingleAtom Method
setLfin Method
setLfout Method
setOeqcheck Method
setParameters Method
setPruneIn Method
setPruneOut Method
setType Method
setVerbosePrinter Method
standardize Method
StructuralFrameworksPlugin.FrameworkTypes Class
StructuralFrameworksPlugin.FrameworkTypes Members
StructuralFrameworksPlugin.FrameworkTypes Fields
allringsystems Field
bemismurcko Field
bemismurckoloose Field
cssr Field
keep Field
largestring Field
largestringsystem Field
mcs Field
sssr Field
StructuralFrameworksPlugin.FrameworkTypes Methods
__<clinit> Method
valueOf Method
values Method
StructuralFrameworksPlugin.FrameworkTypes.__Enum Enumeration
StructuralFrameworksPlugin.VerbosePrinter Interface
StructuralFrameworksPlugin.VerbosePrinter Members
StructuralFrameworksPlugin.VerbosePrinter Methods
verbose Method
TautomerizationPlugin Class
TautomerizationPlugin Members
TautomerizationPlugin Constructor
TautomerizationPlugin Methods
__<clinit> Method
checkMolecule Method
getDominantTautomerDistribution Method
getErrorMessage Method
getProductName Method
getRemark Method
getResult Method
getResultAsString Method
getResultCount Method
getResultDomain Method
getResultSource Method
getResultTypes Method
getStructure Method
getStructureCount Method
getStructures Method
handlesMultiFragmentMolecules Method
isMultiThreadedRunEnabled Method
run Method
setCleanResultStructures Method
setDominantTautomerDistributionCalculation Method
setExcludeAntiAromaticCompounds Method
setInputMoleculeModified Method
setMaximumTautomerizationPathLength Method
setMaxStructureCount Method
setParameters Method
setpH Method
setProgressMonitor Method
setProtectAllTetrahedralStereoCenters Method
setProtectAromaticity Method
setProtectCharge Method
setProtectDoubleBondStereo Method
setProtectEsterGroups Method
setProtectLabeledTetrahedralStereoCenters Method
setRingChainTautomerizationAllowed Method
setSymmetryFiltering Method
setTakeCanonicalForm Method
setTakeDominantTautomers Method
setTakeGenericTautomer Method
setTakeMajorTautomer Method
setTakeMostStableTautomer Method
setTakeStandardForm Method
setWigglyBondVisibility Method
standardize Method
TopologyAnalyserPlugin Class
TopologyAnalyserPlugin Members
TopologyAnalyserPlugin Constructor
TopologyAnalyserPlugin Methods
__<clinit> Method
checkMolecule Method
getAliphaticAtomCount Method
getAliphaticBondCount Method
getAliphaticRingCount Method
getAliphaticRingCount Method
getAliphaticRingCount Method (Int32)
getAliphaticRingCountOfSize Method
getAliphaticRings Method
getAliphaticRings Method
getAliphaticRings Method (Int32)
getAllAtomCount Method
getAromaticAtomCount Method
getAromaticBondCount Method
getAromaticRingCount Method
getAromaticRingCount Method
getAromaticRingCount Method (Int32)
getAromaticRingCountOfSize Method
getAromaticRings Method
getAromaticRings Method
getAromaticRings Method (Int32)
getAsymmetricAtomCount Method
getAsymmetricAtoms Method
getBalabanIndex Method
getBondCount Method
getBondIndex Method
getBondType Method
getCarboaliphaticRingCount Method
getCarboaromaticRingCount Method
getCarboRingCount Method
getCarboRingCount Method
getCarboRingCount Method (Int32)
getCarboRings Method
getCarboRings Method
getCarboRings Method (Int32)
getChainAtomCount Method
getChainBondCount Method
getChiralCenterCount Method
getChiralCenters Method
getCyclomaticNumber Method
getDistanceCount Method
getDistanceDegree Method
getEccentricity Method
getFragmentCount Method
getFusedAliphaticRingCount Method
getFusedAliphaticRingCount Method
getFusedAliphaticRingCount Method (Int32)
getFusedAliphaticRings Method
getFusedAliphaticRings Method
getFusedAliphaticRings Method (Int32)
getFusedAromaticRingCount Method
getFusedAromaticRingCount Method
getFusedAromaticRingCount Method (Int32)
getFusedAromaticRings Method
getFusedAromaticRings Method
getFusedAromaticRings Method (Int32)
getFusedRingCount Method
getHararyIndex Method
getHeteroaliphaticRingCount Method
getHeteroaliphaticRingCount Method
getHeteroaliphaticRingCount Method (Int32)
getHeteroaliphaticRings Method
getHeteroaliphaticRings Method
getHeteroaliphaticRings Method (Int32)
getHeteroaromaticRingCount Method
getHeteroaromaticRingCount Method
getHeteroaromaticRingCount Method (Int32)
getHeteroaromaticRings Method
getHeteroaromaticRings Method
getHeteroaromaticRings Method (Int32)
getHeteroRingCount Method
getHeteroRingCount Method
getHeteroRingCount Method (Int32)
getHeteroRings Method
getHeteroRings Method
getHeteroRings Method (Int32)
getHyperWienerIndex Method
getLargestRing Method
getLargestRingSize Method
getLargestRingSizeOfAtom Method
getLargestRingSystem Method
getLargestRingSystemSize Method
getPlattIndex Method
getProductName Method
getRandicIndex Method
getRemark Method
getResult Method
getResult Method (Object, Int32)
getResult Method (Object, String)
getResultAsString Method
getResultCount Method
getResultDomain Method
getResultMolecule Method
getResultMolecules Method
getResultTypes Method
getRingAtomCount Method
getRingBondCount Method
getRingCount Method
getRingCount Method
getRingCount Method (Int32)
getRingCountOfAtom Method
getRingCountOfSize Method
getRings Method
getRings Method
getRings Method (Int32)
getRingSystemCount Method
getRingSystemCount Method
getRingSystemCount Method (Int32)
getRingSystemCountOfSize Method
getRingSystems Method
getRingSystems Method
getRingSystems Method (Int32)
getRotatableBondCount Method
getShortestPath Method
getSmallestRing Method
getSmallestRingSize Method
getSmallestRingSizeOfAtom Method
getSmallestRingSystem Method
getSmallestRingSystemSize Method
getStereo Method
getStereo Method (Int32)
getStereo Method (Int32, Int32)
getStereoDoubleBondCount Method
getStericEffectIndex Method
getSzegedIndex Method
getTypeString Method
getWienerIndex Method
getWienerPolarity Method
handlesMultiFragmentMolecules Method
isAliphaticAtom Method
isAromaticAtom Method
isAsymmetricAtom Method
isChainAtom Method
isChainBond Method
isChiralCenter Method
isConnected Method
isConnectedGraph Method
isRingAtom Method
isRingBond Method
isRotatableBond Method
run Method
setLicenseEnvironment Method
setParameters Method
standardize Method
TPSAPlugin Class
TPSAPlugin Members
TPSAPlugin Constructor
TPSAPlugin Methods
__<clinit> Method
checkMolecule Method
getErrorMessage Method
getProductName Method
getResult Method
getResultAsString Method
getResultCount Method
getResultDomain Method
getResultMolecule Method
getResultTypes Method
getSurfaceArea Method
getTPSA Method
getTypeString Method
run Method
setExcludePhosphorus Method
setExcludeSulfur Method
setParameters Method
chemaxon.marvin.common Namespace
ParameterConstants Class
ParameterConstants Members
ParameterConstants Fields
ADD_REMOVE_H_ATOMS_ENABLED Field
ANY_BOND Field
ATOM_FONT Field
ATOM_MAPPING_VISIBLE Field
ATOM_NUMBERS_VISIBLE Field
ATOM_PROPERTIES_VISIBLE Field
ATOM_SET_COLOR Field
ATOM_SIZE Field
ATOM_SYMBOL_VISIBLE_3D Field
ATOM_SYMBOLS_VISIBLE Field
AUTOMATIC_FOG_ENABLED Field
BALL_RADIUS Field
BOND_LENGTH_VISIBLE Field
BOND_SET_COLOR Field
BOND_SPACING Field
CACHE_MOLECULES Field
CHIRALITY_SUPPORT Field
CLEANING_2D_OPTIONS Field
CLEANING_3D_OPTIONS Field
CLEANING_DIMENSION Field
CLEANING_OPTIONS Field
COLOR_SCHEME Field
COORDINATE_BOND_STYLE Field
COORDINATE_BOND_STYLE_AT_MULTICENTER Field
COPY_AS_FORMAT Field
COPY_OPTIONS Field
DEBUG Field
DEFAULT_SAVE_FORMAT Field
DISPLAY_QUALITY Field
DOWN_WEDGE Field
ESCAPE_CHAR Field
EXPLICIT_H Field
EZ_VISIBLE Field
FOG_FACTOR Field
IMPLICIT_H Field
IMPORT_CONVERSION Field
INVISIBLE_SETS Field
LICENSE Field
LICENSE_FILE Field
LIGAND_ERROR_VISIBLE Field
LISTEN_PROPERTY_CHANGE Field
LOAD_MOLECULES Field
LONE_PAIRS_VISIBLE Field
MOLECULE Field
MOLECULE_BACKGROUND Field
MOLECULE_FORMAT Field
R_GROUPS_VISIBLE Field
RENDERING Field
SAVE_PROPERTIES Field
SET_COLORING_ENABLED Field
SHOW_SETS Field
SKETCH_ANY_BOND Field
SKETCH_HELP Field
SKETCH_QUICK_HELP Field
SKIN Field
SPLASH_SCREEN_IMAGE Field
STICK_THICKNESS Field
TRANSFER_BUTTON_ICON Field
TRANSFER_BUTTON_TEXT Field
TRANSFER_BUTTON_VISIBLE Field
VALENCE_PROPERTY_VISIBLE Field
VIEW_ANY_BOND Field
VIEW_EXPLICIT_H Field
VIEW_HELP Field
VIEW_NAVIGATION_MODE_2D Field
VIEW_NAVIGATION_MODE_3D Field
VIEW_QUICK_HELP Field
WIRE_THICKNESS Field
UserSettings Class
UserSettings Members
UserSettings Constructor
UserSettings Constructor
UserSettings Constructor (UserSettings)
UserSettings Constructor (String)
UserSettings Fields
CLEAN_H_OPTION Field
DEFAULT_BOND_IN_HAND Field
DEFAULT_LONE_PAIR_AUTOCALC Field
DEFAULT_SKETCH_ARROW_HEAD_LENGTH Field
DEFAULT_SKETCH_ARROW_HEAD_WIDTH Field
DEFAULT_SKETCH_RECENT_FILE_LIST_SIZE Field
DEFAULT_VIEW_RECENT_FILE_LIST_SIZE Field
MARVIN_CONFIG_DEFAULT_PATH Field
MAX_RECENT_FILE_LIST_SIZE Field
MAX_SKETCH_RECENT_FILE_LIST_SIZE Field
MAX_VIEW_RECENT_FILE_LIST_SIZE Field
MIN_RECENT_FILE_LIST_SIZE Field
MIN_SKETCH_RECENT_FILE_LIST_SIZE Field
MIN_VIEW_RECENT_FILE_LIST_SIZE Field
MYTEMPLATES_GROUP_INDEX Field
PROPERTY_TYPE_ALL Field
PROPERTY_TYPE_DEFAULT Field
PROPERTY_TYPE_PERSISTENT Field
PROPERTY_TYPE_TRANSIENT Field
UserSettings Methods
__<clinit> Method
addOwner Method
addPropertyChangeListener Method
addTo Method
addToSketchRecentFileList Method
addToViewRecentFileList Method
addWithLCKeysTo Method
checkBeforeSave Method
get Method
getAbsoluteLabelVisible Method
getAromatizeMethod Method
getAtomFont Method
getAtomMappingMethod Method
getAtomSize Method
getBallRadius Method
getBondSpacing Method
getCheckerConfigFileName Method
getChiralitySupport Method
getClean2dOpts Method
getClean3dOpts Method
getCoordinateBondStyle Method
getCoordinateBondStyleAtMulticenter Method
getCopyAsFormat Method
getDefaultMyTemplatesValue Method
getDefaultProperty Method
getDefaultSaveFormat Method
getDescription Method
getDownWedge Method
getFogFactor Method
getLoadSaveLocation Method
getLoadWorkingDir Method
getMyTemplatesKey Method
getMyTemplatesValue Method
getMyTemplatesValue Method
getMyTemplatesValue Method ()
getOwnerCount Method
getPropertiesDescriptionChangedByOtherApp Method
getProperty Method
getPropertyMap Method
getPropertyMap Method
getPropertyMap Method (String)
getReadGUIPropertiesFromMRV Method
getRLogicVisible Method
getSaveGUIPropertiesInMRV Method
getSaveLoadZoomFactorToMRV Method
getServicesConfigURL Method
getSketchAnyBond Method
getSketchArrowHeadLength Method
getSketchArrowHeadWidth Method
getSketchArrowTailLength Method
getSketchArrowTailWidth Method
getSketchCarbonVisibility Method
getSketchColorScheme Method
getSketchImplicitH Method
getSketchLigandOrderVisibility Method
getSketchLoadWorkingDir Method
getSketchMolbg2d Method
getSketchMolbg3d Method
getSketchRecentFileList Method
getSketchRecentFileListSize Method
getSketchRendering2d Method
getSketchRendering3d Method
getSketchSaveWorkingDir Method
getStickThickness Method
getTerminalBondDeletionStyle Method
getViewAnyBond Method
getViewCarbonVisibility Method
getViewColorScheme Method
getViewExplicitH Method
getViewImplicitH Method
getViewLayout Method
getViewLigandOrderVisibility Method
getViewLoadWorkingDir Method
getViewMolbg2d Method
getViewMolbg3d Method
getViewNavmode2d Method
getViewNavmode3d Method
getViewRecentFileList Method
getViewRecentFileListSize Method
getViewRendering2d Method
getViewRendering3d Method
getViewSaveWorkingDir Method
getWireThickness Method
isAtomPropertiesVisible Method
isAutoCheckStructure Method
isAutomaticFogEnabled Method
isBondDraggedAlong Method
isCleanHOptionEnabled Method
isEZVisible Method
isLigandErrorVisible Method
isLonePairAutoCalc Method
isReactionErrorVisible Method
isTransformationEnabled Method
isValenceErrorVisible Method
isValenceErrorVisibleInView Method
isValencePropertyVisible Method
isvalidateSgroupsAtCreation Method
isViewAtomMarkEnabled Method
keys Method
put Method
removeAllProperty Method
removeOwner Method
removePropertyChangeListener Method
save Method
save Method (String)
save Method (String, Boolean)
save Method (String, String)
setAbsoluteLabelVisible Method
setAromatizeMethod Method
setAtomFont Method
setAtomMappingMethod Method
setAtomPropertiesVisible Method
setAtomSize Method
setAutoCheckStructure Method
setAutomaticFogEnabled Method
setBallRadius Method
setBondDraggedAlong Method
setBondSpacing Method
setCheckerConfigFileName Method
setChiralitySupport Method
setClean2dOpts Method
setClean3dOpts Method
setCleanHOption Method
setCleanHOptionEnabled Method
setCoordinateBondStyle Method
setCoordinateBondStyleAtMulticenter Method
setCopyAsFormat Method
setDefaultSaveFormat Method
setDownWedge Method
setEZVisible Method
setFogFactor Method
setLigandErrorVisible Method
setLoadSaveLocation Method
setLoadWorkingDir Method
setLonePairAutoCalc Method
setProperty Method
setProperty Method (String, String)
setProperty Method (String, String, Boolean)
setReactionErrorVisible Method
setReadGUIPropertiesFromMRV Method
setRLogicVisible Method
setSaveGUIPropertiesInMRV Method
setSaveLoadZoomFactorToMRV Method
setServicesConfigURL Method
setSketchAnyBond Method
setSketchArrowHeadLength Method
setSketchArrowHeadWidth Method
setSketchArrowTailLength Method
setSketchArrowTailWidth Method
setSketchCarbonVisibility Method
setSketchColorScheme Method
setSketchImplicitH Method
setSketchLigandOrderVisibility Method
setSketchLoadWorkingDir Method
setSketchMolbg2d Method
setSketchMolbg3d Method
setSketchRecentFileListSize Method
setSketchRendering2d Method
setSketchRendering3d Method
setSketchSaveWorkingDir Method
setStickThickness Method
setTerminalBondDeletionStyle Method
setTransformationEnabled Method
setValenceErrorVisible Method
setValenceErrorVisibleInView Method
setValencePropertyVisible Method
setvalidateSgroupsAtCreation Method
setViewAnyBond Method
setViewAtomMarkEnabled Method
setViewCarbonVisibility Method
setViewColorScheme Method
setViewExplicitH Method
setViewImplicitH Method
setViewLayout Method
setViewLigandOrderVisibility Method
setViewLoadWorkingDir Method
setViewMolbg2d Method
setViewMolbg3d Method
setViewNavmode2d Method
setViewNavmode3d Method
setViewRecentFileListSize Method
setViewRendering2d Method
setViewRendering3d Method
setViewSaveWorkingDir Method
setWireThickness Method
tryToLoad Method
tryToLoad Method
tryToLoad Method ()
tryToLoadTemplates Method
chemaxon.marvin.io Namespace
ArrayMDocSource Class
ArrayMDocSource Members
ArrayMDocSource Constructor
ArrayMDocSource Constructor (MDocument[])
ArrayMDocSource Constructor (Molecule[])
ArrayMDocSource Constructor ()
ArrayMDocSource Methods
estimateNumRecords Method
getRecordCount Method
getRecordCountMax Method
isEndReached Method
isRewindable Method
nextDoc Method
seekRecord Method
skipRecord Method
MDocSource Class
MDocSource Members
MDocSource Constructor
MDocSource Methods
close Method
estimateNumRecords Method
getDocLabel Method
getMoleculeIterator Method
getRecordCount Method
getRecordCountMax Method
isEndReached Method
isRewindable Method
nextDoc Method
seekForward Method
seekRecord Method
seekRecordAtFraction Method
skipRecord Method
MFieldAccessor Class
MFieldAccessor Members
MFieldAccessor Constructor
MFieldAccessor Methods
getFields Method
getKeys Method
getMainMolecule Method
isEditable Method
setField Method
setFields Method
MolExportException Class
MolExportException Members
MolExportException Constructor
MolExportException Constructor (Exception)
MolExportException Constructor (String)
MolExportException Constructor (String, Exception)
MolExportException Methods
getMolIndex Method
setMolIndex Method
MolExportModule Class
MolExportModule Members
MolExportModule Constructor
MolExportModule Methods
close Method
convert Method
getEncoding Method
getFormat Method
getOptionDescriptors Method
isCleanable Method
isDocumentExport Method
isImplicitHcountImportant Method
isImplicitHcountImportant Method (MolAtom)
isImplicitHcountImportant Method (MoleculeGraph)
open Method
open Method (String)
open Method (String, MPropertyContainer)
setEncoding Method
MolImportModule Class
MolImportModule Members
MolImportModule Constructor
MolImportModule Methods
createMol Method
getLineCount Method
getPreferredView Method
initMolImport Method
initMolImport Method (MolInputStream)
initMolImport Method (MRecord, String)
isDocumentImporter Method
readDocument Method
readMol Method
setOptions Method
MolImportModule.PreferredView Class
MolImportModule.PreferredView Members
MolImportModule.PreferredView Fields
Default Field
Matrix Field
Spreadsheet Field
MolImportModule.PreferredView Methods
__<clinit> Method
valueOf Method
values Method
MolImportModule.PreferredView.__Enum Enumeration
MPropHandler Class
MPropHandler Members
MPropHandler Constructor
MPropHandler Methods
__<clinit> Method
convertToString Method
convertToString Method (MProp, String)
convertToString Method (MPropertyContainer, String)
createArray Method
createArrayXSD Method
createMMoleculeProp Method
createScalar Method
createScalar Method (String, String)
createScalar Method (String, String, Object)
createScalarXSD Method
parseMolecule Method
stringToArray Method
stringToScalar Method
MRecord Class
MRecord Members
MRecord Constructor
MRecord Constructor
MRecord Constructor (Int64, Int64, Int32, String, MPropertyContainer, Int32[])
MRecord Constructor (Int64, Int64, Int32, String, MPropertyContainer, Int32[], Int32)
MRecord Fields
F_MOL_MISSING Field
MRecord Methods
getEncoding Method
getEndLineCount Method
getEndPosition Method
getFlags Method
getFormat Method
getHeaderNewLineCount Method
getInputFormat Method
getLineNumberMap Method
getMolBytes Method
getMolString Method
getPropertyContainer Method
getStartLineCount Method
getStartPosition Method
getString Method
setMolBytes Method
MRecordImporter Class
MRecordImporter Members
MRecordImporter Constructor
MRecordImporter Methods
close Method
createImportMod Method
createImportMod Method (MolInputStream)
createImportMod Method (String)
createMol Method
createMolIfNeeded Method
getFilePointer Method
getFormat Method
getGlobalProperties Method
getLineCount Method
getMoleculeString Method
getMolImportModule Method
getOptions Method
getQueryMode Method
getRecordReader Method
isSeekable Method
length Method
readDoc Method
readMol Method
readMolMovie Method
readMultiSet Method
readRecordAsText Method
seek Method
setOptions Method
setProgressMonitor Method
setQueryMode Method
setThreadCount Method
skipRecord Method
MRecordParseException Class
MRecordParseException Members
MRecordParseException Constructor
MRecordParseException Constructor (MRecordReader.Position, Exception)
MRecordParseException Constructor (MRecordReader.Position, String)
MRecordParseException Constructor (MRecordReader.Position, String, Exception)
MRecordParseException Methods
getPosition Method
MRecordReader Interface
MRecordReader Members
MRecordReader Methods
close Method
detectRecordPositions Method
getEncapsulatedReader Method
getFilePointer Method
getFooterAsString Method
getHeaderAsString Method
getLineCount Method
getMolInputStream Method
getOptions Method
getRecognizedFormat Method
isPropertyRecord Method
isSeekable Method
nextRecord Method
seek Method
setProgressMonitor Method
skipRecord Method
MRecordReader.Position Class
MRecordReader.Position Members
MRecordReader.Position Constructor
MRecordReader.Position Methods
getLineNumber Method
getRecordNumber Method
toString Method
PositionedInputStream Class
PositionedInputStream Members
PositionedInputStream Constructor
PositionedInputStream Constructor ()
PositionedInputStream Constructor (, Int32)
PositionedInputStream Constructor (, String)
PositionedInputStream Constructor (, Int32, String)
PositionedInputStream Methods
__<clinit> Method
endGrabLines Method
getEncoding Method
getFilePointer Method
getGrabbedLines Method
getLineCount Method
isSeekable Method
length Method
putBackLine Method
putBackLine Method
putBackLine Method (Int32)
read Method
read Method
read Method (Byte[], Int32, Int32)
readLine Method
reset Method
seek Method
setDesiredBufferSize Method
setEncoding Method
setEncoding Method (Object)
setEncoding Method (String)
skip Method
skipLine Method
startGrabLines Method
chemaxon.marvin.io.formats Namespace
AbstractMRecordReader Class
AbstractMRecordReader Members
AbstractMRecordReader Constructor
AbstractMRecordReader Methods
close Method
detectRecordPositions Method
getEncapsulatedReader Method
getFilePointer Method
getFooterAsString Method
getHeaderAsString Method
getLineCount Method
getMolInputStream Method
getOptions Method
getRecognizedFormat Method
isPropertyRecord Method
isSeekable Method
nextRecord Method
seek Method
setProgressMonitor Method
skipRecord Method
chemaxon.marvin.io.formats.mdl Namespace
MolExport Class
MolExport Members
MolExport Constructor
MolExport Methods
__<clinit> Method
convert Method
open Method
MolfileUtil Class
MolfileUtil Members
MolfileUtil Constructor
MolfileUtil Fields
SGROUP_TYPENAMES Field
MolfileUtil Methods
__<clinit> Method
getSgroupType Method
isSpecBeilsteinGeneric Method
MolImport Class
MolImport Members
MolImport Constructor
MolImport Methods
__<clinit> Method
createMol Method
initMolImport Method
readMol Method
setOptions Method
chemaxon.marvin.io.formats.smiles Namespace
SmartsAtomQuerifier Class
SmartsAtomQuerifier Members
SmartsAtomQuerifier Constructor
SmartsAtomQuerifier Methods
__<clinit> Method
hasSMARTSProps Method
hasSMARTSPropsExcluding Method
isMarvinCompMode Method
setMarvinCompMode Method
setQuerystr Method
setQuerystr Method (MolAtom, String)
setQuerystr Method (MolAtom, String, Int32)
setSMARTS Method
chemaxon.marvin.modules Namespace
AutoMapper Class
AutoMapper Members
AutoMapper Constructor
AutoMapper Fields
BEST Field
CHANGING Field
CHEMAXON Field
COMPLETE Field
DAYLIGHT Field
DEFAULT_COMPLEXITY_THRESHOLD Field
DEFAULT_MAPPING_STRATEGY Field
DEFAULT_MAPPING_STYLE Field
DEFAULT_STEP_LIMIT Field
EITHER Field
FASTEST Field
MATCHING Field
ORPHANS Field
STANDARD Field
STOP_BADARGSINMODFUNC Field
STOP_FOUND Field
STOP_NOTFOUND Field
STOP_STEPLIMIT Field
STOP_TIMELIMIT Field
STOP_UNKONW Field
UNKNOWN Field
UNMAPPED Field
AutoMapper Methods
__<clinit> Method
clearMaps Method
getDiagnosticMessage Method
getlastStopCause Method
getMapCount Method
guessMappingStyle Method
main Method
map Method
map Method (RxnMolecule)
map Method (Molecule, Int32)
map Method (RxnMolecule, Boolean)
mapReaction Method
modfunc Method
setComplexityThreshold Method
setForbiddenMap Method
setIgnoreH Method
setMap Method
setMappingMode Method
setMappingStrategy Method
setMappingStyle Method
setOption Method
setReaction Method
setStepCountLimit Method
setTimeLimit Method
chemaxon.marvin.modules.datatransfer Namespace
ClipboardHandler Class
ClipboardHandler Members
ClipboardHandler Methods
__<clinit> Method
addTransferable Method
addTransferable Method (TransferableDescriptor)
addTransferable Method (String, String, , , Boolean, Boolean)
addTransferable Method (String, String, , , Boolean, Boolean, Boolean)
clearClipboard Method
getClipboard Method
getCopyAsTransferableNames Method
getLog Method
getObjectFromClipboard Method
getObjectFromTransferable Method
getStringFromClipboard Method
getTransferableFor Method
getTransferableFor Method (Molecule, )
getTransferableFor Method (Molecule, , String)
getWorkOnBackGround Method
isClearClipboardBeforeExport Method
isSupportedTransferFormat Method
putImageToClipboard Method
putMoleculeToClipboard Method
putMoleculeToClipboard Method (Molecule, )
putMoleculeToClipboard Method (Molecule, , String)
putStringToClipboard Method
releasePermanentResources Method
removeOLESupport Method
removeTransferable Method
removeTransferable Method (TransferableDescriptor)
removeTransferable Method (String)
setClearClipboardBeforeExport Method
setWorkOnBackground Method
startPermanentResources Method
MarvinTransferable Class
MarvinTransferable Members
MarvinTransferable Constructor
MarvinTransferable Methods
getTransferData Method
getTransferDataFlavors Method
isDataFlavorSupported Method
isInputAvailable Method
registerNativeNames Method
setMolecule Method
setProperties Method
setTransfer Method
MTransferable Interface
MTransferable Members
MTransferable Fields
CLIPBOARD_OPERATION_GET Field
CLIPBOARD_OPERATION_PUT Field
CLIPBOARD_OPERATION_UNDEFINED Field
MTransferable Methods
isInputAvailable Method
registerNativeNames Method
setMolecule Method
setProperties Method
setTransfer Method
MTransferable.__Fields Class
MTransferable.__Fields Members
MTransferable.__Fields Fields
CLIPBOARD_OPERATION_GET Field
CLIPBOARD_OPERATION_PUT Field
CLIPBOARD_OPERATION_UNDEFINED Field
TransferableDescriptor Class
TransferableDescriptor Members
TransferableDescriptor Constructor
TransferableDescriptor Constructor (String, String, , , Boolean, Boolean)
TransferableDescriptor Constructor (String, String, , , Boolean, Boolean, Boolean)
TransferableDescriptor Methods
compareTo Method
compareTo Method (TransferableDescriptor)
compareTo Method (Object)
equals Method
getInputPriority Method
getName Method
getPriority Method
getRepresentationClass Method
hashCode Method
isCopyAsTransferable Method
isDefaultTransferable Method
isDndTransferable Method
chemaxon.marvin.paint Namespace
DispOptConsts Interface
DispOptConsts Members
DispOptConsts Constructor
DispOptConsts Fields
ABS_FLAG Field
ANYBOND_AUTO Field
ANYBOND_AUTO_S Field
ANYBOND_DASHED Field
ANYBOND_DASHED_S Field
ANYBOND_MASK Field
ANYBOND_OFFSET Field
ANYBOND_SOLID Field
ANYBOND_SOLID_S Field
ANYBOND_STYLES Field
APPLY_DEPTH_CUE Field
ATMAP_FLAG Field
ATNUM_FLAG Field
ATPROP_FLAG Field
ATSYM_FLAG Field
AUTOMATIC_FOG Field
BALLSTICK Field
BALLSTICK_RENDERING_S Field
BONDLEN_FLAG Field
CARBON_VIS_INCHAIN Field
CARBON_VIS_INCHAIN_S Field
CARBON_VIS_MASK Field
CARBON_VIS_OFF Field
CARBON_VIS_OFF_S Field
CARBON_VIS_OFFSET Field
CARBON_VIS_ON Field
CARBON_VIS_ON_S Field
CARBON_VIS_STYLES Field
COLOR_SCHEMES Field
COLORS_MASK Field
COLORS_OFFSET Field
COORDINATE_BOND_ARROW_S Field
COORDINATE_BOND_AT_MULTICENTER_FLAG Field
COORDINATE_BOND_AT_MULTICENTER_OFFSET Field
COORDINATE_BOND_AT_MULTICENTER_STYLES Field
COORDINATE_BOND_HASHED_S Field
COORDINATE_BOND_SOLID_S Field
COORDINATE_BOND_STYLE_FLAG Field
COORDINATE_BOND_STYLE_OFFSET Field
COORDINATE_BOND_STYLES Field
CPK_SCHEME Field
CPK_SCHEME_S Field
DAYLIGHT_DOWNWEDGE_FLAG Field
DAYLIGHT_DOWNWEDGE_S Field
DIM_FLAG Field
DOWNWEDGE_MODES Field
DOWNWEDGE_OFFSET Field
EZ_FLAG Field
GRINV_FLAG Field
GROUP_SCHEME Field
GROUP_SCHEME_S Field
IMPLICITH_ALL Field
IMPLICITH_ALL_S Field
IMPLICITH_HETERO Field
IMPLICITH_HETERO_S Field
IMPLICITH_HETEROTERM Field
IMPLICITH_HETEROTERM_S Field
IMPLICITH_LEVELS Field
IMPLICITH_MASK Field
IMPLICITH_OFF Field
IMPLICITH_OFF_S Field
LIGAND_ERROR_VISIBILITY_FLAG Field
LIGAND_ORDER_MASK Field
LIGAND_ORDER_OFF Field
LIGAND_ORDER_OFF_S Field
LIGAND_ORDER_ON Field
LIGAND_ORDER_ON_S Field
LIGAND_ORDER_ONLY_WITH_DEFINITION Field
LIGAND_ORDER_ONLY_WITH_DEFINITION_S Field
LIGAND_ORDER_STYLES Field
LP_AUTO_FLAG Field
LP_FLAG Field
MDL_DOWNWEDGE_S Field
MM_MASK Field
MM_MODES Field
MM_OFFSET Field
MM_ROT3D Field
MM_ROTZ Field
MM_ZOOM Field
MM_ZOOMROT Field
MONO_SCHEME Field
MONO_SCHEME_S Field
QUALITY_MASK Field
QUALITY_OFFSET Field
RENDERING_MASK Field
RENDERING_OFFSET Field
RENDERING_STYLES Field
RGROUPS_FLAG Field
RLOGIC_FLAG Field
RS_ALL Field
RS_ALL_S Field
RS_MASK Field
RS_OFF Field
RS_OFF_S Field
RS_OFFSET Field
RS_OPTIONS Field
RS_SELECTED Field
RS_SELECTED_S Field
SET_SCHEME_FLAG Field
SHAPELY_SCHEME Field
SHAPELY_SCHEME_S Field
SPACEFILL Field
SPACEFILL_RENDERING_S Field
STICKS Field
STICKS_RENDERING_S Field
VALENCE_PROP_VISIBILITY_FLAG Field
WIREFRAME Field
WIREFRAME_RENDERING_S Field
WIREKNOBS Field
WIREKNOBS_RENDERING_S Field
DispOptConsts Methods
__<clinit> Method
DispOptConsts.__Fields Class
DispOptConsts.__Fields Members
DispOptConsts.__Fields Fields
ABS_FLAG Field
ANYBOND_AUTO Field
ANYBOND_AUTO_S Field
ANYBOND_DASHED Field
ANYBOND_DASHED_S Field
ANYBOND_MASK Field
ANYBOND_OFFSET Field
ANYBOND_SOLID Field
ANYBOND_SOLID_S Field
ANYBOND_STYLES Field
APPLY_DEPTH_CUE Field
ATMAP_FLAG Field
ATNUM_FLAG Field
ATPROP_FLAG Field
ATSYM_FLAG Field
AUTOMATIC_FOG Field
BALLSTICK Field
BALLSTICK_RENDERING_S Field
BONDLEN_FLAG Field
CARBON_VIS_INCHAIN Field
CARBON_VIS_INCHAIN_S Field
CARBON_VIS_MASK Field
CARBON_VIS_OFF Field
CARBON_VIS_OFF_S Field
CARBON_VIS_OFFSET Field
CARBON_VIS_ON Field
CARBON_VIS_ON_S Field
CARBON_VIS_STYLES Field
COLOR_SCHEMES Field
COLORS_MASK Field
COLORS_OFFSET Field
COORDINATE_BOND_ARROW_S Field
COORDINATE_BOND_AT_MULTICENTER_FLAG Field
COORDINATE_BOND_AT_MULTICENTER_OFFSET Field
COORDINATE_BOND_AT_MULTICENTER_STYLES Field
COORDINATE_BOND_HASHED_S Field
COORDINATE_BOND_SOLID_S Field
COORDINATE_BOND_STYLE_FLAG Field
COORDINATE_BOND_STYLE_OFFSET Field
COORDINATE_BOND_STYLES Field
CPK_SCHEME Field
CPK_SCHEME_S Field
DAYLIGHT_DOWNWEDGE_FLAG Field
DAYLIGHT_DOWNWEDGE_S Field
DIM_FLAG Field
DOWNWEDGE_MODES Field
DOWNWEDGE_OFFSET Field
EZ_FLAG Field
GRINV_FLAG Field
GROUP_SCHEME Field
GROUP_SCHEME_S Field
IMPLICITH_ALL Field
IMPLICITH_ALL_S Field
IMPLICITH_HETERO Field
IMPLICITH_HETERO_S Field
IMPLICITH_HETEROTERM Field
IMPLICITH_HETEROTERM_S Field
IMPLICITH_LEVELS Field
IMPLICITH_MASK Field
IMPLICITH_OFF Field
IMPLICITH_OFF_S Field
LIGAND_ERROR_VISIBILITY_FLAG Field
LIGAND_ORDER_MASK Field
LIGAND_ORDER_OFF Field
LIGAND_ORDER_OFF_S Field
LIGAND_ORDER_ON Field
LIGAND_ORDER_ON_S Field
LIGAND_ORDER_ONLY_WITH_DEFINITION Field
LIGAND_ORDER_ONLY_WITH_DEFINITION_S Field
LIGAND_ORDER_STYLES Field
LP_AUTO_FLAG Field
LP_FLAG Field
MDL_DOWNWEDGE_S Field
MM_MASK Field
MM_MODES Field
MM_OFFSET Field
MM_ROT3D Field
MM_ROTZ Field
MM_ZOOM Field
MM_ZOOMROT Field
MONO_SCHEME Field
MONO_SCHEME_S Field
QUALITY_MASK Field
QUALITY_OFFSET Field
RENDERING_MASK Field
RENDERING_OFFSET Field
RENDERING_STYLES Field
RGROUPS_FLAG Field
RLOGIC_FLAG Field
RS_ALL Field
RS_ALL_S Field
RS_MASK Field
RS_OFF Field
RS_OFF_S Field
RS_OFFSET Field
RS_OPTIONS Field
RS_SELECTED Field
RS_SELECTED_S Field
SET_SCHEME_FLAG Field
SHAPELY_SCHEME Field
SHAPELY_SCHEME_S Field
SPACEFILL Field
SPACEFILL_RENDERING_S Field
STICKS Field
STICKS_RENDERING_S Field
VALENCE_PROP_VISIBILITY_FLAG Field
WIREFRAME Field
WIREFRAME_RENDERING_S Field
WIREKNOBS Field
WIREKNOBS_RENDERING_S Field
chemaxon.marvin.plugin Namespace
CalculatorPlugin Class
CalculatorPlugin Members
CalculatorPlugin Constructor
CalculatorPlugin Fields
ATOM Field
BLUE Field
EPSILON Field
MOLECULE Field
MOLECULES Field
PLUGIN_CLASS_KEY Field
PLUGIN_DIR Field
RED Field
CalculatorPlugin Methods
__<clinit> Method
canRepeat Method
checkMolecule Method
create Method
format Method
format Method (Double)
format Method (Double, )
format Method (Double, Int32)
format Method (Double[][], Int32)
getAtomCount Method
getAtomIndex Method
getCalcMolecule Method
getDocument Method
getDoublePrecision Method
getErrorMessage Method
getInputMolDim Method
getpH Method
getPluginResource Method
getProductName Method
getRemark Method
getResult Method
getResult Method (Int32)
getResult Method (String)
getResult Method (Object, Int32)
getResult Method (Object, String)
getResultAsRGB Method
getResultAsRGB Method (Int32, Object)
getResultAsRGB Method (Object, Int32, Object)
getResultAsString Method
getResultAsString Method (Int32, Object)
getResultAsString Method (Object, Int32, Object)
getResultCount Method
getResultCount Method
getResultCount Method (Object)
getResultDomain Method
getResultDomain Method
getResultDomain Method (Object)
getResultMessage Method
getResultMolecule Method
getResultMolecules Method
getResultsAsRGB Method
getResultsAsRGB Method (Int32, Object)
getResultsAsRGB Method (Object, Int32, Object)
getResultsAsString Method
getResultsAsString Method (Int32, Object)
getResultsAsString Method (Object, Int32, Object)
getResultSource Method
getResultTypes Method
getTypeString Method
getWarningMessage Method
handlesMultiFragmentMolecules Method
isInputMoleculeAromatized Method
isLicensed Method
isMultiThreadedRunEnabled Method
isNegligibleResult Method
isOK Method
loadClass Method
readAttribute Method
run Method
setDoublePrecision Method
setDoublePrecision Method (Int32)
setDoublePrecision Method (Int32, Boolean)
setLicenseEnvironment Method
setMolecule Method
setMolecule Method (Molecule)
setMolecule Method (Molecule, Boolean)
setMolecule Method (Molecule, Boolean, Boolean)
setParameters Method
setProgressMonitor Method
standardize Method
CalculatorPluginDisplay Class
CalculatorPluginDisplay Members
CalculatorPluginDisplay Constructor
CalculatorPluginDisplay Methods
clear Method
getErrorComponent Method
getLabels Method
getParameterPanel Method
getProgressMonitor Method
getRemark Method
getResultComponent Method
getTitle Method
isMultipleDisplay Method
pop Method
setCellIndex Method
setParameters Method
setParent Method
setPlugin Method
setReactionArrow Method
setTitle Method
store Method
CalculatorPluginOutput Class
CalculatorPluginOutput Members
CalculatorPluginOutput Constructor
CalculatorPluginOutput Constructor
CalculatorPluginOutput Constructor (CalculatorPlugin)
CalculatorPluginOutput Methods
close Method
close Method
close Method (Int32)
getCachedResults Method
getHeader Method
getPlugin Method
getPluginParameters Method
getRemark Method
getResult Method
getResultDomain Method
getResultMessage Method
getResultMolecule Method
getResultMolecules Method
getSpecResult Method
getThrowable Method
isMolecular Method
isOK Method
isStreamOutput Method
setOutputParameters Method
setOutputStream Method
setParameters Method
setPlugin Method
setSeparator Method
setThrowable Method
ParameterPanelHandler Interface
ParameterPanelHandler Members
ParameterPanelHandler Methods
getComponent Method
getParameters Method
getStoredParameters Method
isOkActionEnabled Method
reloadParameters Method
restoreDefaultParameters Method
saveParameters Method
verifyParameters Method
PluginException Class
PluginException Members
PluginException Constructor
PluginException Constructor
PluginException Constructor (Exception)
PluginException Constructor (String)
PluginException Constructor (Exception, Int32)
PluginException Constructor (String, Exception)
PluginException Constructor (String, Int32)
PluginException Methods
getErrorLevel Method
getException Method
PluginFactory Class
PluginFactory Members
PluginFactory Constructor
PluginFactory Fields
DEFAULT_CONFIG_FILE Field
NOPARAMS Field
PRELOAD Field
SEPARATOR Field
PluginFactory Methods
createDefaultParameterPanel Method
createDefaultParameterPanel Method (String, )
createDefaultParameterPanel Method (, String, )
getCount Method
getDisplay Method
getGroup Method
getGroupMnemonic Method
getKey Method
getMenu Method
getMnemonic Method
getOptionsPane Method
getParameterPanel Method
getPlugin Method
getPluginIndex Method
getSeparator Method
hasParameters Method
isOptionsPaneLoaded Method
load Method
load Method
load Method ()
load Method (String, String)
saveParameterSettings Method
setOKActionListener Method
setParentComponent Method
PluginFactory.PluginRecord Class
PluginFactory.PluginRecord Members
PluginFactory.PluginRecord Methods
compareTo Method
getDisplay Method
getOptionsPane Method
getParameterPanel Method
getPlugin Method
saveParameterSettings Method
chemaxon.marvin.plugin.concurrent Namespace
DefaultPluginWorkUnit Class
DefaultPluginWorkUnit Members
DefaultPluginWorkUnit Constructor
DefaultPluginWorkUnit Methods
getResult Method
PluginExecutionException Class
PluginExecutionException Members
PluginExecutionException Constructor
PluginExecutionException Constructor (CalculatorPlugin, Exception)
PluginExecutionException Constructor (CalculatorPlugin, String, Exception)
PluginExecutionException Methods
getPlugin Method
PluginWorkUnit Class
PluginWorkUnit Members
PluginWorkUnit Constructor
PluginWorkUnit Constructor
PluginWorkUnit Constructor (CalculatorPlugin)
PluginWorkUnit Methods
call Method
getResult Method
getWrapperException Method
setInput Method
setPlugin Method
ReusablePluginWorkUnit Class
ReusablePluginWorkUnit Members
ReusablePluginWorkUnit Constructor
ReusablePluginWorkUnit Methods
call Method
getResult Method
getWrapperException Method
setInput Method
chemaxon.marvin.plugin.gui Namespace
OptionsPane Class
OptionsPane Members
OptionsPane Constructor
OptionsPane Constructor (String, String, ParameterPanelHandler, )
OptionsPane Constructor (, String, String, ParameterPanelHandler, )
OptionsPane Constructor (, String, String, ParameterPanelHandler, )
OptionsPane Methods
__<clinit> Method
actionPerformed Method
getKey Method
getParameters Method
setActionsEnabled Method
windowActivated Method
windowClosed Method
windowClosing Method
windowDeactivated Method
windowDeiconified Method
windowIconified Method
windowOpened Method
ParameterPanel Class
ParameterPanel Members
ParameterPanel Constructor
ParameterPanel Constructor (ParameterTab, ParameterTab[])
ParameterPanel Constructor (ParameterTab, ParameterTab[], Object)
ParameterPanel Methods
__<clinit> Method
getComponent Method
getParameters Method
getStoredParameters Method
isOkActionEnabled Method
reloadParameters Method
restoreDefaultParameters Method
saveParameters Method
verifyParameters Method
ParameterTab Class
ParameterTab Members
ParameterTab Constructor
chemaxon.marvin.services Namespace
AsyncCallback Interface
AsyncCallback Members
AsyncCallback Methods
onFailure Method
onSuccess Method
DynamicArgument Class
DynamicArgument Members
DynamicArgument Methods
evaluate Method
getExpression Method
getPlaceholderText Method
isValid Method
setExpression Method
toString Method
ServiceArgument Class
ServiceArgument Members
ServiceArgument Methods
createArgument Method
createArgument Method (Object)
createArgument Method (String, Object)
createArgumentAs Method
createArgumentAs Method (Object, )
createArgumentAs Method (String, Object, )
createConstantFromString Method
getAlias Method
getName Method
getType Method
getValue Method
isValid Method
setAlias Method
setName Method
setType Method
setValue Method
toString Method
ServiceDescriptorEditor Interface
ServiceDescriptorEditor Members
ServiceDescriptorEditor Fields
PROPERTY_KEY_PREFERRED_DESCRIPTION Field
PROPERTY_KEY_PREFERRED_NAME Field
PROPERTY_KEY_USERSETTINGS Field
PROPERTY_KEY_VALID Field
ServiceDescriptorEditor Methods
getDescriptor Method
getEditor Method
getPropertyChangeSupport Method
isValid Method
setDescriptor Method
ServiceDescriptorEditor.__Fields Class
ServiceDescriptorEditor.__Fields Members
ServiceDescriptorEditor.__Fields Fields
PROPERTY_KEY_PREFERRED_DESCRIPTION Field
PROPERTY_KEY_PREFERRED_NAME Field
PROPERTY_KEY_USERSETTINGS Field
PROPERTY_KEY_VALID Field
ServiceDescriptorEditorProvider Interface
ServiceDescriptorEditorProvider Members
ServiceDescriptorEditorProvider Methods
getEditor Method
getSupportedDescriptors Method
ServiceDescriptorReader Interface
ServiceDescriptorReader Members
ServiceDescriptorReader Methods
readServiceDescriptors Method
ServiceDescriptorTools Class
ServiceDescriptorTools Members
ServiceDescriptorTools Constructor
ServiceDescriptorTools Fields
DEFAULT_SERVICE_CONFIGURATION_PATH Field
DEFAULT_SERVICE_DESCRIPTOR_EDITOR_PROVIDER_CLASSNAME Field
DEFAULT_SERVICE_DESCRIPTOR_READER_CLASSNAME Field
DEFAULT_SERVICE_DESCRIPTOR_WRITER_CLASSNAME Field
DEFAULT_SERVICE_DIALOG_PROVIDER_CLASSNAME Field
DEFAULT_USER_SERVICE_CONFIGURATION_FILENAME Field
ServiceDescriptorTools Methods
getDefaultServiceDescriptorEditorProvider Method
getDefaultServiceDescriptorReader Method
getDefaultServiceDescriptorWriter Method
getDefaultServiceDialogProvider Method
getServiceDescriptorConfigurationAsStream Method
getServiceDescriptorConfigurationAsStream Method
getServiceDescriptorConfigurationAsStream Method (UserSettings)
getServiceDescriptorEditorProvider Method
getServiceDescriptorReader Method
getServiceDescriptorWriter Method
getServiceDialogProvider Method
ServiceDescriptorWriter Interface
ServiceDescriptorWriter Members
ServiceDescriptorWriter Methods
writeServiceDescriptors Method
ServiceDialogProvider Interface
ServiceDialogProvider Members
ServiceDialogProvider Methods
getDialog Method
ServiceException Class
ServiceException Members
ServiceException Constructor
ServiceException Constructor (Exception)
ServiceException Constructor (String)
ServiceException Constructor (String, Exception)
ServiceHandler Class
ServiceHandler Members
ServiceHandler Constructor
ServiceHandler Methods
callService Method
callService Method (, Object[])
callService Method (, AsyncCallback, Object[])
chemaxon.marvin.services.httpservice Namespace
HTTPServiceDescriptor Class
HTTPServiceDescriptor Members
HTTPServiceDescriptor Constructor
HTTPServiceDescriptor Methods
__<clinit> Method
<bridge>getServiceHandler Method
getServiceHandler Method
getSimpleName Method
chemaxon.marvin.services.json Namespace
JsonServiceDescriptor Class
JsonServiceDescriptor Members
JsonServiceDescriptor Constructor
JsonServiceDescriptor Fields
DESCRIPTOR_URI Field
JsonServiceDescriptor Methods
__<clinit> Method
<bridge>getServiceHandler Method
getDescriptorURI Method
getId Method
getRequestMethod Method
getServiceHandler Method
getSimpleName Method
setDescriptorURI Method
setRequestMethod Method
JsonServiceDescriptor.Method Class
JsonServiceDescriptor.Method Members
JsonServiceDescriptor.Method Fields
GET Field
POST Field
JsonServiceDescriptor.Method Methods
__<clinit> Method
valueOf Method
values Method
JsonServiceDescriptor.Method.__Enum Enumeration
chemaxon.marvin.services.localservice Namespace
LocalServiceDescriptor Class
LocalServiceDescriptor Members
LocalServiceDescriptor Constructor
LocalServiceDescriptor Fields
CLASS Field
LocalServiceDescriptor Methods
__<clinit> Method
getClassName Method
getIcon Method
getServiceHandler Method
getSimpleName Method
setClassName Method
chemaxon.marvin.services.soap Namespace
SoapServiceDescriptor Class
SoapServiceDescriptor Members
SoapServiceDescriptor Constructor
SoapServiceDescriptor Fields
NAMESPACE Field
PORT Field
SERVICE Field
WSDL Field
SoapServiceDescriptor Methods
__<clinit> Method
<bridge>getServiceHandler Method
getNameSpace Method
getPortName Method
getReturnTypes Method
getServiceHandler Method
getSimpleName Method
getWebServiceName Method
getWsdlURI Method
setNameSpace Method
setPortName Method
setReturnTypes Method
setWebServiceName Method
setWsdlURI Method
chemaxon.marvin.services.xmlrpcservice Namespace
XMLRPCServiceDescriptor Class
XMLRPCServiceDescriptor Members
XMLRPCServiceDescriptor Constructor
XMLRPCServiceDescriptor Methods
__<clinit> Method
getIcon Method
getServiceHandler Method
getSimpleName Method
chemaxon.marvin.sketch Namespace
SketchParameterConstants Class
SketchParameterConstants Members
SketchParameterConstants Fields
ABBREVIATED_GROUPS Field
ABBREVIATED_GROUPS_ALLOWED Field
ABSOLUTE_LABEL_VISIBLE Field
ATOM_STRINGS Field
AUTO_SCALE Field
BACKGROUNDLOAD_ENABLED Field
BACKGROUNDLOAD_PRIORITY Field
BOND_DRAGGED_ALONG Field
BUTTON_MENUBAR Field
CUSTOMIZATION_ENABLED Field
DEFAULT_TOOL Field
DETACH Field
ELEMENTS Field
ENABLED_2D_VIEWER Field
ENABLED_3D_VIEWER Field
EXTRA_BONDS Field
EXTRA_TEMPLATES Field
GRAPH_INVARIANTS_VISIBLE Field
GROUPTYPE_ALTERNATING_COPOLYMER_GROUP Field
GROUPTYPE_ANYPOLYMER_GROUP Field
GROUPTYPE_BLOCK_COPOLYMER_GROUP Field
GROUPTYPE_COMPONENT_GROUP Field
GROUPTYPE_COPOLYMER_GROUP Field
GROUPTYPE_CROSSLINK_GROUP Field
GROUPTYPE_GENERIC_GROUP Field
GROUPTYPE_GRAFT_GROUP Field
GROUPTYPE_MER_GROUP Field
GROUPTYPE_MODIFICATION_GROUP Field
GROUPTYPE_MONOMER_GROUP Field
GROUPTYPE_MULTIPLE_GROUP Field
GROUPTYPE_ORDERED_MIXTURE_GROUP Field
GROUPTYPE_RANDOM_COPOLYMER_GROUP Field
GROUPTYPE_RANGE_GROUP Field
GROUPTYPE_SRU_GROUP Field
GROUPTYPE_SUPERATOM_GROUP Field
GROUPTYPE_UNORDERED_MIXTURE_GROUP Field
IMAGE_SAVE_FORMAT Field
IMAGE_SAVE_URL Field
IMAGE_SHOW_URL Field
LONE_PAIRS_AUTO_CALCULATION Field
MAX_SCALE Field
MENU_CUSTOMIZATION_FILE Field
MENUBAR Field
MERGE_DISTANCE Field
MOL_LOADER_FINISHED_EVENT Field
MORE_ENABLED Field
PRELOAD Field
QUERY_ATOMS Field
REACTION_ERROR_VISIBLE Field
REACTION_SUPPORT Field
RLOGIC_VISIBLE Field
SCALE Field
SHORTCUTS Field
SIMPLE_VIEW Field
SKETCH_ARROW_HEAD_LENGTH Field
SKETCH_ARROW_HEAD_WIDTH Field
SKETCH_ARROW_TAIL_LENGTH Field
SKETCH_ARROW_TAIL_WIDTH Field
SKETCH_CARBON_VISIBILITY Field
SKETCH_LIGAND_ORDER_VISIBILITY Field
STATUS_BAR Field
STICK_DISTANCE Field
TEMPLATE_TOOLBAR_CUSTOMIZABLE Field
TEMPLATES Field
TOOLBAR_FLOATABLE Field
TOOLBAR_TEMPLATES Field
TRANSFORMATION_ENABLED Field
UI_DISABLED_GROUP_TYPES Field
UNDETACH_BY_X Field
UNDO Field
USED_JARS Field
VALENCE_CHECK_ENABLED Field
VALENCE_ERROR_VISIBLE Field
VIEW_ONLY Field
chemaxon.marvin.space Namespace
AtomProperty Class
AtomProperty Members
AtomProperty Constructor
AtomProperty Methods
getAtomProperty Method
getSmoleculeAtomProperty Method
AtomProperty.MoleculeAtomProperty Class
AtomProperty.MoleculeAtomProperty Members
AtomProperty.MoleculeAtomProperty Constructor
AtomProperty.MoleculeAtomProperty Methods
getBFactor Method
getCharge Method
getLabel Method
getPartialAtomCharge Method
getResidueTypeId Method
getSecondaryStructureType Method
getType Method
getX Method
getY Method
getZ Method
setMolecule Method
AtomProperty.SmoleculeAtomProperty Class
AtomProperty.SmoleculeAtomProperty Members
AtomProperty.SmoleculeAtomProperty Constructor
AtomProperty.SmoleculeAtomProperty Fields
xCoords Field
yCoords Field
zCoords Field
AtomProperty.SmoleculeAtomProperty Methods
getBFactor Method
getCharge Method
getLabel Method
getPartialAtomCharge Method
getResidueTypeId Method
getSecondaryStructureType Method
getType Method
getX Method
getY Method
getZ Method
setCoordinates Method
setMolecule Method
BoundingBox Class
BoundingBox Members
BoundingBox Constructor
BoundingBox Constructor
BoundingBox Constructor (Single, Single, Single, Single, Single, Single)
BoundingBox Methods
centerx Method
centery Method
centerz Method
clear Method
contains Method
draw Method
extend Method
finalize Method
getBoundingCenter Method
getBoundingRadius Method
getMaxX Method
getMaxY Method
getMaxZ Method
getMinX Method
getMinY Method
getMinZ Method
maxx Method
maxy Method
maxz Method
minx Method
miny Method
minz Method
ready Method
set Method
setMax Method
setMaxX Method
setMaxY Method
setMaxZ Method
setMin Method
setMinX Method
setMinY Method
setMinZ Method
setWithCondition Method
setWithCondition Method (BoundingBox)
setWithCondition Method (Single, Single, Single)
toString Method
translate Method
CellOrComponentId Class
CellOrComponentId Members
CellOrComponentId Constructor
CellOrComponentId Constructor (Int32)
CellOrComponentId Constructor (Int32, Int32)
CellOrComponentId Methods
getCellIndex Method
getComponentIndex Method
isCell Method
isComponent Method
setCellIndex Method
setComponentIndex Method
toString Method
ComponentElement Class
ComponentElement Members
ComponentElement Constructor
ComponentElement Constructor (ComponentElement)
ComponentElement Constructor (, Int32, )
ComponentElement Constructor (, Int32, Int32)
ComponentElement Constructor (, Int32, Int32, )
ComponentElement Constructor (, Int32, Int32, Int32)
ComponentElement Methods
getColor Method
getComponent Method
getComponentPartId Method
getCoordinates Method
getDescription Method
getElementIndex Method
getElementType Method
isComponentPart Method
isVisible Method
setColor Method
setCoordinates Method
setDescription Method
toString Method
GraphicCell Class
GraphicCell Members
GraphicCell Constructor
GraphicCell Constructor
GraphicCell Constructor (Object, Object)
GraphicCell Methods
addComponent Method
clearSelections Method
componentBecameSelected Method
componentBecameUnselected Method
containsComponent Method
draw Method
drawBorders Method
drawCell Method
drawSmoothBackground Method
drawSphere Method
exclusiveSelection Method
extendSelection Method
fadeSelectedComponents Method
fadeUnselectedComponents Method
getBottom Method
getBoundingBoxAndSetSphereRadius Method
getCameraZ Method
getCellDrawProperty Method
getComponent Method
getComponentCount Method
getComponentIterator Method
getControllableObject Method
getFarClip Method
getFovY Method
getHeight Method
getId Method
getIndex Method
getLeft Method
getNearClip Method
getRight Method
getRotateMatrix Method
getShiftX Method
getShiftY Method
getTop Method
getTransformationCenter Method
getVerboseLevel Method
getWidth Method
hasSelectedComponent Method
hasSelectedComponentElement Method
hideAllComponents Method
hideAllMonitors Method
hideSelectedComponents Method
hideUnselectedComponents Method
invertSelection Method
isActive Method
isSelectedComponent Method
isVerbose Method
locateObject Method
locateObject Method (Int32, Int32)
locateObject Method (Int32, Int32, )
locationNearEdgeX Method
locationNearEdgeY Method
notifyZCoordinateChange Method
removeAllComponents Method
removeComponent Method
removeComponent Method ()
removeComponent Method ()
removeComponent Method (Int32)
removeSelectedComponents Method
removeUnselectedComponents Method
removeUnselectedMonitors Method
resetView Method
resetZoom Method
rotate Method
selectComponentElementsInside Method
setActive Method
setAntialias Method
setBackgroundColor Method
setCellDrawProperties Method
setContexts Method
setDrawProperty Method
setDrawSphere Method
setInactive Method
setIndex Method
setIndices Method
setMotionMode Method
setNearEdgeTolerance Method
setOrigin Method
setPickMatrix Method
setRotateMatrix Method
setSize Method
setSmoothBackgroud Method
setTransformationCenter Method
setTransformationCenter Method (Object)
setTransformationCenter Method (Single, Single, Single)
setTransformationCenterX Method
setTransformationCenterY Method
setTransformationCenterZ Method
setVerbose Method
setVerbose Method (Boolean)
setVerbose Method (Int32)
shift Method
showAllComponents Method
showAllComponents Method
showAllComponents Method ()
showAllMonitors Method
showFaded Method
updateRotationMatrix Method
zoom Method
MacroMoleculeComponent Class
MacroMoleculeComponent Members
MacroMoleculeComponent Constructor
MacroMoleculeComponent Fields
B_FACTOR_MODE Field
RAINBOW_MODE Field
MacroMoleculeComponent Methods
__<clinit> Method
draw Method
draw2DPart Method
drawTransparentPart Method
exclusiveSelection Method
extendSelection Method
fadeSelected Method
fadeUnselected Method
getBFactorPalette Method
getComponent Method
getComponentElement Method
getComponentElement Method
getComponentElement Method (MacroMoleculeComponent.MoleculeVisualizer)
getComponentIterator Method
getComponents Method
getCoordinates Method
getDescription Method
getLabelInformation Method
getMacroMolecule Method
getMolecule Method
getRainbowPalette Method
getUsableObject Method
getUsableObjectId Method
has2DPart Method
hasSelectedElements Method
hasTransparentPart Method
hideSelected Method
hideUnselected Method
invertSelection Method
isControllable Method
isVisible Method
isVisible Method
isVisible Method (ComponentElement)
onRemoveGraphicComponent Method
rotate Method
select Method
selectComponentElementsInside Method
setDrawProperty Method
setDrawProperty Method (String, String)
setDrawProperty Method (String, String, MacroMoleculeComponent.MoleculeVisualizer)
setGL Method
setProgressBar Method
setVisible Method
showFaded Method
translate Method
unSelect Method
MacroMoleculeComponent.MoleculeVisualizer Interface
MacroMoleculeComponent.MoleculeVisualizer Members
MacroMoleculeComponent.MoleculeVisualizer Methods
draw Method
drawAtomSelection Method
drawTransparentPart Method
fadeSelected Method
fadeUnselected Method
getBoundingBox Method
getColor Method
getColorType Method
getDescription Method
getDrawProperty Method
getLabelInformation Method
getMacroMoleculeComponent Method
getName Method
getVisibleAtomCount Method
hasTransparentPart Method
hideSelected Method
hideUnselected Method
initDraw Method
isAtomFaded Method
isAtomVisible Method
isHighlighted Method
isSelected Method
isSelectedAtom Method
isVisible Method
onRemove Method
select Method
selectAtom Method
selectComponentElementsInside Method
selectedAtomCount Method
setDrawProperty Method
setGL Method
setHighlighted Method
setVisible Method
showFaded Method
unSelect Method
unSelectAtom Method
MolecularSurfaceComponent Class
MolecularSurfaceComponent Members
MolecularSurfaceComponent Constructor
MolecularSurfaceComponent Constructor
MolecularSurfaceComponent Constructor ()
MolecularSurfaceComponent Constructor (., Object)
MolecularSurfaceComponent Constructor (, String)
MolecularSurfaceComponent Constructor (., Object, Single)
MolecularSurfaceComponent Fields
DEFAULT_ISOVALUE Field
DEFAULT_PROBE_RADIUS Field
DEFAULT_RESOLUTION Field
SURFACE_COLOR_GRID_MAPPING Field
SURFACE_COLOR_PROPERTY_MAPPING Field
SURFACE_COLOR_TYPE_ATOMTYPE Field
SURFACE_COLOR_TYPE_B_FACTOR Field
SURFACE_COLOR_TYPE_CHAIN Field
SURFACE_COLOR_TYPE_CONSTANT Field
SURFACE_COLOR_TYPE_EP Field
SURFACE_COLOR_TYPE_RAINBOW Field
SURFACE_COLOR_TYPE_RESIDUE Field
SURFACE_COLOR_TYPE_SS Field
SURFACE_TYPE_BLOBBY Field
SURFACE_TYPE_CONNOLLY Field
SURFACE_TYPE_GAUSSIAN Field
SURFACE_TYPE_SAS Field
SURFACE_TYPE_VDW Field
MolecularSurfaceComponent Methods
__<clinit> Method
callback Method
draw Method
drawTransparentPart Method
getColor Method
getColorType Method
getDrawType Method
getMaximumMappedValue Method
getMinimumMappedValue Method
getPalette Method
getPaletteString Method
getProbeRadius Method
getSurface Method
getSurfacePrecision Method
getSurfaceSimplificationEnabled Method
getSurfaceSmoothnessFactor Method
getSurfaceThreshold Method
getSurfaceType Method
getSurfaceType Method
getSurfaceType Method (String)
getSurfaceTypeString Method
hasTransparentPart Method
isColorMapperEnabled Method
isControllable Method
isVolumeVisible Method
mapPropertyToSurface Method
mapPropertyToSurface_0 Method
onRemoveGraphicComponent Method
receiveNotificationOnCoordinateChange Method
refreshColoring Method
resize Method
select Method
setAtomPropertyList Method
setColor Method
setDrawProperty Method
setExclusiveDrawing Method
setGL Method
setMolecules Method
setNegativeCriterium Method
setPalette Method
setPalette Method (Byte[][])
setPalette Method (Int32)
setPaletteMaximum Method
setPaletteMinimum Method
setPositiveCriterium Method
setProbeRadius Method
setProgressBar Method
setRotateMatrix Method
setSurfacePrecision Method
setSurfacePrecision Method
setSurfacePrecision Method (Single)
setSurfacePrecision Method (String)
setSurfaceSimplificationEnabled Method
setSurfaceType Method
setVisible Method
showVolume Method
surfaceOf Method
surfaceSimplification Method
translate Method
updatePropertyMapping Method
MoleculeComponent Class
MoleculeComponent Members
MoleculeComponent Constructor
MoleculeComponent Constructor (Molecule)
MoleculeComponent Constructor (Object, MacroMoleculeComponent)
MoleculeComponent Fields
elementList Field
LONE_PAIR_TYPE Field
MoleculeComponent Methods
__<clinit> Method
draw Method
drawAtomSelection Method
drawTransparentPart Method
exclusiveSelection Method
extendSelection Method
fadeSelected Method
fadeUnselected Method
getAtomCount Method
getAtomIterator Method
getAtomProperty Method
getAtomSelections Method
getBondCount Method
getBondIterator Method
getBoundingBox Method
getColor Method
getColorType Method
getComponentElement Method
getCoordinates Method
getDescription Method
getGraphicComponent Method
getId Method
getLabelInformation Method
getLabelInformation Method (String)
getLabelInformation Method (String, Boolean)
getMacroMoleculeComponent Method
getMolecule Method
getSelectedAtom Method
getVisibleAtomCount Method
hasSelectedElements Method
hasTransparentPart Method
hideSelected Method
hideUnselected Method
initDraw Method
invertSelection Method
isAtomFaded Method
isAtomVisible Method
isControllable Method
isGraphicComponent Method
isHighlighted Method
isLigand Method
isMacromoleculePart Method
isSelected Method
isSelected Method
isSelected Method (ComponentElement)
isSelectedAtom Method
isVisible Method
isVisible Method
isVisible Method (ComponentElement)
onRemove Method
onRemoveGraphicComponent Method
rotate Method
select Method
selectAllAtoms Method
selectAtom Method
selectComponentElementsInside Method
selectedAtomCount Method
setColor Method
setColor Method ()
setColor Method (Single, Single, Single)
setDrawProperty Method
setGL Method
setHighlighted Method
setMacroMoleculeComponent Method
setMolecule Method
setVisible Method
showFaded Method
torsion Method
translate Method
unSelect Method
unSelectAllAtoms Method
unSelectAtom Method
MSpaceEasy Class
MSpaceEasy Members
MSpaceEasy Constructor
MSpaceEasy Constructor (Boolean)
MSpaceEasy Constructor (Boolean, Boolean, )
MSpaceEasy Constructor (Int32, Int32, Boolean)
MSpaceEasy Constructor (Int32, Int32, Boolean, Boolean, )
MSpaceEasy Methods
__<clinit> Method
addCanvas Method
addMenuBar Method
addMolecule Method
addMolecule Method (Molecule)
addMolecule Method (String)
addMoleculeTo Method
addMoleculeToEmptyCell Method
addMoleculeToEmptyCell Method (Molecule)
addMoleculeToEmptyCell Method (String)
addMoleculeWithoutChange Method
addPDB Method
addPopupMenu Method
addSelectionPanel Method
addSelectionPanelAndProgressBar Method
addToolBar Method
callback Method
computeSurface Method
computeSurface Method (MacroMoleculeComponent.MoleculeVisualizer)
computeSurface Method (String)
createSelectionPanel Method
createSelectionPanelAndProgressBar Method
getEventHandler Method
getGraphicScene Method
getInputStream Method
getMolInputStream Method
getRCSBLink Method
getRCSBLink Method (String)
getRCSBLink Method (String, Boolean)
isURL Method
mapPropertyFile Method
openMolecule Method
processArguments Method
readPDB Method
readPropertyFile Method
refresh Method
removeAllComponents Method
removeComponent Method
resetAll Method
setCellProperty Method
setComponentProperty Method
setIconImage Method
setLayout Method
setProperty Method
setSize Method
setVerbose Method
PharmacophoreArrow Class
PharmacophoreArrow Members
PharmacophoreArrow Constructor
PharmacophoreArrow Constructor
PharmacophoreArrow Constructor (ComponentElement)
PharmacophoreArrow Constructor (Double, Double, Double)
PharmacophoreArrow Fields
DRAW_TYPES Field
PharmacophoreArrow Methods
__<clinit> Method
draw Method
drawTransparentPart Method
getColor Method
getCoordinates Method
getDescription Method
getDrawType Method
getName Method
getRadius Method
hasTransparentPart Method
isControllable Method
isHighlighted Method
onRemoveGraphicComponent Method
resize Method
rotate Method
select Method
setDrawProperty Method
setDrawType Method
setHighlighted Method
setPosition Method
setRadius Method
setRenderingQuality Method
setRenderingQuality Method (Int32)
setRenderingQuality Method (String)
toString Method
translate Method
unSelect Method
PharmacophorePoint Class
PharmacophorePoint Members
PharmacophorePoint Constructor
PharmacophorePoint Constructor
PharmacophorePoint Constructor (ComponentElement)
PharmacophorePoint Constructor (Double, Double, Double)
PharmacophorePoint Fields
ACCEPTOR_TYPE Field
ANIONIC_TYPE Field
AROMATIC_TYPE Field
CATIONIC_TYPE Field
DEFAULT_RADIUS Field
DONOR_TYPE Field
DRAW_TYPES Field
EXCLUDED_TYPE Field
HYDROPHOBIC_TYPE Field
UNKONWN_TYPE Field
PharmacophorePoint Methods
__<clinit> Method
draw Method
drawTransparentPart Method
getColor Method
getCoordinates Method
getDescription Method
getDrawType Method
getName Method
getRadius Method
hasTransparentPart Method
isAcceptor Method
isAnionic Method
isAromatic Method
isCationic Method
isControllable Method
isDonor Method
isExcluded Method
isHighlighted Method
isHydrophobic Method
resize Method
select Method
setAcceptor Method
setAnionic Method
setAromatic Method
setCationic Method
setDonor Method
setDrawProperty Method
setDrawType Method
setExcluded Method
setHighlighted Method
setHydrophobic Method
setPosition Method
setRadius Method
setRenderingQuality Method
setRenderingQuality Method (Int32)
setRenderingQuality Method (String)
toString Method
translate Method
unSelect Method
SurfaceColoring Class
SurfaceColoring Members
SurfaceColoring Constructor
SurfaceColoring Constructor (SurfaceComponent)
SurfaceColoring Constructor (, SurfaceComponent)
SurfaceColoring Constructor (, SurfaceComponent, Single)
SurfaceColoring Fields
ATOM_PROPERTY_MAPPING Field
BUILT_IN_CHAIN_MAPPING Field
BUILT_IN_CPK_MAPPING Field
BUILT_IN_RAINBOW_MAPPING Field
BUILT_IN_RESIDUE_MAPPING Field
BUILT_IN_SECONDARY_STRUCTURE_MAPPING Field
COLOR_MAPPER_BLUE_TO_GREEN Field
COLOR_MAPPER_BLUE_TO_RED Field
COLOR_MAPPER_FIRE Field
COLOR_MAPPER_GREEN_TO_BLUE Field
COLOR_MAPPER_RAINBOW Field
COLOR_MAPPER_RED_TO_BLUE Field
COLOR_MAPPER_REVERSE_RAINBOW Field
DECREASE_LINEAR Field
DECREASE_RECIPROCAL_SQUARE Field
DECREASE_SQUARE Field
DISTANCE_CONSTANT Field
DISTANCE_FROM_VDW Field
DISTANCE_FROM_VDW_EXTENDED Field
DISTANCE_WEIGHTED Field
GRID_MAPPING Field
MEAN_VALUE Field
NEAREST_VALUE Field
NO_DECREASE Field
RADIUS_CONSTANT Field
RADIUS_VDW Field
RADIUS_VDW_EXTENDED Field
SUM_OF_VALUES Field
SurfaceColoring Methods
changeColorMapperColors Method
doColoring Method
doColoring Method
doColoring Method (Int32)
getBuiltInPalette Method
getBuiltInPalette Method (Int32)
getBuiltInPalette Method (Object)
getBuiltInPalettes Method
getMaximumValue Method
getMinimumValue Method
reset Method
setAtomRadiusExtension Method
setBuiltInColorMapperMethod Method
setBuiltInColorMapperMethod Method (Int32)
setBuiltInColorMapperMethod Method (Int32, Boolean)
setConstantAtomRadius Method
setConstantDistanceRadius Method
setDistanceRadiusExtension Method
setDistanceRadiusMode Method
setEnrtyRadiusMode Method
setHomogeneousPaletteColors Method
setLowerCutoffValue Method
setMaximumValue Method
setMinimumValue Method
setProgressBar Method
setPropertyColorMapperMethod Method
setPropertyColorMapperRange Method
setPropertyColorObject Method
setPropertyMethod Method
setPropertyObject Method
setPropertyValueDecreasement Method
setReciprocalConstant Method
setSmoothColoringToCutoffValues Method
setSurface Method
setUpperCutoffValue Method
setWeightMode Method
updateColors Method
SurfaceComponent Class
SurfaceComponent Members
SurfaceComponent Constructor
SurfaceComponent Constructor (Int32)
SurfaceComponent Constructor (Int32, Int32)
SurfaceComponent Constructor (Int32, Int32, Int32, Int32)
SurfaceComponent Fields
DOTTED_TYPE Field
FILLED_TYPE Field
MESH_TYPE Field
TRANSPARENT_TYPE Field
SurfaceComponent Methods
__<clinit> Method
clipSurface Method
coloring Method
draw Method
drawTransparentPart Method
getColor Method
getColor3 Method
getDrawType Method
getNormal Method
getPrimitives Method
getVertexCount Method
getVertexX Method
getVertexY Method
getVertexZ Method
hasTransparentPart Method
isClipped Method
manuallySetNormals Method
onRemoveGraphicComponent Method
putColor Method
putColorComponent Method
putNormal Method
putNormal Method (Single[])
putNormal Method (Single, Single, Single)
putPolygon Method
putTriangle Method
putVertex Method
putVertex Method (Single[])
putVertex Method (Single, Single, Single)
setColor Method
setDrawing Method
setDrawingPrimitiveType Method
setDrawingPrimitiveType Method (Int32)
setDrawingPrimitiveType Method (Int32, Int32)
setDrawProperty Method
setDrawType Method
setExclusiveColor Method
setExclusiveDrawing Method
chemaxon.marvin.space.monitor Namespace
AngleMonitor Class
AngleMonitor Members
AngleMonitor Constructor
AngleMonitor Methods
draw Method
getCoordinates Method
maximumItemCount Method
measurement Method
Control Class
Control Members
Control Constructor
Control Methods
control Method
control Method (Int32)
control Method (Int32, Int32)
getCenter Method
getColor Method
setCenter Method
setComponent Method
DihedralControl Class
DihedralControl Members
DihedralControl Constructor
DihedralControl Methods
__<clinit> Method
control Method
control Method (Int32)
control Method (Int32, Int32)
finalize Method
flip Method
getColor Method
setAtoms Method
setComponent Method
DihedralMonitor Class
DihedralMonitor Members
DihedralMonitor Constructor
DihedralMonitor Methods
control Method
draw Method
getComponent Method
getCoordinates Method
maximumItemCount Method
measurement Method
select Method
setControl Method
unSelect Method
DistanceMonitor Class
DistanceMonitor Members
DistanceMonitor Constructor
DistanceMonitor Methods
draw Method
maximumItemCount Method
measurement Method
GlobalLocationControl Class
GlobalLocationControl Members
GlobalLocationControl Constructor
GlobalLocationControl Methods
__<clinit> Method
control Method
control Method (Int32)
control Method (Int32, Int32)
getColor Method
GlobalOrientationControl Class
GlobalOrientationControl Members
GlobalOrientationControl Constructor
GlobalOrientationControl Methods
__<clinit> Method
control Method
control Method (Int32)
control Method (Int32, Int32)
getColor Method
Label Class
Label Members
Label Constructor
Label Fields
BACKGROUND_MODE_NONE Field
BACKGROUND_MODE_OWN_COLOR Field
BORDER_MODE_BRIGHTER_FOREGROUND Field
BORDER_MODE_FOREGROUND_COLOR Field
BORDER_MODE_NONE Field
BORDER_MODE_OWN_COLOR Field
LARGE_FONT_SIZE Field
MEDIUM_FONT_SIZE Field
SMALL_FONT_SIZE Field
Label Methods
draw Method
draw2DPart Method
drawTransparentPart Method
getBackgroundColor Method
getBorderColor Method
getComponent Method
getCoordinates Method
getCoordinates Method (Single[])
getCoordinates Method (ComponentElement, Single[])
getForegroundColor Method
getSelectedItem Method
getText Method
getZCoordinateTo2DPart Method
has2DPart Method
hasInvisibleItem Method
hasTransparentPart Method
ignoreDrawProperties Method
locateObject Method
maximumItemCount Method
receiveNotificationOnCoordinateChange Method
refresh Method
select Method
selectItem Method
selectItem Method (ComponentElement)
selectItem Method ()
setBackgroundColor Method
setBackgroundColorMode Method
setBorderColor Method
setBorderColorMode Method
setDrawProperty Method
setForegroundColor Method
setLabel2DDrawing Method
setPosition Method
setPosition Method (Single[])
setPosition Method (Single, Single)
setPosition Method (Single, Single, Single)
setRelativeXCoordinate Method
setRelativeYCoordinate Method
setText Method
shift Method
unSelect Method
unSelect Method
unSelect Method (ComponentElement)
LocalLocationControl Class
LocalLocationControl Members
LocalLocationControl Constructor
LocalLocationControl Methods
__<clinit> Method
control Method
control Method (Int32)
control Method (Int32, Int32)
getColor Method
LocalOrientationControl Class
LocalOrientationControl Members
LocalOrientationControl Constructor
LocalOrientationControl Methods
__<clinit> Method
control Method
control Method (Int32)
control Method (Int32, Int32)
getColor Method
MeasurementMonitor Class
MeasurementMonitor Members
MeasurementMonitor Methods
getCoordinates Method
getCoordinates Method (Single[])
getCoordinates Method (ComponentElement, Single[])
getDescription Method
getDescription Method
getDescription Method (ComponentElement)
measurement Method
receiveNotificationOnCoordinateChange Method
refresh Method
selectItem Method
setLabel Method
PositionMonitor Class
PositionMonitor Members
PositionMonitor Constructor
PositionMonitor Methods
control Method
control Method (Int32)
control Method (Int32, Int32)
draw Method
draw2DPart Method
getComponent Method
getControl Method
getCoordinates Method
getCoordinates Method (Single[])
getCoordinates Method (ComponentElement, Single[])
getPosition Method
has2DPart Method
isVisible Method
locateObject Method
maximumItemCount Method
refresh Method
selectItem Method
selectItem Method (ComponentElement)
selectItem Method ()
setControl Method
setPosition Method
setPosition Method (Single[])
setPosition Method (Single, Single, Single)
ResizeControl Class
ResizeControl Members
ResizeControl Constructor
ResizeControl Methods
__<clinit> Method
control Method
control Method (Int32)
control Method (Int32, Int32)
getColor Method
chemaxon.marvin.util Namespace
CleanUtil Class
CleanUtil Members
CleanUtil Constructor
CleanUtil Methods
arrangeComponents Method
arrangeComponents Method (MoleculeGraph)
arrangeComponents Method (MoleculeGraph, Boolean)
arrangeComponents Method (MoleculeGraph, Boolean, Boolean)
arrangeDataSgroupData Method
arrangeMolecules Method
arrangeReaction Method
arrangeSgBrackets Method
calcBadness Method
calcBracketEndPoints Method
calcDividingPoint Method
calcSimplePolymerBracket Method
createBracket Method
createRotationAboutBond Method
createSavedCoordsArray Method
generateBracketCoords Method
generateBracketCoords Method (Sgroup, Int32)
generateBracketCoords Method (Sgroup, Int32, Boolean)
hasWiggly Method
isNonPreferredStereoAtom Method
removeCTflagFromSmallRings Method
restoreCoords Method
saveCoords Method
setBestLigandPosition Method
setBestLigandPosition Method (MolAtom, MolAtom)
setBestLigandPosition Method (MolAtom, MolAtom, Double)
setCTCrossedBond Method
setCTWigglyBond Method
setCTWigglyBond Method (MoleculeGraph)
setCTWigglyBond Method (MoleculeGraph, Int32)
sumDistanceSquare Method
ClipboardHandler Class
ClipboardHandler Members
ClipboardHandler Constructor
ClipboardHandler Methods
clearClipboard Method
getClipboard Method
getClipboardClearerTask Method
getDataFromClipboardOLE Method
getDefaultOutputTransferFormatIds Method
getDefaultTransferFormatId Method
getImageToClipboardTask Method
getMoleculeToClipboardTask Method
getObjectFromClipboard Method
getObjectFromTransferable Method
getOLEToClipboardTask Method
getOutputTransferFormatIds Method
getStringFromClipboard Method
getStringToClipboardTask Method
getTransferableFor Method
getTransferableFor Method (Molecule, )
getTransferableFor Method (Molecule, , String)
isSupportedTransferFormat Method
putImageToClipboard Method
putMoleculeToClipboard Method
putMoleculeToClipboard Method (Molecule, )
putMoleculeToClipboard Method (Molecule, , String)
putOLEToClipboard Method
putStringToClipboard Method
removePermanentOLEEnsurerReference Method
removePermanentOLESupport Method
ColorGenerator Class
ColorGenerator Members
ColorGenerator Constructor
ColorGenerator Methods
gatherBaseColors Method
gatherBaseColorsAndBaseMoleculeColors Method
gatherBaseMoleculeColors Method
gatherBlackAndWhite Method
generateColors Method
generateColors Method (Int32)
generateColors Method (Int32, )
CopyOptConstants Interface
CopyOptConstants Members
CopyOptConstants Fields
COPY_AS_IMAGE_BITMAP Field
COPY_AS_IMAGE_EMF Field
COPY_AS_OLE Field
COPY_AS_TEXT Field
FMT_EMF Field
FMT_IMAGE Field
FMT_MOL Field
FMT_MRV Field
FMT_OLE Field
FMT_PLAINTEXT Field
FMT_RXN Field
FMT_SMILES Field
FMT_STRING Field
FMT_STRUCTURE Field
CopyOptConstants.__Fields Class
CopyOptConstants.__Fields Members
CopyOptConstants.__Fields Fields
COPY_AS_IMAGE_BITMAP Field
COPY_AS_IMAGE_EMF Field
COPY_AS_OLE Field
COPY_AS_TEXT Field
FMT_EMF Field
FMT_IMAGE Field
FMT_MOL Field
FMT_MRV Field
FMT_OLE Field
FMT_PLAINTEXT Field
FMT_RXN Field
FMT_SMILES Field
FMT_STRING Field
FMT_STRUCTURE Field
MoleculeUtil Class
MoleculeUtil Members
MoleculeUtil Constructor
MoleculeUtil Methods
arrangeCrossingBonds Method
getCrossingBonds Method
MolExportException Class
MolExportException Members
MolExportException Constructor
MolExportException Constructor (Exception)
MolExportException Constructor (String)
MolExportException Constructor (String, Exception)
MolExportModule Class
MolExportModule Members
MolExportModule Constructor
MolFragLoader Class
MolFragLoader Members
MolFragLoader Constructor
MolFragLoader Constructor
MolFragLoader Constructor (MolImporter)
MolFragLoader Constructor (MoleculeIterator)
MolFragLoader Fields
FILTER_ONE_ATTACHMENT Field
FILTER_TWO_ATTACHMENTS Field
MolFragLoader Methods
__<clinit> Method
arrangeRgroupMembers Method
loadFrags Method
loadFrags Method
loadFrags Method (Boolean)
loadFrags Method (MoleculeGraph, Boolean)
loadFrags Method (MoleculeGraph, Int32, Boolean)
loadRgroupMembers Method
setFilter Method
setImporter Method
setIterator Method
setRange Method
MolFragLoader.RgroupAttachmentCountFilter Class
MolFragLoader.RgroupAttachmentCountFilter Members
MolFragLoader.RgroupAttachmentCountFilter Constructor
MolFragLoader.RgroupAttachmentCountFilter Methods
accept Method
MolImageSize Class
MolImageSize Members
MolImageSize Constructor
MolImageSize Constructor
MolImageSize Constructor (MolImageSize)
MolImageSize Constructor (Int32, Int32, Double)
MolImageSize Fields
height Field
scale Field
width Field
MolImageSize Methods
clone Method
Implicit Method
Implicit Operator
Implicit Operator
toString Method
OptionDescriptor Class
OptionDescriptor Members
OptionDescriptor Constructor
OptionDescriptor Fields
BOOL Field
NONNEGATIVE_REAL Field
OptionDescriptor Methods
getDescription Method
getInverseName Method
getName Method
getOptionsToDeselect Method
getOptionsToDisable Method
getOptionsToEnable Method
getType Method
isDefaultSelected Method
parseType Method
toString Method
SwingUtil Class
SwingUtil Members
SwingUtil Constructor
SwingUtil Methods
addHyperlinkListener Method
createMenu Method
createMenu Method (, String)
createMenu Method (, String, Boolean)
createMenuItem Method
createMenuItem Method (, String)
createMenuItem Method (, String, Boolean)
createMenuItem Method (, String, , Boolean)
createMessagePane Method
createSubPanel Method
createTopLeftConstraints Method
decorateSubPanel Method
getCommandKeyStroke Method
Implicit Operator
initAction Method
initButton Method
initButton Method (, , String)
initButton Method (, , String, Boolean)
initCtrlShortcutForMac Method
initInApplet Method
invokeAndWait Method
invokeLater Method
setDefaultFont Method
chemaxon.marvin.util.codeassist Namespace
CodeAssistFactory Class
CodeAssistFactory Members
CodeAssistFactory Fields
PROPERTY_KEY_FACTORY_INSTANCE Field
CodeAssistFactory Methods
__<clinit> Method
createChemicalTermsTextPane Method
createChemicalTermsTextPane Method
createChemicalTermsTextPane Method (CodeAssistFactory.CodeAssistConfiguration)
createChemicalTermsTextPane Method (Boolean)
createChemicalTermsTextPane Method (Object)
createChemicalTermsTextPane Method (String)
createChemicalTermsTextPane Method (Boolean, Boolean)
createChemicalTermsTextPane Method (Boolean, Object)
createChemicalTermsTextPane Method (String, Boolean)
createChemicalTermsTextPane Method (String, Object)
createChemicalTermsTextPane Method (String, String)
createChemicalTermsTextPane Method (Boolean, Boolean, Boolean)
createChemicalTermsTextPane Method (Boolean, Boolean, Object)
createChemicalTermsTextPane Method (String, Boolean, Boolean)
createChemicalTermsTextPane Method (String, Boolean, Object)
createChemicalTermsTextPane Method (String, String, Boolean)
createChemicalTermsTextPane Method (String, Boolean, Boolean, Boolean)
createChemicalTermsTextPane Method (String, Boolean, Boolean, Object)
createChemicalTermsTextPane Method (String, String, Boolean, Boolean)
createChemicalTermsTextPane Method (String, String, Boolean, Object)
createChemicalTermsTextPane Method (String, String, Boolean, String)
createChemicalTermsTextPane Method (String, String, Boolean, String, Boolean)
createChemicalTermsTextPane Method (String, String, Boolean, String, Object)
createChemicalTermsTextPane Method (String, String, Boolean, String, Boolean, Object)
getCusromToolBar Method
getFavoritesComboBox Method
getOperatorToolBar Method
getToolBar Method
getValidationResultLabel Method
getValidationResultLabel Method ()
getValidationResultLabel Method (, Object)
getValidationResultLabelForReactionContext Method
insertText Method
saveAsMacro Method
showInsertFunctionDialog Method
showManageFavoritesDialog Method
showManageMacrosDialog Method
CodeAssistFactory.CodeAssistConfiguration Class
CodeAssistFactory.CodeAssistConfiguration Members
CodeAssistFactory.CodeAssistConfiguration Constructor
CodeAssistFactory.CodeAssistConfiguration Methods
getContext Method
getHelpText Method
getPrefix Method
getToolbarConfigPath Method
isAddServices Method
isAutoPopup Method
isExpertMode Method
setAddServices Method
setAutoPopup Method
setContext Method
setExpertMode Method
setHelpText Method
setPrefix Method
setToolbarConfigPath Method
chemaxon.marvin.view Namespace
MDocStorage Class
MDocStorage Members
MDocStorage Constructor
MDocStorage Constructor
MDocStorage Constructor (Int32)
MDocStorage Methods
addListener Method
aromatize Method
aromatizeAll Method
clean Method
cleanAll Method
contractOrExpandSgroups Method
contractOrExpandSgroupsAll Method
countRecords Method
countRecordsInFraction Method
doSetSetSeqs Method
fillWithNulls Method
getCacheCapacity Method
getCachedDoc Method
getCachedDocIndices Method
getCacheLock Method
getCapacity Method
getDoc Method
getDoc Method (Int32, String)
getDoc Method (Int32, String, Object)
getDocLabel Method
getDocSource Method
getDocSourcePosition Method
getFieldAccessor Method
getGlobalGUIProperties Method
getIDBackgroundRGBA Method
getIDForegroundRGBA Method
getL Method
getListeners Method
getMainDoc Method
getMainDoc Method (Int32)
getMainDoc Method (Int32, Object)
getMaxDimCached Method
getMolCenter Method
getMolPainter Method
getOffset Method
getSelectedAtoms Method
getSize Method
getT Method
hydrogenize Method
hydrogenizeAll Method
isEnabledT Method
isFixed Method
isFractionQuicklyAvailable Method
isRewindable Method
isSizeFinal Method
removeListener Method
setAtomSetSeq Method
setAtomSetSeq Method (Int32, String, Int32, Int32)
setAtomSetSeq Method (Int32, String, String, Int32)
setAtomSetSeqs Method
setBondSetSeq Method
setBondSetSeq Method (Int32, String, String, Int32)
setBondSetSeq Method (Int32, String, Int32, Int32, Int32)
setBondSetSeqAll Method
setBondSetSeqs Method
setCacheCapacity Method
setDocSource Method
setEnabledT Method
setFieldAccessor Method
setFixed Method
setIDBackgroundRGBA Method
setIDForegroundRGBA Method
setL Method
setListeners Method
setMolCenter Method
setMolPainter Method
setSelectedAtoms Method
setSelectedAtoms Method (Int32, String, Int32[])
setSelectedAtoms Method (Int32, String, String)
setSize Method
setT Method
storeDoc Method
storeMainDoc Method
MDocStorage.CancellationException Class
MDocStorage.CancellationException Members
MDocStorage.CancellationException Methods
finishCancel Method
MDocStorage.Listener Interface
MDocStorage.Listener Members
MDocStorage.Listener Methods
docProduced Method
storageSizeChanged Method
storageSizeFinalized Method
MDocStorage.RecordUnavailableException Class
MDocStorage.RecordUnavailableException Members
MDocStorage.RecordUnavailableException Methods
getRecordIndex Method
getRecordIndexMax Method
getRecordIndexMin Method
isEndReached Method
TaskScheduler Interface
TaskScheduler Members
TaskScheduler Methods
invokeAndWait Method
invokeLater Method
waitForAll Method
ViewParameterConstants Class
ViewParameterConstants Members
ViewParameterConstants Fields
ANIMATE Field
ANIMATION_DELAY Field
ANIMATION_FPS Field
ANIMATION_SYNCHRONIZATION Field
ATOM_SET Field
AUTO_TAB_SCALE Field
BACKGROUND Field
BOND_SET Field
BORDER Field
CELL Field
COLS Field
CONFIRM_TRANSFER Field
DETACHABLE Field
DRAGGABLE Field
EDITABLE Field
GRAPH_INVARIANTS Field
IMPORT_ENABLED Field
LAYOUT Field
LAYOUT_HEADER Field
LISTEN_MOUSE_EVENT Field
MOLECULE_CHANGED Field
NAVIGATION_MODE Field
PARAMETERS Field
PARAMETERS_HEADER Field
ROWS Field
SCRIPT Field
SELECTABLE Field
SELECTED_INDEX Field
SELECTION Field
SPIN Field
TAB_SCALE Field
VALENCE_ERROR_VISIBLE_IN_VIEW Field
VIEW_CARBON_VISIBILITY Field
VIEW_LIGAND_ORDER_VISIBILITY Field
VISIBLE_COLS Field
VISIBLE_ROWS Field
WINDOW_SCALE Field
chemaxon.marvin.view.swing Namespace
TableOptions Class
TableOptions Members
TableOptions Fields
MMF_FIELD Field
MMF_NOT_FIELD Field
MMF_UNSET Field
VH_AUTO Field
VH_GRIDBAG Field
VH_SPREADSHEET Field
TableOptions Methods
__<clinit> Method
addActionListener Method
getColumnWidth Method
getColumnWidth Method
getColumnWidth Method (Int32)
getColumnWidthsString Method
getFieldFontSize Method
getFieldsShown Method
getGenNameFontSize Method
getMainMolFieldness Method
getMaxCols Method
getMaxRows Method
getMaxSize Method
getMolNameFontSize Method
getRowHeight Method
getSelectedFieldCount Method
getSelectedFields Method
getSelectedFieldTypes Method
getSMILESFontSize Method
getStartAt Method
getViewHandlerType Method
initFields Method
isGenNameShown Method
isMolNameShown Method
isSingleCellLabelShown Method
isSMILESShown Method
isSubsetChangable Method
removeActionListener Method
setColumnWidth Method
setColumnWidth Method (Int32)
setColumnWidth Method (Int32, Int32)
setFieldFontSize Method
setFieldsShown Method
setGenNameFontSize Method
setGenNameShown Method
setListFont Method
setMaxCols Method
setMaxRows Method
setMaxSize Method
setMolNameFontSize Method
setMolNameShown Method
setRowHeight Method
setSelectedFields Method
setSingleCellLabelShown Method
setSMILESFontSize Method
setSMILESShown Method
setStartAt Method
setSubsetChangable Method
setViewHandlerType Method
showDialog Method
updateFields Method
updateFields Method (MDocument)
updateFields Method (MDocument[])
TableSupport Class
TableSupport Members
TableSupport Fields
scheduler Field
TableSupport Methods
enqueueUpdate Method
getDefaultSize Method
getDocStorage Method
getTableOptions Method
makeTableMenu Method
setCellSize Method
setDocument Method
setSDFColoring Method
start Method
startNow Method
chemaxon.metabolizer Namespace
Metabolizer Class
Metabolizer Members
Metabolizer Constructor
Metabolizer Constructor (Boolean)
Metabolizer Constructor (Boolean, )
Metabolizer Constructor (Int32, Boolean)
Metabolizer Constructor (Int32, RxnMolecule[], MetabolizerTemporaryStorage)
Metabolizer Constructor (Int32, RxnMolecule[], Boolean)
Metabolizer Constructor (Int32, Boolean, )
Metabolizer Constructor (Int32, RxnMolecule[], MetabolizerTemporaryStorage, )
Metabolizer Constructor (Int32, RxnMolecule[], Boolean, )
Metabolizer Constructor (Int32, RxnMolecule[], Boolean, Boolean)
Metabolizer Constructor (Int32, RxnMolecule[], String, MetabolizerTemporaryStorage)
Metabolizer Constructor (Int32, RxnMolecule[], String, Boolean)
Metabolizer Constructor (Int32, RxnMolecule[], Boolean, Boolean, )
Metabolizer Constructor (Int32, RxnMolecule[], String, MetabolizerTemporaryStorage, )
Metabolizer Constructor (Int32, RxnMolecule[], String, MetabolizerTemporaryStorage, Boolean)
Metabolizer Constructor (Int32, RxnMolecule[], String, Boolean, )
Metabolizer Constructor (Int32, RxnMolecule[], String, MetabolizerTemporaryStorage, Boolean, )
Metabolizer Methods
__<clinit> Method
closeTemporaryStorage Method
getCurrentLevelLength Method
getLevelCount Method
getLevelCounter Method
getMetabolicPathwayTolerance Method
getNeededMetaboliteSmiles Method
getSubstrateCounter Method
getTermCondition Method
hasMoreLevel Method
ignoreSelectivity Method
isCurrentLevelEnded Method
isGeneratingSubstrates Method
isLicensed Method
main Method
next Method
nextLevel Method
setExcludedMetabolites Method
setGeneratingSubstrates Method
setLevelCount Method
setLicenseEnvironment Method
setMetabolicPathwayTolerance Method
setNeededMetabolites Method
setProgressMonitor Method
setReactions Method
setRunInMemory Method
setSubstrates Method
setTemporaryStorage Method
setTermCondition Method
MetabolizerConstants Class
MetabolizerConstants Members
MetabolizerConstants Fields
DEFAULT_SERVER_NAME Field
LOG_FILE_PATH Field
MAX_STABILITY Field
OUTPUT_TYPE_PRODUCT Field
OUTPUT_TYPE_REACTION Field
PERSISTENT_PROPERTY_FILENAME Field
PROPERTY_LOAD_ERROR Field
SERVER_NAME Field
SERVER_REGISTER_ERROR Field
MetabolizerException Class
MetabolizerException Members
MetabolizerException Constructor
MetabolizerException Constructor
MetabolizerException Constructor (Exception)
MetabolizerException Constructor (String)
MetabolizerException Constructor (String, Exception)
MetabolizerExporter Interface
MetabolizerExporter Members
MetabolizerExporter Methods
close Method
export Method
MetabolizerFileExporter Class
MetabolizerFileExporter Members
MetabolizerFileExporter Constructor
MetabolizerFileExporter Constructor (, String)
MetabolizerFileExporter Constructor (String, String)
MetabolizerFileExporter Methods
close Method
export Method
MetabolizerFileImporter Class
MetabolizerFileImporter Members
MetabolizerFileImporter Constructor
MetabolizerFileImporter Constructor ()
MetabolizerFileImporter Constructor (String)
MetabolizerFileImporter Methods
close Method
getMoleculeCount Method
hasNext Method
next Method
MetabolizerImporter Interface
MetabolizerImporter Members
MetabolizerImporter Methods
close Method
getMoleculeCount Method
hasNext Method
next Method
MetabolizerIOException Class
MetabolizerIOException Members
MetabolizerIOException Constructor
MetabolizerIOException Constructor
MetabolizerIOException Constructor (Exception)
MetabolizerIOException Constructor (String)
MetabolizerIOException Constructor (String, Exception)
MetabolizerMemoryExporter Class
MetabolizerMemoryExporter Members
MetabolizerMemoryExporter Constructor
MetabolizerMemoryExporter Methods
close Method
export Method
MetabolizerMemoryImporter Class
MetabolizerMemoryImporter Members
MetabolizerMemoryImporter Constructor
MetabolizerMemoryImporter Methods
close Method
getMoleculeCount Method
hasNext Method
next Method
MetabolizerProperties Class
MetabolizerProperties Members
MetabolizerProperties Fields
METABOLIZER_FILE_STORAGE_SMILES_OUTPUT_FILEFORMAT Field
METABOLIZER_OUT_TEMP_FILE_NAME Field
METABOLIZER_SMILES_OUTPUT_FILEFORMAT_WITH_DOMINANCE Field
PARENTS Field
PROPERTY_METABOLIZER_ACCUMULATION Field
PROPERTY_METABOLIZER_CHILDDEPTH Field
PROPERTY_METABOLIZER_EXACTMASS Field
PROPERTY_METABOLIZER_IGNORED Field
PROPERTY_METABOLIZER_METABOLIC_STABILITY Field
PROPERTY_METABOLIZER_PARENTSYNTHESISCODE Field
PROPERTY_METABOLIZER_PRODUCTION Field
PROPERTY_METABOLIZER_SPEED_CATEGORY Field
PROPERTY_METABOLIZER_SYNTHESISCODE Field
PROPERTY_METABOLIZER_SYNTHESISLEVEL Field
PROPERTY_METABOLIZER_TRANSMISSIVITY Field
PROPERTY_METABOLIZER_TREE_ROOT_SYNTHESIS_CODE Field
MetabolizerTemporaryFileStorage Class
MetabolizerTemporaryFileStorage Members
MetabolizerTemporaryFileStorage Constructor
MetabolizerTemporaryFileStorage Constructor
MetabolizerTemporaryFileStorage Constructor ()
MetabolizerTemporaryFileStorage Constructor (String)
MetabolizerTemporaryFileStorage Methods
close Method
getExporter Method
getImporter Method
newIteration Method
MetabolizerTemporaryMemoryStorage Class
MetabolizerTemporaryMemoryStorage Members
MetabolizerTemporaryMemoryStorage Constructor
MetabolizerTemporaryMemoryStorage Methods
close Method
getExporter Method
getImporter Method
newIteration Method
MetabolizerTemporaryStorage Interface
MetabolizerTemporaryStorage Members
MetabolizerTemporaryStorage Methods
close Method
getExporter Method
getImporter Method
newIteration Method
MetabolizerUtilities Class
MetabolizerUtilities Members
MetabolizerUtilities Constructor
MetabolizerUtilities Methods
cancel Method
copyProperties Method
generateChildDepth Method
generateChildDepth Method (, , String)
generateChildDepth Method (, , String)
generateMajorMetabolites Method
generateMajorMetabolites Method (Metabolizer, MolExporter, String, String, Single)
generateMajorMetabolites Method (Metabolizer, , String, String, Single)
generateMetabolites Method
generateMetabolites Method (Metabolizer, , String, String)
generateMetabolites Method (Metabolizer, , String, String)
generateMetabolitesWithChildDepth Method
generateMetabolitesWithChildDepth Method (Metabolizer, MolExporter, String, String)
generateMetabolitesWithChildDepth Method (Metabolizer, , String, String)
generateMetabolitesWithChildDepth Method (Metabolizer, , String, String)
isCanceled Method
setCanceled Method
chemaxon.naming Namespace
DocumentExtractor Class
DocumentExtractor Members
DocumentExtractor Constructor
DocumentExtractor Constructor
DocumentExtractor Constructor ()
DocumentExtractor Constructor ()
DocumentExtractor Constructor ()
DocumentExtractor Constructor ()
DocumentExtractor Constructor (String)
DocumentExtractor Constructor (, String)
DocumentExtractor Fields
propertyPage Field
propertySourceDocument Field
DocumentExtractor Methods
acceptElements Method
acceptGenericNames Method
acceptIons Method
clearHits Method
getHits Method
main Method
printEncodingError Method
processHTML Method
processHTML Method
processHTML Method (DocumentExtractor.ProgressListener)
processHTML Method ()
processPlainText Method
processPlainText Method
processPlainText Method (DocumentExtractor.ProgressListener)
processPlainText Method ()
readPDF Method
readPDF Method ()
readPDF Method ()
setCasNumberLookup Method
DocumentExtractor.Hit Class
DocumentExtractor.Hit Members
DocumentExtractor.Hit Fields
position Field
structure Field
text Field
DocumentExtractor.Hit Methods
getAllPositions Method
getPageNumber Method
getPositionsString Method
toString Method
DocumentExtractor.ProgressInfo Class
DocumentExtractor.ProgressInfo Members
DocumentExtractor.ProgressInfo Constructor
DocumentExtractor.ProgressInfo Methods
getCharactersRead Method
getEstimatedTotalCharacters Method
getHitsFound Method
getWordsRead Method
Implicit Operator
DocumentExtractor.ProgressListener Interface
DocumentExtractor.ProgressListener Members
DocumentExtractor.ProgressListener Methods
progress Method
DocumentToStructure Class
DocumentToStructure Members
DocumentToStructure Constructor
DocumentToStructure Fields
BYTE Field
CHARACTER Field
CONFIDENCE Field
DOCUMENT Field
PAGE Field
SOURCE_TEXT Field
TYPE Field
TYPE_CAS Field
TYPE_CDX Field
TYPE_COMMON Field
TYPE_GENERIC Field
TYPE_INCHI Field
TYPE_MRV Field
TYPE_OSR Field
TYPE_SMILES Field
TYPE_SYMYX Field
TYPE_SYSTEMATIC Field
DocumentToStructure Methods
process Method
process Method (String)
process Method (String, String)
NameConverter Interface
NameConverter Members
NameConverter Methods
convert Method
setPrefixMode Method
NameConverters Class
NameConverters Members
NameConverters Methods
__<clinit> Method
add Method
add Method (NameConverter, Int32)
add Method (NameConverter, Int32, Boolean)
remove Method
NameFormatException Class
NameFormatException Members
NameFormatException Constructor
NameFormatException Constructor (Exception)
NameFormatException Constructor (String)
NameFormatException Methods
__<clinit> Method
fillInStackTrace Method
NameFormatException.FilteredCase Class
NameFormatException.FilteredCase Members
NameFormatException.FilteredCase Constructor
NameFormatException.FilteredCase Methods
__<clinit> Method
NamePrefixException Class
NamePrefixException Members
NamePrefixException Constructor
NamePrefixException Constructor
NamePrefixException Constructor (String)
NamePrefixException Constructor (String, String)
NamePrefixException Fields
token Field
NamePrefixException Methods
__<clinit> Method
getParsed Method
chemaxon.pharmacophore Namespace
PMap Class
PMap Members
PMap Constructor
PMap Constructor (Int32, [])
PMap Constructor (Int32, Int32)
PMap Methods
clear Method
clearFeatures Method
clone Method
create Method
getAtomCount Method
getAtoms Method
getAtoms Method (Int32)
getAtoms Method (Int32, Int32[])
getFeatureCount Method
getFeatureCount Method
getFeatureCount Method (Int32)
getFeatures Method
hasFeature Method
hasFeature Method (Int32)
hasFeature Method (Int32, Int32)
setFeature Method
toString Method
PMapper Class
PMapper Members
PMapper Constructor
PMapper Constructor ()
PMapper Constructor (Object)
PMapper Constructor (String)
PMapper Constructor (, Standardizer)
PMapper Constructor (Object, Standardizer)
PMapper Constructor (Object, Object)
PMapper Constructor (Object, String)
PMapper Constructor (String, Standardizer)
PMapper Constructor (Object, Standardizer, String)
PMapper Constructor (Object, Object, String)
PMapper Fields
DEFAULT_TAG_NAME Field
PMapper Methods
__<clinit> Method
createFeatureMap Method
getID Method
getMolConstant Method
getSymbols Method
isLicensed Method
main Method
setLicenseEnvironment Method
setVerbose Method
PSymbols Class
PSymbols Members
PSymbols Constructor
PSymbols Constructor ()
PSymbols Constructor (String[])
PSymbols Methods
getIndex Method
getSymbol Method
getSymbolCount Method
chemaxon.reaction Namespace
ConcurrentReactorProcessor Class
ConcurrentReactorProcessor Members
ConcurrentReactorProcessor Constructor
ConcurrentReactorProcessor Fields
MODE_COMBINATORIAL Field
MODE_SEQUENTIAL Field
ConcurrentReactorProcessor Methods
__<clinit> Method
getProgress Method
getReactants Method
initialize Method
main Method
react Method
reactNext Method
setReactantIterators Method
setReactantIterators Method (MoleculeIterator[], Int32)
setReactantIterators Method (MoleculeIterator[], Int32, String, Double, Boolean)
setReactantSetEnumerator Method
setReactor Method
setWorkerThreadCount Method
ConcurrentStandardizerProcessor Class
ConcurrentStandardizerProcessor Members
ConcurrentStandardizerProcessor Constructor
ConcurrentStandardizerProcessor Fields
F:chemaxon.reaction.ConcurrentStandardizerProcessor.TRANSFORMER_SET_DIM_0/chemaxon.util.MolTransformer
PREPROCESS_SET_DIM_0 Field
ConcurrentStandardizerProcessor Methods
__<clinit> Method
getAppliedTaskIDs Method
getAppliedTaskIndexes Method
getInputMolecule Method
getProgress Method
main Method
setMoleculeIterator Method
setPreprocessing Method
setPreprocessor Method
setStandardizer Method
setStoreAppliedTaskData Method
setWorkerThreadCount Method
standardize Method
ReactantSetEnumeration Interface
ReactantSetEnumeration Members
ReactantSetEnumeration Methods
getProgress Method
hasNext Method
next Method
Reaction Class
Reaction Members
Reaction Constructor
Reaction Constructor
Reaction Constructor (Molecule)
Reaction Constructor (String)
Reaction Fields
ALL_SIDE Field
DATA_ALL Field
DATA_ATOMS Field
DATA_BONDS Field
DATA_DOUBLE_BOND_STEREO Field
DATA_PARITY Field
PRODUCT_SIDE Field
REACTANT_SIDE Field
Reaction Methods
__<clinit> Method
getChangingAtoms Method
getChangingBondData Method
getID Method
getReactant Method
getReactantCount Method
getReaction Method
getReactivity Method
getTolerances Method
Implicit Operator
setFID Method
setID Method
setReaction Method
setReaction Method (Molecule)
setReaction Method (Molecule, Boolean)
setReaction Method (Molecule, Boolean, Boolean)
setReaction Method (Molecule, Boolean, Boolean, Boolean)
setReactivityRule Method
setRequiredData Method
setSelectivityRule Method
setSelectivityRule Method (String, Evaluator)
setSelectivityRule Method (String, Double[], Evaluator)
setSelectivityRule Method (String, String, Evaluator)
ReactionException Class
ReactionException Members
ReactionException Constructor
ReactionException Constructor
ReactionException Constructor (Exception)
ReactionException Constructor (String)
ReactionException Constructor (String, Exception)
Reactor Class
Reactor Members
Reactor Constructor
Reactor Fields
DEF_MAX_TRANSFORM_COUNT Field
DEF_TOLERANCE Field
FUSED_REACTION_OUTPUT Field
IGNORE_REACTIVITY Field
IGNORE_SELECTIVITY Field
IGNORE_TOLERANCE Field
MAPPING_STYLE_CHANGING Field
MAPPING_STYLE_COMPLETE Field
MAPPING_STYLE_MATCHING Field
MAPPING_STYLE_NONE Field
NO_DUPLICATE_FILTERING Field
ORDER_INSENSITIVE_DUPLICATE_FILTERING Field
ORDER_SENSITIVE_DUPLICATE_FILTERING Field
PRODUCT_OUTPUT Field
REACTION_OUTPUT Field
Reactor Methods
__<clinit> Method
createReactionObject Method
createReactionObject Method (Molecule, String, String, String, Double[])
createReactionObject Method (Molecule, String, String, String, String)
getProductCount Method
getProductStandardizer Method
getReactantCount Method
getReactants Method
getReaction Method
getReactionID Method
getReactionIDPropertyName Method
getReactionProduct Method
getReactionReactant Method
getStandardizer Method
Implicit Operator
isCached Method
isLicensed Method
isReverse Method
isSingle Method
main Method
react Method
restart Method
setCached Method
setComponentIDPropertyNames Method
setComponentIDPropertyNames Method (String, String)
setComponentIDPropertyNames Method (String[], String[])
setCopyAllReactantProperties Method
setCopyReactantProperties Method
setCopyReactantProperties Method ()
setCopyReactantProperties Method (String[][])
setCopyReactantProperties Method (String[][], String[][])
setDuplicateFiltering Method
setIgnoreReactionDefinedStandardizer Method
setIgnoreRules Method
setLicenseEnvironment Method
setMaxNumberOfProductSets Method
setOutputReactionMappingStyle Method
setProductIndexes Method
setProductStandardizer Method
setRatio Method
setReactant Method
setReactants Method
setReactants Method (Molecule[])
setReactants Method (String)
setReaction Method
setReaction Method (Reaction)
setReaction Method (Molecule)
setReaction Method (Molecule, String)
setReaction Method (Molecule, String, String, String, Double[])
setReaction Method (Molecule, String, String, String, String)
setReactionIDPropertyName Method
setReactionString Method
setReactionString Method (String)
setReactionString Method (String, String)
setRemoveDuplicateProductReferences Method
setResultType Method
setReverse Method
setSearchOptions Method
setShowUnsuccessfulReactions Method
setSingle Method
setSkipReactionMappingCheck Method
setStandardizer Method
setTransform Method
Standardizer Class
Standardizer Members
Standardizer Constructor
Standardizer Constructor ()
Standardizer Constructor ()
Standardizer Constructor (Object)
Standardizer Constructor (String)
Standardizer Constructor (Object, String)
Standardizer Fields
FINAL_CLEAN_ID Field
GROUP_QUERY Field
GROUP_TARGET Field
SET_TARGET Field
Standardizer Methods
__<clinit> Method
addInactiveTasks Method
clearInactiveTasks Method
getActiveGroups Method
getAppliedTaskIDs Method
getAppliedTaskIndexes Method
getNewToOld Method
getOldToNew Method
Implicit Operator
isLastTaskClean Method
isLicensed Method
main Method
removeInactiveTasks Method
setActiveGroup Method
setActiveGroups Method
setAtomIndexQuery Method
setCleanTemplates Method
setFinalClean Method
setFinalClean Method
setFinalClean Method (Int32)
setFinalClean Method (Int32, Boolean)
setFinalClean Method (Int32, Boolean, )
setInactiveTasks Method
setLicenseEnvironment Method
standardize Method
standardize Method (Molecule)
standardize Method (Molecule[])
StandardizerException Class
StandardizerException Members
StandardizerException Constructor
StandardizerException Constructor
StandardizerException Constructor (Exception)
StandardizerException Constructor (String)
StandardizerException Constructor (String, Exception)
chemaxon.sss Namespace
SearchConstants Interface
SearchConstants Members
SearchConstants Constructor
SearchConstants Fields
ABS_STEREO_ALWAYS_ON Field
ABS_STEREO_CHIRAL_FLAG Field
ABS_STEREO_TABLE_OPTION Field
ATTACHED_DATA_MATCH_EXACT Field
ATTACHED_DATA_MATCH_GENERAL Field
ATTACHED_DATA_MATCH_IGNORE Field
CHARGE_MATCHING_DEFAULT Field
CHARGE_MATCHING_EXACT Field
CHARGE_MATCHING_IGNORE Field
DEFAULT_DISSIMILARITY_THRESHOLD Field
DEFAULT_SEARCHTYPE Field
DISSIMILARITY_PROPERTY_NAME Field
DUPLICATE Field
FULL Field
FULL_FRAGMENT Field
HCOUNT_MATCHING_AUTO Field
HCOUNT_MATCHING_EQUAL Field
HCOUNT_MATCHING_GREATER_OR_EQUAL Field
HIT_EXCLUDEDQ Field
HIT_LP Field
HIT_MULTICENTER Field
HIT_NON_R Field
HIT_ORDERING_NONE Field
HIT_ORDERING_UNDEF_R_MATCHING_GROUP_FIRST Field
HIT_R Field
HIT_R_EMPTY_MATCH Field
HIT_UNMAPABLE Field
IMPLICIT_H_MATCHING_DEFAULT Field
IMPLICIT_H_MATCHING_DISABLED Field
IMPLICIT_H_MATCHING_ENABLED Field
IMPLICIT_H_MATCHING_IGNORE Field
ISOTOPE_MATCHING_DEFAULT Field
ISOTOPE_MATCHING_EXACT Field
ISOTOPE_MATCHING_IGNORE Field
MARKUSH_AROM_FINAL_CHECK Field
MARKUSH_AROM_NO_FINAL_CHECK Field
MARKUSH_AROM_OFF Field
MARKUSH_HIT_INNER Field
MARKUSH_HIT_ORIGINAL Field
MARKUSH_MCS Field
MATCH_COUNT_BETWEEN Field
MATCH_COUNT_RELATION Field
NO_ABAS Field
NO_SCREEN Field
RADICAL_MATCHING_DEFAULT Field
RADICAL_MATCHING_EXACT Field
RADICAL_MATCHING_IGNORE Field
SEARCH_MODE_NAMES Field
SEARCH_OPTIONS_LENGTH Field
SIMILARITY Field
STEREO_DIASTEREOMER Field
STEREO_ENANTIOMER Field
STEREO_EXACT Field
STEREO_IGNORE Field
STEREO_MODEL_COMPREHENSIVE Field
STEREO_MODEL_DEFAULT Field
STEREO_MODEL_GLOBAL Field
STEREO_MODEL_LOCAL Field
STEREO_SPECIFIC Field
SUBSTRUCTURE Field
SUPERSTRUCTURE Field
TAUTOMER_SEARCH_DEFAULT Field
TAUTOMER_SEARCH_OFF Field
TAUTOMER_SEARCH_ON Field
UNDEF_R_MATCHING_ALL Field
UNDEF_R_MATCHING_GROUP Field
UNDEF_R_MATCHING_GROUP_H Field
UNDEF_R_MATCHING_GROUP_H_EMPTY Field
UNDEF_R_MATCHING_UNDEF_R Field
VAGUE_BOND_DEFAULT Field
VAGUE_BOND_LEVEL_HALF Field
VAGUE_BOND_LEVEL1 Field
VAGUE_BOND_LEVEL2 Field
VAGUE_BOND_LEVEL3 Field
VAGUE_BOND_LEVEL4 Field
VAGUE_BOND_OFF Field
SearchConstants Methods
__<clinit> Method
SearchConstants.__Fields Class
SearchConstants.__Fields Members
SearchConstants.__Fields Fields
ABS_STEREO_ALWAYS_ON Field
ABS_STEREO_CHIRAL_FLAG Field
ABS_STEREO_TABLE_OPTION Field
ATTACHED_DATA_MATCH_EXACT Field
ATTACHED_DATA_MATCH_GENERAL Field
ATTACHED_DATA_MATCH_IGNORE Field
CHARGE_MATCHING_DEFAULT Field
CHARGE_MATCHING_EXACT Field
CHARGE_MATCHING_IGNORE Field
DEFAULT_DISSIMILARITY_THRESHOLD Field
DEFAULT_SEARCHTYPE Field
DISSIMILARITY_PROPERTY_NAME Field
DUPLICATE Field
FULL Field
FULL_FRAGMENT Field
HCOUNT_MATCHING_AUTO Field
HCOUNT_MATCHING_EQUAL Field
HCOUNT_MATCHING_GREATER_OR_EQUAL Field
HIT_EXCLUDEDQ Field
HIT_LP Field
HIT_MULTICENTER Field
HIT_NON_R Field
HIT_ORDERING_NONE Field
HIT_ORDERING_UNDEF_R_MATCHING_GROUP_FIRST Field
HIT_R Field
HIT_R_EMPTY_MATCH Field
HIT_UNMAPABLE Field
IMPLICIT_H_MATCHING_DEFAULT Field
IMPLICIT_H_MATCHING_DISABLED Field
IMPLICIT_H_MATCHING_ENABLED Field
IMPLICIT_H_MATCHING_IGNORE Field
ISOTOPE_MATCHING_DEFAULT Field
ISOTOPE_MATCHING_EXACT Field
ISOTOPE_MATCHING_IGNORE Field
MARKUSH_AROM_FINAL_CHECK Field
MARKUSH_AROM_NO_FINAL_CHECK Field
MARKUSH_AROM_OFF Field
MARKUSH_HIT_INNER Field
MARKUSH_HIT_ORIGINAL Field
MARKUSH_MCS Field
MATCH_COUNT_BETWEEN Field
MATCH_COUNT_RELATION Field
NO_ABAS Field
NO_SCREEN Field
RADICAL_MATCHING_DEFAULT Field
RADICAL_MATCHING_EXACT Field
RADICAL_MATCHING_IGNORE Field
SEARCH_MODE_NAMES Field
SEARCH_OPTIONS_LENGTH Field
SIMILARITY Field
STEREO_DIASTEREOMER Field
STEREO_ENANTIOMER Field
STEREO_EXACT Field
STEREO_IGNORE Field
STEREO_MODEL_COMPREHENSIVE Field
STEREO_MODEL_DEFAULT Field
STEREO_MODEL_GLOBAL Field
STEREO_MODEL_LOCAL Field
STEREO_SPECIFIC Field
SUBSTRUCTURE Field
SUPERSTRUCTURE Field
TAUTOMER_SEARCH_DEFAULT Field
TAUTOMER_SEARCH_OFF Field
TAUTOMER_SEARCH_ON Field
UNDEF_R_MATCHING_ALL Field
UNDEF_R_MATCHING_GROUP Field
UNDEF_R_MATCHING_GROUP_H Field
UNDEF_R_MATCHING_GROUP_H_EMPTY Field
UNDEF_R_MATCHING_UNDEF_R Field
VAGUE_BOND_DEFAULT Field
VAGUE_BOND_LEVEL_HALF Field
VAGUE_BOND_LEVEL1 Field
VAGUE_BOND_LEVEL2 Field
VAGUE_BOND_LEVEL3 Field
VAGUE_BOND_LEVEL4 Field
VAGUE_BOND_OFF Field
chemaxon.sss.formula Namespace
FormulaSearch Class
FormulaSearch Members
FormulaSearch Constructor
FormulaSearch Fields
EXACT Field
EXACT_SUBFORMULA Field
NONE Field
SUBFORMULA Field
FormulaSearch Methods
__<clinit> Method
getQuery Method
getSearchType Method
getTarget Method
isMatching Method
setQuery Method
setSearchType Method
setTarget Method
chemaxon.sss.screen Namespace
HashCode Class
HashCode Members
HashCode Constructor
HashCode Fields
DEFAULT_RECURSION_LEVEL Field
HashCode Methods
getHashCode Method
getHashCode Method (Molecule)
getHashCode Method (Molecule, Int32)
getHashCode Method (Molecule, Int32[])
getHashCode Method (Molecule, Int32[], Int32)
Similarity Class
Similarity Members
Similarity Constructor
Similarity Methods
__<clinit> Method
getTanimoto Method
getTanimoto Method (Byte[], Byte[])
getTanimoto Method (Byte[], Byte[], Int32)
getTanimoto Method (Int32[], Int32[], Int32)
Tanimoto Method
StrucFPConfig Class
StrucFPConfig Members
StrucFPConfig Constructor
StrucFPConfig Methods
getConfig Method
getMolecules Method
getMolStrings Method
getNumberOfIntegersNeeded Method
getNumberOfKeys Method
getSmartsMode Method
parseConfig Method
readMolecules Method
setMolStrings Method
chemaxon.sss.search Namespace
Decomposition Class
Decomposition Members
Decomposition Fields
ATTACHMENT_ATOM Field
ATTACHMENT_LABEL Field
ATTACHMENT_MAP Field
ATTACHMENT_NONE Field
ATTACHMENT_POINT Field
ATTACHMENT_RLABEL Field
Decomposition Methods
__<clinit> Method
color Method
color Method
color Method (Molecule)
color Method (String)
color Method (Molecule, String)
equals Method
getGroupHit Method
getLigandIds Method
getLigands Method
getQuery Method
getScaffold Method
getTarget Method
JChemSearchOptions Class
JChemSearchOptions Members
JChemSearchOptions Constructor
JChemSearchOptions Constructor
JChemSearchOptions Constructor (Int32)
JChemSearchOptions Methods
__<clinit> Method
clone Method
clonecopy Method
clonecopyOptions Method
getAbsoluteStereo Method
getDescriptorConfig Method
getDescriptorName Method
getDissimilarityMetric Method
getDissimilarityMetricParameters Method
getDissimilarityThreshold Method
getFilterQuery Method
getFormulaSearchQuery Method
getFormulaSearchType Method
getHaltOnError Method
getMarkushScreeningType Method
getMatchCountOptions Method
getMaxResultCount Method
getMaxTime Method
getOption Method
Implicit Method
Implicit Operator
Implicit Operator
isCacheRegistrationNeeded Method
isDissimilarityThresholdExcluded Method
isMarkushScreeningEnabled Method
isOptimizeQueries Method
isReturnsNonHits Method
setAbsoluteStereo Method
setCacheRegistrationNeeded Method
setDescriptorConfig Method
setDescriptorName Method
setDissimilarityMetric Method
setDissimilarityMetricParameters Method
setDissimilarityThreshold Method
setDissimilarityThresholdExcluded Method
setFilterQuery Method
setFormulaSearchQuery Method
setFormulaSearchType Method
setHaltOnError Method
setMarkushScreeningEnabled Method
setMarkushScreeningType Method
setMarkushScreeningTypes Method
setMatchCountOptions Method
setMaxResultCount Method
setMaxTime Method
setOptimizeQueries Method
setOption Method
setReturnsNonHits Method
toList Method
MarkushFeature Class
MarkushFeature Members
MarkushFeature Constructor
MarkushFeature Constructor (Int32[])
MarkushFeature Constructor (Int32, Int32[])
MarkushFeature Fields
ATOMLIST Field
BONDLIST Field
LINKNODE Field
MULTIBOND Field
REPUNIT Field
RGROUP Field
MarkushFeature Methods
equals Method
getData Method
getType Method
hashCode Method
Implicit Operator
toString Method
MarkushGenerator Class
MarkushGenerator Members
MarkushGenerator Constructor
MarkushGenerator Fields
NO_UNDEF_RGROUP Field
MarkushGenerator Methods
__<clinit> Method
generate Method
getQuery Method
getSearchOptions Method
getSkippedTargetIndexes Method
getTargets Method
setQuery Method
setSearchOptions Method
setStandardizer Method
setTargets Method
MarkushTagger Class
MarkushTagger Members
MarkushTagger Constructor
MarkushTagger Fields
COLORING_GRADUAL Field
COLORING_NONE Field
COLORING_SOLID Field
MarkushTagger Methods
__<clinit> Method
getFeatureCoverageTable Method
getFeatureTable Method
getLoggingLevel Method
getMarkush Method
getSearchOptions Method
restore Method
setAllHits Method
setColor Method
setColoringStyle Method
setExpandHomology Method
setLoggingLevel Method
setMarkush Method
setQueries Method
setSearchOptions Method
store Method
tag Method
MatchCountOptions Class
MatchCountOptions Members
MatchCountOptions Constructor
MatchCountOptions Constructor (String, Int32)
MatchCountOptions Constructor (Int32, Boolean, Int32, Boolean)
MatchCountOptions Methods
__<clinit> Method
getMatchCountHighLimit Method
getMatchCounthitLimit Method
getMatchCountLowLimit Method
getMatchCountRelation Method
getMode Method
Implicit Operator
isMatchCountHighLimitInclusive Method
isMatchCountIncludesZero Method
isMatchCountLowLimitInclusive Method
setMatchCountHighLimit Method
setMatchCountHighLimitInclusive Method
setMatchCounthitLimit Method
setMatchCountIncludesZero Method
setMatchCountLowLimit Method
setMatchCountLowLimitInclusive Method
setMatchCountRelation Method
toString Method
MCES Class
MCES Members
MCES Constructor
MCES Fields
DEFAULT_MIN_COMPONENT_SIZE Field
MCES Methods
__<clinit> Method
disableAromatization Method
enableAromatization Method
enableAromatization Method
enableAromatization Method (Int32)
getAromatizationMethod Method
getAsMolecule Method
getAtomCount Method
getAtomMapMatch Method
getAtomMapping Method
getAtomReverseMapping Method
getAtomTypeMatch Method
getBondCount Method
getBondMapping Method
getBondReverseMapping Method
getBondTypeMatch Method
getChargeMatch Method
getComponentCount Method
getHybridizationMatch Method
getIsotopeMatch Method
getKeepLargestComponent Method
getMatchedQueryAtoms Method
getMatchedQueryBonds Method
getMatchedTargetAtoms Method
getMatchedTargetBonds Method
getMinComponentSize Method
getQueryMolecule Method
getSearchMode Method
getStepCountLimit Method
getTargetMolecule Method
getTerminationCause Method
getTimeLimit Method
getUnmatchedQueryAtoms Method
getUnmatchedQueryBonds Method
getUnmatchedTargetAtoms Method
getUnmatchedTargetBonds Method
isLicensed Method
main Method
search Method
setAtomMapMatch Method
setAtomTypeMatch Method
setBondTypeMatch Method
setChargeMatch Method
setHybridizationMatch Method
setIsotopeMatch Method
setKeepLargestComponent Method
setLicenseEnvironment Method
setMinComponentSize Method
setMolecules Method
setQueryMolecule Method
setSearchMode Method
setStepCountLimit Method
setTargetMolecule Method
setTimeLimit Method
MCES.SearchMode Class
MCES.SearchMode Members
MCES.SearchMode Fields
EXHAUSTIVE Field
FAST Field
STANDARD Field
MCES.SearchMode Methods
__<clinit> Method
valueOf Method
values Method
MCES.SearchMode.__Enum Enumeration
MCES.TerminationCause Class
MCES.TerminationCause Members
MCES.TerminationCause Fields
FINISHED Field
OPTIMAL Field
STEP_LIMIT Field
TIME_LIMIT Field
MCES.TerminationCause Methods
__<clinit> Method
valueOf Method
values Method
MCES.TerminationCause.__Enum Enumeration
MCS Class
MCS Members
MCS Constructor
MCS Fields
DEFAULT_MIN_COMMON_SIZE Field
MODE_EXACT Field
MODE_FAST Field
MODE_TURBO Field
MCS Methods
findFirst Method
findNext Method
getResult Method
getResultAsMolecule Method
getResultAsSmiles Method
getResultQueryAtoms Method
getResultQueryBonds Method
getResultSize Method
getResultTargetAtoms Method
getResultTargetBonds Method
isLicensed Method
search Method
setDontBreakRingBonds Method
setFastSearch Method
setIgnoreAtomType Method
setIgnoreBondType Method
setIgnoreCharge Method
setIgnoreHybridization Method
setIgnoreIsotopes Method
setIgnoreQueryProperties Method
setLicenseEnvironment Method
setMCESMode Method
setMCSMode Method
setMinimumCommonSize Method
setMode Method
setMolecules Method
setQuery Method
setSSSMode Method
setTarget Method
MolComparator Class
MolComparator Members
MolComparator Constructor
MolComparator Fields
MAYBE_USEFUL Field
NOT_USEFUL Field
USEFUL Field
MolComparator Methods
compareAtoms Method
compareBonds Method
compareHit Method
getOrigQueryAtom Method
getOrigQueryAtom1 Method
getOrigQueryAtom2 Method
getOrigQueryBond Method
getOrigQueryNeighbour Method
getOrigTargetAtom Method
getOrigTargetAtom1 Method
getOrigTargetAtom2 Method
getOrigTargetBond Method
getOrigTargetNeighbour Method
initAll Method
isUsefulForQuery Method
isUsefulForTarget Method
setQuery Method
setSearcher Method
setTarget Method
MolSearch Class
MolSearch Members
MolSearch Constructor
MolSearch Methods
__<clinit> Method
addComparator Method
addMatch Method
addMatch Method (Int32, Int32)
addMatch Method (Int32[], Int32[], Int32)
checkFilter Method
checkFilter Method (String)
checkFilter Method (String, )
clearComparators Method
clearMatch Method
findAllHits Method
findFirstHit Method
findNextHit Method
getFilter Method
getMatchingQuery Method
getMatchingTarget Method
getQuery Method
getTarget Method
isLicensed Method
isMatching Method
removeComparator Method
setFilter Method
setFilterConfig Method
setLicenseEnvironment Method
setOrigTargetMayBeMarkush Method
setQuery Method
setQuery Method (Molecule)
setQuery Method (String)
setQuery Method (Molecule, Int32[])
setSearchOptions Method
setStandardizer Method
setTarget Method
setTarget Method (Molecule)
setTarget Method (Molecule, Int32[])
stop Method
MolSearchOptions Class
MolSearchOptions Members
MolSearchOptions Constructor
MolSearchOptions Constructor
MolSearchOptions Constructor (Int32)
MolSearchOptions Methods
__<clinit> Method
clone Method
clonecopy Method
clonecopyOptions Method
getHitIndexType Method
getMarkushArom Method
getOption Method
Implicit Operator
isDistinctFirstAtomMatching Method
isHitIncludesRNodes Method
isMarkushEnabled Method
isQueryAbsoluteStereo Method
isSubgraphSearch Method
isSwitchOffAllProtectsForTDF Method
isTargetAbsoluteStereo Method
setDistinctFirstAtomMatching Method
setHitIncludesRNodes Method
setHitIndexType Method
setMarkushArom Method
setMarkushEnabled Method
setOption Method
setQueryAbsoluteStereo Method
setSubgraphSearch Method
setSwitchOffAllProtectsForTDF Method
setTargetAbsoluteStereo Method
toList Method
RgDecompResults Class
RgDecompResults Members
RgDecompResults Constructor
RgDecompResults Constructor (Molecule, Molecule[], SearchOptions, Int32)
RgDecompResults Constructor (Molecule, Molecule[], SearchOptions, Int32, Int32[])
RgDecompResults Constructor (Molecule, Int32, Molecule[][], RgMolecule, Int32[])
RgDecompResults Constructor (Molecule, Int32, Molecule[][], RgMolecule, Int32[], Int32[])
RgDecompResults Methods
getHitsAsMarkush Method
getHitsAsRgDecomp Method
getHitsAsTable Method
getIncludedIds Method
getLigandsNumber Method
getScaffold Method
getSkippedIds Method
hasResults Method
run Method
setAttachmentType Method
setOriginalIds Method
setQuery Method
setSearchOptions Method
setTargets Method
RGroupDecomposition Class
RGroupDecomposition Members
RGroupDecomposition Constructor
RGroupDecomposition Fields
ATTACHMENT_ATOM Field
ATTACHMENT_LABEL Field
ATTACHMENT_MAP Field
ATTACHMENT_NONE Field
ATTACHMENT_POINT Field
ATTACHMENT_RLABEL Field
COL_MOLECULE Field
COL_SCAFFOLD Field
HEADER_MAP Field
HEADER_NONE Field
HEADER_RGROUP Field
SEPARATOR Field
RGroupDecomposition Methods
__<clinit> Method
addHydrogens Method
addRGroups Method
addRGroups Method (Molecule)
addRGroups Method (Molecule, Int32)
findDecomposition Method
findDecomposition Method
findDecomposition Method (Boolean)
findFirstDecomposition Method
findLigandTable Method
findLigandTable Method (Int32, Int32)
findLigandTable Method (Int32, Int32, String)
findLigandTableRow Method
findLigandTableRow Method (Int32)
findLigandTableRow Method (Int32, String)
findNextDecomposition Method
getLigandTableHeader Method
getLigandTableHeader Method (Int32, Int32)
getLigandTableHeader Method (Int32, Int32, String)
getQuery Method
getRGroupedQuery Method
isLicensed Method
isMarkushQuery Method
setAlign Method
setAttachmentType Method
setLicenseEnvironment Method
setQuery Method
setQuery Method (Molecule)
setQuery Method (Molecule, Int32)
setSameRGroupSameStructure Method
setTarget Method
Search Class
Search Members
Search Constructor
Search Methods
addMatch Method
addMatch Method (Int32, Int32)
addMatch Method (Int32[], Int32[], Int32)
areMatchingBondTypes Method
clearMatch Method
findAll Method
findAllGroups Method
findFirst Method
findFirstGroup Method
findNext Method
findNextGroup Method
getMatchCount Method
getMatchingQuery Method
getQuery Method
getSearchOptions Method
getTarget Method
isMatchCountBetween Method
isMatchCountInRelation Method
isMatching Method
isVerbose Method
setQuery Method
setQuery Method (Molecule)
setQuery Method (Molecule, Int32[])
setSearchOptions Method
setTarget Method
setTarget Method (Molecule)
setTarget Method (Molecule, Int32[])
setVerbose Method
stop Method
SearchHit Class
SearchHit Members
SearchHit Constructor
SearchHit Constructor (Int32[])
SearchHit Constructor (Int32[][])
SearchHit Constructor (Int32[], Int32[][])
SearchHit Methods
__<clinit> Method
getGroupHit Method
getSingleHit Method
setGroupHit Method
setSingleHit Method
toString Method
SearchOptions Class
SearchOptions Members
SearchOptions Constructor
SearchOptions Constructor
SearchOptions Constructor (Int32)
SearchOptions Fields
verbose Field
SearchOptions Methods
__<clinit> Method
addUserComparator Method
areMonomersTransformed Method
clearChangesInUserComparators Method
clone Method
clonecopy Method
clonecopyOptions Method
deleteAllUserComparators Method
deleteUserComparator Method
getAllOptionsAsString Method
getAllOptionsAsString Method
getAllOptionsAsString Method (String)
getAttachedDataMatch Method
getAttachedDataPrefixes Method
getChargeMatching Method
getCheckSpHyb Method
getChemTermsFilter Method
getChemTermsFilterConfig Method
getCompleteHG Method
getDoubleBondStereoMatchingMode Method
getExactSpecialAtomMatching Method
getExhaustiveModeLimit Method
getHCountMatching Method
getHitOrdering Method
getHomologyBroadTranslation Method
getHomologyNarrowTranslation Method
getImplicitHMatching Method
getIsotopeMatching Method
getOption Method
getRadicalMatching Method
getRLigandEqualityCheck Method
getSearchType Method
getSearchType Method
getSearchType Method (String)
getSSRType Method
getStereoModel Method
getStereoSearchType Method
getTautomerSearch Method
getTimeoutLimit Method
getTimeoutLimitMilliseconds Method
getUndefinedRAtom Method
getUserComparators Method
getVagueBondLevel Method
hasChangesInUserComparators Method
hasUserComparators Method
Implicit Method
Implicit Operator
Implicit Operator
isBridgingRAllowed Method
isCopolymerMatching Method
isDirty Method
isEndgroupMatching Method
isExactBondMatching Method
isExactFragment Method
isExactQueryAtomMatching Method
isFullFragment Method
isIgnoreAlleneStereo Method
isIgnoreAxialStereo Method
isIgnoreCTExceptions Method
isIgnoreDoubleBondStereo Method
isIgnoreSynAntiStereo Method
isIgnoreTetrahedralStereo Method
isKeepQueryOrder Method
isMixSgroupMatching Method
isOrderSensitiveSearch Method
isPerfectSearchType Method
isPhaseShiftedMatching Method
isPolymerMatching Method
isQHomologyHandling Method
isReactionUnpairedMapMatching Method
isSubgraphSearch Method
isSuperstructureSearch Method
isTautomerDuplicateFiltering Method
isThrowExceptionOnTimeout Method
isUndefinedRAtomMatchingGroup Method
isValenceMatching Method
isVerbose Method
setAttachedDataMatch Method
setAttachedDataPrefixes Method
setBridgingRAllowed Method
setChargeMatching Method
setCheckSpHyb Method
setChemTermsFilter Method
setChemTermsFilterConfig Method
setCompleteHG Method
setCopolymerMatching Method
setDirty Method
setDoubleBondStereoMatchingMode Method
setEndgroupMatching Method
setExactBondMatching Method
setExactFragment Method
setExactQueryAtomMatching Method
setExactSpecialAtomMatching Method
setExhaustiveModeLimit Method
setFullFragment Method
setHCountMatching Method
setHitOrdering Method
setHomologyBroadTranslation Method
setHomologyNarrowTranslation Method
setIgnoreAlleneStereo Method
setIgnoreAxialStereo Method
setIgnoreCTExceptions Method
setIgnoreDoubleBondStereo Method
setIgnoreSynAntiStereo Method
setIgnoreTetrahedralStereo Method
setImplicitHMatching Method
setIsotopeMatching Method
setKeepQueryOrder Method
setMixSgroupMatching Method
setMonomerTransform Method
setOption Method
setOptions Method
setOrderSensitiveSearch Method
setPhaseShiftedMatching Method
setPolymerMatching Method
setQHomologyHandling Method
setRadicalMatching Method
setReactionUnpairedMapMatching Method
setRLigandEqualityCheck Method
setSearchType Method
setSSRType Method
setStereoModel Method
setStereoSearchType Method
setSubgraphSearch Method
setSuperstructureSearch Method
setTautomerDuplicateFiltering Method
setTautomerSearch Method
setThrowExceptionOnTimeout Method
setTimeoutLimit Method
setTimeoutLimitMilliseconds Method
setUndefinedRAtom Method
setVagueBondLevel Method
setValenceMatching Method
setVerbose Method
toList Method
toString Method
toString Method
toString Method (String)
StandardizedMolSearch Class
StandardizedMolSearch Members
StandardizedMolSearch Constructor
StandardizedMolSearch Methods
__<clinit> Method
setStandardizer Method
chemaxon.sss.search.options Namespace
HomologyTranslationOption Class
HomologyTranslationOption Members
HomologyTranslationOption Fields
ALL Field
MARKED Field
NONE Field
HomologyTranslationOption Methods
__<clinit> Method
fromString Method
toString Method
valueOf Method
values Method
HomologyTranslationOption.__Enum Enumeration
SetOfSmallestRingsOption Class
SetOfSmallestRingsOption Members
SetOfSmallestRingsOption Fields
CSSR Field
SSSR Field
SetOfSmallestRingsOption Methods
__<clinit> Method
fromString Method
toString Method
valueOf Method
values Method
SetOfSmallestRingsOption.__Enum Enumeration
chemaxon.struc Namespace
CEdge Interface
CGraph Interface
CNode Interface
CTransform3D Class
CTransform3D Members
CTransform3D Constructor
CTransform3D Constructor
CTransform3D Constructor (CTransform3D)
CTransform3D Fields
m00 Field
m01 Field
m02 Field
m03 Field
m10 Field
m11 Field
m12 Field
m13 Field
m20 Field
m21 Field
m22 Field
m23 Field
m30 Field
m31 Field
m32 Field
m33 Field
CTransform3D Methods
determinant Method
determinant2D Method
getEuler Method
getScale Method
Implicit Operator
invert Method
is3d Method
mul Method
read16doubles Method
read16floats Method
readExternal Method
set Method
setEuler Method
setIdentity Method
setRotation Method
setRotationCenter Method
setScale Method
setTranslation Method
setTranslation Method (DPoint3)
setTranslation Method (Double, Double, Double)
setZero Method
toString Method
transform Method
write16doubles Method
write16floats Method
writeExternal Method
DPoint3 Class
DPoint3 Members
DPoint3 Constructor
DPoint3 Constructor
DPoint3 Constructor (DPoint3)
DPoint3 Constructor (Double, Double, Double)
DPoint3 Fields
x Field
y Field
z Field
DPoint3 Methods
add Method
add Method (DPoint3)
add Method (DPoint3, DPoint3)
angle2D Method
angle3D Method
clone Method
cross Method
distance Method
distance2D Method
equals Method
Implicit Method
Implicit Operator
Implicit Operator
readExternal Method
set Method
subtract Method
toString Method
writeExternal Method
HybridizationStateConsts Interface
HybridizationStateConsts Members
HybridizationStateConsts Fields
HS_S Field
HS_SP Field
HS_SP2 Field
HS_SP3 Field
HS_UNKNOWN Field
HybridizationStateConsts.__Fields Class
HybridizationStateConsts.__Fields Members
HybridizationStateConsts.__Fields Fields
HS_S Field
HS_SP Field
HS_SP2 Field
HS_SP3 Field
HS_UNKNOWN Field
Incomplecule Interface
Incomplecule Members
Incomplecule Methods
getAtomCount Method
getBondCount Method
getName Method
properties Method
MDocument Class
MDocument Members
MDocument Constructor
MDocument Constructor (MDocument)
MDocument Constructor (Molecule[])
MDocument Constructor (MoleculeGraph)
MDocument Fields
SETCOLOR_COLORLESS Field
SETCOLOR_DEFAULT Field
SETCOLOR_SPECIFIED Field
MDocument Methods
addCheckerMark Method
addObject Method
calcCenter Method
calcCenter Method
calcCenter Method (CTransform3D)
clear Method
clearCheckerMarks Method
clearSets Method
clone Method
cloneDocument Method
cloneMainMolecule Method
cloneMainMoleculeGraph Method
cloneSets Method
contains Method
contains Method (MDocument)
contains Method (MObject)
containsOnlyOne Method
exportToBinFormat Method
exportToFormat Method
exportToObject Method
getAllMolecules Method
getAllNonEmptyMolecules Method
getAllObjects Method
getAtomSetColor Method
getAtomSetColorMode Method
getAtomSetFont Method
getAtomSetRGB Method
getAtomSetSize Method
getBondSetColor Method
getBondSetColorMode Method
getBondSetRGB Method
getBondSetSize Method
getBondSetThickness Method
getCheckerMarks Method
getConnectedObject Method
getConnectedObjectCount Method
getDraggedObject Method
getEndPosition Method
getExtraLabelSetColorMode Method
getExtraLabelSetFont Method
getExtraLabelSetRGBs Method
getExtraLabelSetSize Method
getFocus Method
getGUIPropertyContainer Method
getInputFormat Method
getMainMoleculeGraph Method
getMoleculeMovie Method
getMProp Method
getObject Method
getObjectContainingSelection Method
getObjectCount Method
getPageSettings Method
getPrimaryMolecule Method
getPrimaryMolecules Method
getStartPosition Method
highlight Method
Implicit Operator
indexOf Method
isAtomSetColorModeSet Method
isEmpty Method
isExtraObject Method
isHighlighted Method
isSimpleMolecule Method
moveMainMoleculeGraphToFront Method
moveMoleculeMovieToFront Method
moveObject Method
parseMRV Method
properties Method
removeAtom Method
removeAtom Method (MolAtom)
removeAtom Method (MolAtom, Int32)
removeAtomFromGraphs Method
removeObject Method
removeObject Method (MObject)
removeObject Method (Int32)
selectAllConnectedObjects Method
selectAllObjects Method
setAtomSetColorMode Method
setAtomSetFont Method
setAtomSetRGB Method
setBondSetColorMode Method
setBondSetRGB Method
setBondSetThickness Method
setDraggedObject Method
setEndPosition Method
setExtraLabelColorsForDocument Method
setExtraLabelSetColorMode Method
setExtraLabelSetRGBs Method
setExtraLabelSetRGBs Method (Int32, Int32)
setExtraLabelSetRGBs Method (Int32, Int32, Int32)
setFocus Method
setGUIPropertyContainer Method
setGUIProperyContainer Method
setInputFormat Method
setMainMoleculeGraph Method
setMoleculeMovie Method
setObject Method
setObjectContainingSelection Method
setPageSettings Method
setStartPosition Method
simplifyMolecule Method
toString Method
transform Method
transform Method (CTransform3D)
transform Method (CTransform3D, Int32)
transform Method (CTransform3D, Int32, CTransform3D)
unhighlight Method
unhighlightAll Method
MDocument.CheckerMark Class
MDocument.CheckerMark Members
MDocument.CheckerMark Constructor
MDocument.CheckerMark Methods
getAtoms Method
getBonds Method
getColor Method
MDocument.Prop Class
MDocument.Prop Members
MDocument.Prop Constructor
MDocument.Prop Methods
cloneProp Method
convertToString Method
getPropArraySize Method
getPropType Method
getPropValue Method
getPropXSDType Method
MObject Class
MObject Members
MObject Fields
PAINT_ANTIALIAS Field
PAINT_FOCUSED Field
TRANSFORM_DISTORT Field
MObject Methods
addAttributeKeys Method
addCdataAttributeKeys Method
addNotify Method
calcCenter Method
checkValidity Method
clone Method
containsAtom Method
containsPoint Method
distanceFrom Method
distanceFrom Method (Double, Double)
distanceFrom Method (Double, Double, CTransform3D)
finishCloning Method
fixClonedPoints Method
getAttribute Method
getBackground Method
getColor Method
getLineColor Method
getPoint Method
getPointCount Method
getPointRef Method
getPointRefCount Method
hasBackground Method
hasColor Method
hasLineColor Method
Implicit Method
Implicit Operator
Implicit Operator
isChildOf Method
isEmpty Method
isInternalSelectable Method
isReactionArrow Method
isSelectableNow Method
isSelected Method
isTransformable Method
removeAtom Method
removeChild Method
removeNotify Method
replaceAtom Method
setAttribute Method
setBackground Method
setColor Method
setLineColor Method
setSelected Method
toString Method
transform Method
unselectContents Method
updateBoundingRect Method
MolAtom Class
MolAtom Members
MolAtom Constructor
MolAtom Constructor (Int32)
MolAtom Constructor (Double, Double)
MolAtom Constructor (Int32, Double, Double, Double)
MolAtom Fields
AAMAP_MASK Field
AAMAP_MAX Field
AAMAP_OFF Field
ALIPHATIC Field
ALL_H Field
ANY Field
AROMATIC Field
AROMATIC_OR_ALIPHATIC Field
ATOM_TYPE_COUNT Field
ATOM_TYPE_MAX Field
ATTACH_BOTH Field
ATTACH1 Field
ATTACH2 Field
CHARGED_H Field
CTSPECIFIC_H Field
ELEMENT_COUNT Field
EMPTY Field
FIX_CHARGE Field
HCONNECTED_H Field
HETERO Field
HS_S Field
HS_SP Field
HS_SP2 Field
HS_SP3 Field
HS_UNKNOWN Field
ISOTOPE_H Field
LDIR_ABOVE Field
LDIR_BELOW Field
LDIR_LEFT Field
LDIR_RIGHT Field
LIST Field
LONELY_H Field
LP Field
MAPPED_H Field
MULTICENTER Field
NOTLIST Field
POLYMERENDGROUP_H Field
PSEUDO Field
RAD_COUNT_MASK Field
RAD_MASK Field
RAD_OFF Field
RAD1 Field
RAD2 Field
RAD2_SINGLET Field
RAD2_TRIPLET Field
RAD3 Field
RAD3_DOUBLET Field
RAD3_QUARTET Field
RAD4 Field
RADICAL_CHAR Field
RADICAL_H Field
RESSEQ_MAX Field
RESTYPE_MAX Field
RGROUP Field
RGROUP_ATTACHMENT Field
RGROUP_MAX Field
RXNSTEREO_INVERSION Field
RXNSTEREO_NONE Field
RXNSTEREO_RETENTION Field
SETSEQ_MAX Field
SGROUP Field
SGROUPEND_H Field
SMARTS_H_DAYLIGHT_COMP_MODE Field
SMARTS_H_MARVIN_COMP_MODE Field
STAR Field
SYM_CX Field
SYM_EXPLH Field
SYM_IMPLH Field
SYM_MOLEX Field
SYM_NEUTRAL Field
SYM_SMARTS Field
SYM_SQBRACKETS Field
UNSPECIFIED_AROMATICITY Field
VALENCE_CHECKED Field
VALENCE_ERROR Field
VALENCEERROR_H Field
WEDGED_H Field
MolAtom Methods
__<clinit> Method
addRgroupAttachmentPoint Method
bondweights Method
checkAtno Method
clear Method
clearExtraLabel Method
clearProperties Method
clearQProps Method
clone Method
containsPropertyKey Method
covalentRadiusOf Method
decQProp Method
decValenceProp Method
electronegOf Method
getAliasstr Method
getAtno Method
getAtomicNumber Method
getAtomMap Method
getAtomSymbol Method
getAttach Method
getAttachParentSgroup Method
getBicycloStereo Method
getBond Method
getBondCount Method
getBondTo Method
getCharge Method
getColumn Method
getEdge Method
getEdgeCount Method
getEdgeTo Method
getElectronProp Method
getExplicitHcount Method
getExtraLabel Method
getExtraLabelColor Method
getExtraLabelColor Method
getExtraLabelColor Method (Int32)
getExtraLabelColor Method (Int64, Int32)
getExtraLabelSetSeq Method
getFlags Method
getHybridizationState Method
getImplicitHcount Method
getLigand Method
getLigandIndex Method
getLigandOrder Method
getLigands Method
getLinkNodeOuterAtom Method
getList Method
getLocation Method
getLocation Method
getLocation Method (DPoint3)
getLonePairCount Method
getMass Method
getMassno Method
getMaxRepetitions Method
getMinRepetitions Method
getNonQueryImplicitHcount Method
getParent Method
getPreferredLabelDir Method
getProperty Method
getQProp Method
getQPropAsInt Method
getQPropMinMax Method
getQPropNames Method
getQPropNameSet Method
getQueryAromaticity Method
getQueryLabel Method
getQuerystr Method
getQueryString Method
getRadical Method
getRadicalCount Method
getReactionStereo Method
getRealBondCount Method
getRelativeNegativity Method
getResidueAtomId Method
getResidueSeq Method
getResidueType Method
getRgroup Method
getRgroupAttachmentPointOrder Method
getRow Method
getSetSeq Method
getStereoCare Method
getStereoGroupNumber Method
getStereoGroupType Method
getSymbol Method
getTemporaryObject Method
getValence Method
getValenceProp Method
getValencePropMinMax Method
getX Method
getY Method
getZ Method
hasAromaticBond Method
hasQProps Method
hasQueryBonds Method
hasSMARTSProps Method
hasSMARTSPropsExcluding Method
hasValenceError Method
hasWedgedBond Method
haveEqualProperties Method
haveSimilarBonds Method
haveSimilarEdges Method
Implicit Operator
incQProp Method
incQueryAromaticity Method
incValenceProp Method
indexOf Method
insideLabel Method
ionChargeOf Method
isAmbiguousStereo Method
isAromaticSMILESSubset Method
isArrowEnd Method
isBoundTo Method
isGeneric Method
isImplicitizableH Method
isLinkNode Method
isMappable Method
isNobleGas Method
isotopeType Method
isPseudo Method
isQProp Method
isQuery Method
isSameParityClass Method
isSelected Method
isSpecIsotopeSymbolPreferred Method
isSpecIsotopeSymbolUsed Method
isTerminalAtom Method
maxAbsOxStateOf Method
moveCorners Method
nameOf Method
naturalWeightOf Method
negOxOf Method
numOf Method
numoxstatesOf Method
oxstateOf Method
pack Method
paritySign Method
posOxOf Method
propertyCount Method
propertyKeySet Method
propertySet Method
putProperty Method
qpropCheck Method
removeProperty Method
residueSymbolOf Method
residueTypeOf Method
set Method
setAliasstr Method
setAtno Method
setAtomMap Method
setAttach Method
setAttach Method (Int32)
setAttach Method (Int32, Sgroup)
setBicycloStereo Method
setCharge Method
setCorners Method
setElectronProp Method
setExtraLabel Method
setExtraLabelColor Method
setExtraLabelColor Method (Int64)
setExtraLabelColor Method (Int32, Int32)
setExtraLabelSetSeq Method
setFlags Method
setFlags Method (Int32)
setFlags Method (Int32, Int32)
setForSpecIsotopeSymbol Method
setHybridizationState Method
setImplicitHcount Method
setLigandOrder Method
setLinkNodeDefaultOuters Method
setLinkNodeOuterAtom Method
setList Method
setList Method (Int32[])
setList Method (Int32[], Int32)
setLocation Method
setMassno Method
setMassnoIfKnown Method
setMaxRepetitions Method
setMinRepetitions Method
setNonQueryImplicitHcount Method
setQProp Method
setQProp Method (String, Int32)
setQProp Method (String, Object)
setQueryAromaticity Method
setQuerystr Method
setQuerystr Method (String)
setQuerystr Method (String, Int32)
setQueryString Method
setRadical Method
setReactionStereo Method
setResidueAtomId Method
setResidueSeq Method
setResidueType Method
setRgroup Method
setRgroupAttachmentPointOrder Method
setSelected Method
setSetSeq Method
setSMARTS Method
setSpecIsotopeSymbolPreferred Method
setStereoGroupNumber Method
setStereoGroupType Method
setValenceError Method
setValenceProp Method
setX Method
setXY Method
setXYZ Method
setY Method
setZ Method
sringsize Method
storeTemporaryObject Method
symbolOf Method
symbolOf Method (Int32)
symbolOf Method (Int32, Int32)
toString Method
transform Method
twicesumbonds Method
valenceCheck Method
valenceCheck Method
valenceCheck Method (Int32)
MolBond Class
MolBond Members
MolBond Constructor
MolBond Constructor (MolAtom, MolAtom)
MolBond Constructor (MolAtom, MolAtom, Int32)
MolBond Fields
ANY Field
AROMATIC Field
ARROW Field
BOLD Field
CCLENGTH Field
CONJUGATED Field
COORDINATE Field
DOUBLE_OR_AROMATIC Field
DOWN Field
HASHED Field
RC_CHANGE Field
RC_MAKE_AND_CHANGE Field
RC_MAKE_OR_BREAK Field
RC_NOT_CENTER Field
RC_NOT_MODIFIED Field
RC_REACTING_CENTER Field
RC_UNMAPPED Field
REACTING_CENTER_MASK Field
SETSEQ_MAX Field
SETSEQ_OFF Field
SINGLE_OR_AROMATIC Field
SINGLE_OR_DOUBLE Field
STEREO_MASK Field
STEREO1_MASK Field
STEREO2_CARE Field
TOPOLOGY_CHAIN Field
TOPOLOGY_MASK Field
TOPOLOGY_RING Field
TYPE_MASK Field
UP Field
WAVY Field
MolBond Methods
__<clinit> Method
calcOrderFromLength Method
calcOrderFromValence Method
calcStereo2 Method
calcStereo2 Method
calcStereo2 Method (MolAtom, MolAtom)
calcStereo2 Method (MolAtom, MolAtom, MolAtom, MolAtom)
clone Method
cloneBond Method
cloneEdge Method
desiredLength Method
equals Method
getAtom1 Method
getAtom2 Method
getCTAtom1 Method
getCTAtom4 Method
getFlags Method
getLength Method
getNode1 Method
getNode2 Method
getOtherAtom Method
getOtherNode Method
getParent Method
getQuerystr Method
getSetSeq Method
getStereo1 Method
getType Method
haveEqualProperties Method
Implicit Operator
isArrow Method
isBold Method
isCollinear Method
isConjugated Method
isCoordinate Method
isCoordinative Method
isHashed Method
isPositionVariation Method
isQuery Method
setFlags Method
setFlags Method (Int32)
setFlags Method (Int32, Int32)
setSetSeq Method
setStereo2Flags Method
setType Method
stepWedge Method
stepWedge Method
stepWedge Method (MolBond[])
swap Method
toString Method
transformCT Method
Molecule Class
Molecule Members
Molecule Constructor
Molecule Constructor
Molecule Constructor (Molecule, MolAtom)
Molecule Constructor (Molecule, MolBond)
Molecule Constructor (Molecule, Int32, Int32)
Molecule Fields
DEFAULT_UNGROUP Field
RECURSIVE_UNGROUP Field
RMCLEANUP_FROMSGROUPS Field
RMCLEANUP_SGROUPATOMS Field
Molecule Methods
add Method
addExplicitHydrogens Method
addSgroup Method
aromatize Method
aromatize Method (Int32)
aromatize Method (Int32, Boolean)
bondlength Method
calcCenter Method
calcOutRect Method
calcOutRectCenter Method
canBeCT Method
canBeReactionComponent Method
checkConsistency Method
clean Method
clear Method
clearExtraLabels Method
clearForImport Method
clearObjects Method
clearProperties Method
clone Method
clonecopy Method
clonecopy Method (MoleculeGraph)
clonecopy Method (Int32[], MoleculeGraph)
clonelesscopy Method
cloneMolecule Method
cloneMoleculeWithDocument Method
contains Method
contains Method (MolAtom)
contractSgroups Method
convertToFrags Method
countExpandableContractableSgroups Method
countOrderedComponentSgroups Method
dearomatize Method
dearomatize Method
endReuse Method
expandSgroups Method
expandSgroups Method
expandSgroups Method (Int32)
exportToBinFormat Method
exportToFormat Method
exportToObject Method
findAllSgroupContaining Method
findComponentIds Method
findContainingMulticenterSgroup Method
findContractableSgroup Method
findExpandableSgroup Method
findFrag Method
findFragById Method
findFrags Method
findFrags Method
findSgroupContaining Method
findSgroupOf Method
findSmallestSgroupContaining Method
fuse Method
getAllObjects Method
getAromrings Method
getAtomCount Method
getComment Method
getDesiredLength Method
getEndPosition Method
getFragCount Method
getFragIds Method
getGrinv Method
getInputFormat Method
getName Method
getNonAromrings Method
getObjectCount Method
getProperty Method
getPropertyCount Method
getPropertyKey Method
getPropertyKeys Method
getPropertyObject Method
getRootSgroups Method
getSgroup Method
getSgroupArray Method
getSgroupCount Method
getSgroupLigands Method
getSimplifiedMolecule Method
getSortedSgroups Method
getStartPosition Method
getStereo2 Method
getVisibleCoords Method
implicitizeHydrogens Method
indexOf Method
indexOf Method (Sgroup)
isEmpty Method
isExpandable Method
isGUIContracted Method
isMolecule Method
isReaction Method
isSgroup Method
mergeAtoms Method
mergeFrags Method
mergeFrags Method
newInstance Method
newSelectionMolecule Method
partialClean Method
removeAll Method
removeAllBonds Method
removeAtom Method
removeAtom Method (MolAtom, Int32)
removeAtom Method (Int32, Int32)
removeBond Method
removeEdge Method
removeNode Method
removeObject Method
replaceSgroup Method
residueSymbolOf Method
residueTypeOf Method
reuseAtom Method
selectAllObjects Method
setComment Method
setDim Method
setEndPosition Method
setGUIContracted Method
setGUIContracted Method (Boolean)
setGUIContracted Method (Boolean, Int32)
setInputFormat Method
setLocalParity Method
setName Method
setParity Method
setProperty Method
setPropertyObject Method
setSgroupParent Method
setStartPosition Method
sortSgroupXBonds Method
toBinFormat Method
toFormat Method
toObject Method
transform Method
transform Method (CTransform3D, Boolean)
ungroupSgroup Method
ungroupSgroup Method (Sgroup)
ungroupSgroup Method (Int32)
ungroupSgroup Method (Sgroup, Int32)
ungroupSgroup Method (Int32, Int32)
ungroupSgroups Method
ungroupSgroups Method
ungroupSgroups Method (Int32)
valenceCheck Method
MoleculeGraph Class
MoleculeGraph Members
MoleculeGraph Constructor
MoleculeGraph Constructor
MoleculeGraph Constructor (MoleculeGraph, Int32, Int32)
MoleculeGraph Fields
AROM_AMBIGUOUS Field
AROM_BASIC Field
AROM_CHEMAXON Field
AROM_DAYLIGHT Field
AROM_GENERAL Field
AROM_LOOSE Field
AROM_SUBSTRUCTURE Field
CACHE_REMOVE_ALL Field
CACHE_REMOVE_AROMATAMODULE Field
CACHE_REMOVE_CACHEMEMORY Field
CACHE_REMOVE_GRINVMODULE Field
CACHE_REMOVE_PARITYMODULE Field
CACHE_REMOVE_SSSRMODULE Field
CACHE_REMOVE_TABS Field
DEAROM_GENERAL Field
DEAROM_HUCKELCHECK Field
DEAROM_HUCKELCHECK_EX Field
FRAG_BASIC Field
FRAG_KEEPING_MULTICENTERS Field
FRAG_KEEPING_SGROUPS Field
FRAG_TYPE_COUNT Field
GRINV_DONT_STORE Field
GRINV_NOHYDROGEN Field
GRINV_OLDSTEREO Field
GRINV_STEREO Field
GRINV_USEMAPS Field
GRINV_VALUE_OPTIONS Field
INVALID_LINKNODE_MESSAGE Field
MIN_RING_SIZE_FOR_TRANS_DB Field
OMIT_POSTCLEAN Field
RMCLEANUP_ALL Field
RMCLEANUP_EDGES Field
RMCLEANUP_MOBJECT Field
RMCLEANUP_NONE Field
RMCLEANUP_PARENTDOC Field
RMCLEANUP_STEREO Field
MoleculeGraph Methods
add Method
add Method (MolAtom)
add Method (MolBond)
addExplicitHydrogens Method
addExplicitHydrogens Method (Int32)
addExplicitHydrogens Method (Int32, MolAtom[])
addExplicitLonePairs Method
adjustMultiChiralFlag Method
aromatize Method
aromatize Method
aromatize Method (Boolean)
aromatize Method (Int32)
aromatize Method (Int32, Boolean)
arrangeComponents Method
bondlength Method
calcCenter Method
calcCenter Method
calcCenter Method (DPoint3)
calcDehydrogenizedGrinv Method
calcHeight Method
calcHybridization Method
calcOutRect Method
calcOutRect Method
calcOutRect Method (DPoint3)
calcOutRectCenter Method
calcOutRectCenter Method
calcOutRectCenter Method (DPoint3)
calcWidth Method
canBeCT Method
canBeCT Method (MolBond)
canBeCT Method (Int32, Int32)
canBeCT Method (Int32, Int32, Boolean)
checkConsistency Method
clean Method
clean Method (Int32, String)
clean Method (Int32, String, Object)
clear Method
clearCachedInfo Method
clearForImport Method
clone Method
clonecopy Method
clonecopy Method (MoleculeGraph)
clonecopy Method (Int32[], MoleculeGraph)
clonelesscopy Method
contains Method
contains Method (MolAtom)
contains Method (MolBond)
contains Method (MoleculeGraph)
createBHtab Method
createCHtab Method
dearomatize Method
dearomatize Method
dearomatize Method (Int32)
findAtomClone Method
findBasicFrags Method
findComponentIds Method
findComponentIds Method
findComponentIds Method (Int32[])
findFrag Method
findFrag Method (Int32, MoleculeGraph)
findFrag Method (Int32, Int32, MoleculeGraph)
findFragById Method
findFragById Method (Int32, MoleculeGraph)
findFragById Method (Int32, Int32, MoleculeGraph)
findFrags Method
findFrags Method ()
findFrags Method (, Int32)
fuse Method
fuse Method (MoleculeGraph)
fuse Method (MoleculeGraph, Boolean)
getAromaticAndAliphaticRings Method
getAromrings Method
getAromrings Method
getAromrings Method (Int32)
getAtom Method
getAtomArray Method
getAtomCount Method
getAtomCount Method
getAtomCount Method (Int32)
getBond Method
getBondArray Method
getBondCount Method
getBondTable Method
getBtab Method
getChirality Method
getCSSR Method
getCtab Method
getDesiredLength Method
getDesiredLength Method (MolBond)
getDesiredLength Method (Int32, Int32, Int32)
getDim Method
getDocument Method
getEdge Method
getEdgeArray Method
getEdgeCount Method
getEdgeVector Method
getEnclosingCube Method
getExactMass Method
getExplicitHcount Method
getExplicitLonePairCount Method
getFlags Method
getForefather Method
getFormalCharge Method
getFormula Method
getFragCount Method
getFragCount Method
getFragCount Method (Int32)
getFragIds Method
getFragIds Method
getFragIds Method (Int32)
getGraphUnion Method
getGrinv Method
getGrinv Method (Int32[])
getGrinv Method (Int32[], Boolean)
getGrinv Method (Int32[], Int32)
getGrinvCC Method
getGrinvOptions Method
getImplicitHcount Method
getLocalParity Method
getLocation Method
getLock Method
getLonePairCount Method
getMass Method
getMaxRgroupAttachmentPointOrder Method
getName Method
getNode Method
getNodeCount Method
getNodeVector Method
getNonAromrings Method
getNonAromrings Method
getNonAromrings Method (Int32)
getParent Method
getParity Method
getParityType Method
getPoints Method
getSmallestRingSizeForIdx Method
getSSSR Method
getSSSRBonds Method
getSSSRBondSet Method
getSSSRBondSetInLong Method
getSSSRIdxesForAtoms Method
getStereo2 Method
getStereo2 Method (MolBond)
getStereo2 Method (MolBond, MolAtom, MolAtom)
getStereo2 Method (MolAtom, Int32, Int32, MolAtom)
getStereo2 Method (MolBond, MolAtom, MolAtom, Boolean)
getStereo2 Method (Int32, Int32, Int32, Int32)
getSubGraphs Method
getTotalCharge Method
getValenceCheckState Method
getVisibleCoords Method
hasAtomSet Method
hasBondSet Method
hasExplicitLonePairs Method
hasExtraLabelSet Method
hasImplicitH Method
hasSelfReferringProperty Method
hasValenceError Method
hydrogenize Method
Implicit Operator
implicitizeHydrogens Method
implicitizeHydrogens Method (Int32)
implicitizeHydrogens Method (Int32, MolAtom[])
implicitizeHydrogens Method (Int32, MolAtom[], Boolean)
incGrinvCCOnly Method
indexOf Method
indexOf Method (MolAtom)
indexOf Method (MolBond)
insertAtom Method
insertBond Method
insertBondInOrder Method
insertEdge Method
insertEdgeInOrder Method
insertNode Method
isAbsStereo Method
isAtom Method
isBond Method
isEmpty Method
isLargeMolecule Method
isMolecule Method
isMultiChiral Method
isOnlyFirstAtomInStereoCalculation Method
isQuery Method
isRing Method
isRingBond Method
isSelfReference Method
isSimilarTo Method
isSymmetric Method
isValenceCheckEnabled Method
isValidLinkNode Method
mergeAtoms Method
mergeFrags Method
mergeFrags Method
mergeFrags Method (Int32, Int32)
mergeFrags Method (Int32, Int32, Int32)
mergeNodes Method
moveTo Method
newInstance Method
pack Method
partialClean Method
partialClean Method (Molecule[], String)
partialClean Method (MoleculeGraph, Int32[], String)
partialClean Method (Int32, Int32[], String)
properties Method
qpropCheck Method
regenBonds Method
regenEdges Method
removeAll Method
removeAllBonds Method
removeAllEdges Method
removeAtom Method
removeAtom Method (MolAtom)
removeAtom Method (Int32)
removeAtom Method (MolAtom, Int32)
removeAtom Method (Int32, Int32)
removeBond Method
removeBond Method (MolBond)
removeBond Method (Int32)
removeEdge Method
removeEdge Method (MolBond)
removeEdge Method (Int32)
removeExplicitLonePairs Method
removeNode Method
removeNode Method (MolAtom)
removeNode Method (Int32)
removeNode Method (MolAtom, Int32)
removeNode Method (Int32, Int32)
replaceBond Method
replaceEdge Method
revalidateCoordDependentProps Method
setAbsStereo Method
setAtom Method
setAtomSetSeqs Method
setBond Method
setBondSetSeqs Method
setChirality Method
setDim Method
setEdge Method
setGrinvOptions Method
setLinkNodeDefaultOuters Method
setLocalParity Method
setLocalParity Method (Int32[], Boolean)
setLocalParity Method (Int32[], Int32[], Boolean)
setLocation Method
setNode Method
setParity Method
setParity Method (Int32[])
setParity Method (Int32, Int32)
setParity Method (Int32[], Boolean)
setSetSeqs Method
setValenceCheckEnabled Method
setValenceCheckState Method
smol Method
sortBondsAccordingTo Method
sortEdgesAccordingTo Method
stereoClean Method
toString Method
transform Method
transform Method (CTransform3D)
transform Method (CTransform3D, Boolean)
useOnlyFirstAtomInStereoCalculation Method
valenceCheck Method
valenceCheck Method
valenceCheck Method ()
MoleculeGraph.ValenceCheckState Class
MoleculeGraph.ValenceCheckState Members
MoleculeGraph.ValenceCheckState Fields
AMBIGUOUS_AROMATIC_ATOMS_IGNORED Field
FULL Field
OFF Field
MoleculeGraph.ValenceCheckState Methods
__<clinit> Method
valueOf Method
values Method
MoleculeGraph.ValenceCheckState.__Enum Enumeration
MPoint Class
MPoint Members
MPoint Constructor
MPoint Constructor (DPoint3)
MPoint Constructor (MPoint)
MPoint Constructor (Double, Double)
MPoint Constructor (Double, Double, Double)
MPoint Methods
calcCenter Method
clone Method
distanceFrom Method
equals Method
equals Method (MPoint)
equals Method (Object)
getLocation Method
getLocation Method
getLocation Method (CTransform3D)
getLocation Method (DPoint3, CTransform3D)
getPoint Method
getPointCount Method
getPointRef Method
getPointRefCount Method
isChildOf Method
isInternalSelectable Method
setLocation Method
transform Method
MProp Class
MProp Members
MProp Constructor
MProp Fields
CONV_SELFREF Field
COORDDEP Field
MProp Methods
cloneProp Method
convertToString Method
convertToString Method (String)
convertToString Method (String, Int32)
getPropArraySize Method
getPropType Method
getPropValue Method
getPropXSDType Method
Implicit Method
Implicit Operator
Implicit Operator
isCoordDependent Method
toString Method
MPropertyContainer Class
MPropertyContainer Members
MPropertyContainer Constructor
MPropertyContainer Methods
clear Method
clone Method
contains Method
flatten Method
get Method
getKey Method
getKeys Method
getObject Method
getPropList Method
getString Method
hierarchize Method
Implicit Method
Implicit Operator
Implicit Operator
isHierarchic Method
isSelfReference Method
isValid Method
readExternal Method
remove Method
replace Method
set Method
set Method (String, MProp)
set Method (String, MProp, Int32)
setObject Method
setString Method
size Method
writeExternal Method
MSelectionDocument Class
MSelectionDocument Members
MSelectionDocument Constructor
MSelectionDocument Constructor (MSelectionDocument)
MSelectionDocument Constructor (SelectionMolecule)
MSelectionDocument Methods
addObject Method
clear Method
cloneDocument Method
findSelectedSgroup Method
removeObject Method
removeObject Method (MObject)
removeObject Method (Int32)
setObject Method
MTransformable Interface
MTransformable Members
MTransformable Methods
transform Method
PeriodicSystem Class
PeriodicSystem Members
PeriodicSystem Constructor
PeriodicSystem Fields
Ac Field
Ag Field
Al Field
Am Field
Ar Field
As Field
At Field
Au Field
B Field
Ba Field
Be Field
Bh Field
Bi Field
Bk Field
Br Field
C Field
Ca Field
Cd Field
Ce Field
Cf Field
Cl Field
Cm Field
Co Field
Cr Field
Cs Field
Cu Field
Db Field
Ds Field
Dy Field
Er Field
Es Field
Eu Field
F Field
Fe Field
Fm Field
Fr Field
Ga Field
Gd Field
Ge Field
H Field
He Field
Hf Field
Hg Field
Ho Field
Hs Field
I Field
In Field
Ir Field
K Field
Kr Field
La Field
Li Field
Lr Field
Lu Field
Md Field
Mg Field
Mn Field
Mo Field
Mt Field
N Field
Na Field
Nb Field
Nd Field
Ne Field
Ni Field
No Field
Np Field
O Field
Os Field
P Field
Pa Field
Pb Field
Pd Field
Pm Field
Po Field
Pr Field
Pt Field
Pu Field
Ra Field
Rb Field
Re Field
Rf Field
Rg Field
Rh Field
Rn Field
Ru Field
S Field
Sb Field
Sc Field
Se Field
Sg Field
Si Field
Sm Field
Sn Field
Sr Field
Ta Field
Tb Field
Tc Field
Te Field
Th Field
Ti Field
Tl Field
Tm Field
U Field
V Field
W Field
Xe Field
Y Field
Yb Field
Zn Field
Zr Field
PeriodicSystem Methods
__<clinit> Method
findAtomicNumber Method
getAbundance Method
getAtomicNumber Method
getAtomicRadius Method
getColumn Method
getCovalentRadius Method
getCovalentRadius Method (Int32)
getCovalentRadius Method (Int32, Int32)
getElementCount Method
getIsotope Method
getIsotopeCount Method
getIsotopeCount Method
getIsotopeCount Method (Int32)
getMass Method
getMass Method (Int32)
getMass Method (Int32, Int32)
getMassPrecision Method
getMassPrecision Method (Int32)
getMassPrecision Method (Int32, Int32)
getMostFrequentNaturalIsotope Method
getName Method
getRow Method
getSymbol Method
getVanDerWaalsRadius Method
isActinideMetal Method
isAlkaliMetal Method
isAlkalineEarthMetal Method
isAtomicSymbol Method
isHalogen Method
isLanthanideMetal Method
isMetal Method
isMetalloid Method
isNobleGas Method
isOtherMetal Method
isTransitionMetal Method
QueryBond Class
QueryBond Members
QueryBond Constructor
QueryBond Constructor (QueryBond)
QueryBond Constructor (MolAtom, MolAtom)
QueryBond Constructor (MolAtom, MolAtom, Int32)
QueryBond Constructor (MolAtom, MolAtom, String)
QueryBond Methods
__<clinit> Method
clone Method
cloneBond Method
getQuerystr Method
haveEqualProperties Method
setQuerystr Method
RgMolecule Class
RgMolecule Members
RgMolecule Constructor
RgMolecule Fields
RG_ID_MASK Field
RG_ID2_FLAG Field
RG_ID2_MASK Field
RG_ID2_OFF Field
RG_RESTH Field
RgMolecule Methods
add Method
add Method (MolAtom)
add Method (MolBond)
addRgroup Method
addRgroupsTo Method
aromatize Method
aromatize Method (Int32)
aromatize Method (Int32, Boolean)
canBeReactionComponent Method
checkConsistency Method
checkRlogicRange Method
cleanupRemovedRgroupMember Method
clearForImport Method
clearObjects Method
clonecopy Method
clonecopy Method (MoleculeGraph)
clonecopy Method (Int32[], MoleculeGraph)
clonelesscopy Method
cloneMolecule Method
contains Method
contains Method (MolAtom)
contains Method (MolBond)
createMol Method
endReuse Method
findRgroupIndex Method
fuse Method
getAllObjects Method
getAtom Method
getAtomCount Method
getAtomCount Method
getAtomCount Method (Int32)
getBond Method
getBondCount Method
getBondTable Method
getBtab Method
getComment Method
getCtab Method
getFlags Method
getFormula Method
getGraphUnion Method
getLocalParity Method
getLonePairCount Method
getMass Method
getMaxAttachmentPointOrder Method
getName Method
getObjectCount Method
getParity Method
getRgroupCount Method
getRgroupId Method
getRgroupIndex Method
getRgroupMember Method
getRgroupMemberCount Method
getRgroupMemberG Method
getRgroupMemberID Method
getRgroupMemberIndex Method
getRlogic Method
getRlogicRange Method
getRoot Method
getRootG Method
hasAtomSet Method
hasBondSet Method
hasRgroupContainedBy Method
indexOf Method
indexOf Method (MolAtom)
indexOf Method (MolBond)
isAtom Method
isBond Method
isEmpty Method
isIncompleteReaction Method
isQuery Method
isReaction Method
isSelfReference Method
mergeAtoms Method
newInstance Method
newSelectionMolecule Method
properties Method
regenBonds Method
removeAll Method
removeAllBonds Method
removeAtom Method
removeAtom Method (MolAtom, Int32)
removeAtom Method (Int32, Int32)
removeObject Method
replaceAtomsWithNewRgroup Method
replaceBond Method
reuseAtom Method
revalidateCoordDependentProps Method
rgroupIdOf Method
rgroupIndexOf Method
selectAllObjects Method
setAbsStereo Method
setAbsStereo Method (Boolean)
setAbsStereo Method (Boolean, Int32, Int32)
setAtom Method
setBond Method
setComment Method
setDim Method
setInputFormat Method
setLocation Method
setName Method
setRlogic Method
setRlogicRange Method
setRoot Method
setSgroupParent Method
sortBondsAccordingTo Method
stereoClean Method
toString Method
transform Method
unRgroupAtoms Method
RxnMolecule Class
RxnMolecule Members
RxnMolecule Constructor
RxnMolecule Fields
AGENTS Field
EQUILIBRIUM Field
PRODUCTS Field
REACTANTS Field
REGULAR_DOUBLE Field
REGULAR_SINGLE Field
RESONANCE Field
RETROSYNTHETIC Field
RGROUPED Field
TWO_HEADED_DOUBLE Field
TWO_HEADED_SINGLE Field
TYPE_COUNT Field
TYPE_MASK Field
RxnMolecule Methods
__<clinit> Method
add Method
add Method (MolAtom)
add Method (MolBond)
addComponent Method
addComponent Method (Molecule, Int32)
addComponent Method (Molecule, Int32, Boolean)
addReactionStep Method
addStructure Method
addStructure Method (Molecule, Int32)
addStructure Method (Molecule, Int32, Boolean)
canBeReactionComponent Method
clearForImport Method
clearObjects Method
clonecopy Method
clonecopy Method (MoleculeGraph)
clonecopy Method (Int32[], MoleculeGraph)
clonelesscopy Method
cloneMolecule Method
contains Method
contains Method (MolAtom)
contains Method (MolBond)
createBHtab Method
createCHtab Method
createReaction Method
createReaction Method (MoleculeGraph, DPoint3[])
createReaction Method (Molecule, DPoint3[], Int32)
determineArrowDistance Method
determineType Method
determineType Method (Double, Double, Double)
determineType Method (Double, Double, Double, DPoint3[])
fuse Method
getAgent Method
getAgentCount Method
getAgents Method
getAllFragments Method
getAllObjects Method
getArrowAsProperty Method
getAtom Method
getAtomCount Method
getAtomCount Method
getAtomCount Method (Int32)
getBond Method
getBondCount Method
getBondTable Method
getBtab Method
getCenter Method
getComponent Method
getComponent Method (Int64)
getComponent Method (Int32, Int32)
getComponentCount Method
getComponentFlags Method
getComponentID Method
getComponentID Method (MolAtom)
getComponentID Method (MolBond)
getComponentID Method (Molecule)
getComponentIndex Method
getComponentType Method
getCtab Method
getFormula Method
getGraphUnion Method
getItsArrow Method
getLocalParity Method
getMass Method
getMSLogic Method
getObjectCount Method
getParity Method
getProduct Method
getProductCount Method
getProducts Method
getReactant Method
getReactantCount Method
getReactants Method
getReaction Method
getReactionArrow Method
getReactionArrow Method
getReactionArrow Method (Boolean)
getReactionArrowList Method
getReactionArrowType Method
getReactionArrowTypeName Method
getReactionSteps Method
getStructure Method
getStructureCount Method
getType Method
hasAtomSet Method
hasBondSet Method
indexOf Method
indexOf Method (MolAtom)
indexOf Method (MolBond)
isAtom Method
isBond Method
isEmpty Method
isIncompleteReaction Method
isMergedComponent Method
isReaction Method
isSingleStepReaction Method
mergeAtoms Method
mergeComponentParts Method
newInstance Method
rebuildStructures Method
rebuildStructures Method
rebuildStructures Method (DPoint3[], Int32)
recalcReactionArrow Method
regenBonds Method
removeAll Method
removeAllBonds Method
removeAtom Method
removeAtom Method (MolAtom, Int32)
removeAtom Method (Int32, Int32)
removeComponent Method
removeEmptyComponents Method
removeObject Method
removeReactionArrow Method
removeStructure Method
replaceBond Method
revalidateCoordDependentProps Method
selectAllObjects Method
setAbsStereo Method
setAtom Method
setBond Method
setDim Method
setLocation Method
setMSLogic Method
setReactionArrow Method
setReactionArrow Method
setReactionArrow Method (DPoint3[])
setReactionArrow Method (Object)
setReactionArrow0 Method
setReactionArrowEndPoints Method
setReactionArrowType Method
setReactionArrowType Method (Int32)
setReactionArrowType Method (String)
setSgroupParent Method
simplifyIncompleteReactionToMolecule Method
simplifyToMolecule Method
sortBondsAccordingTo Method
splitAllDisconnectedComponents Method
splitComponentParts Method
splitDisconnectedComponent Method
splitDisconnectedComponent Method (Int64)
splitDisconnectedComponent Method (Int32, Int32)
stereoClean Method
toString Method
transform Method
updateComponentRoles Method
SelectionMolecule Class
SelectionMolecule Members
SelectionMolecule Constructor
SelectionMolecule Methods
add Method
clone Method
clonecopy Method
removeAtom Method
removeAtom Method (MolAtom)
removeAtom Method (Int32)
removeBond Method
removeBond Method (MolBond)
removeBond Method (Int32)
setBond Method
swapAtoms Method
transform Method
Sgroup Class
Sgroup Members
Sgroup Constructor
Sgroup Constructor (Molecule, Int32)
Sgroup Constructor (Molecule, Int32, Int32)
Sgroup Fields
CHARGE_ON_ATOMS Field
CHARGE_ON_GROUP Field
PR_ATSYMS Field
SCN_EITHER_UNKNOWN Field
SCN_HEAD_TO_HEAD Field
SCN_HEAD_TO_TAIL Field
SGROUP_TYPE_COUNT Field
SORT_CHILD_PARENT Field
SORT_PARENT_CHILD Field
SST_ALTERNATING Field
SST_BLOCK Field
SST_RANDOM Field
ST_ANY Field
ST_COMPONENT Field
ST_COPOLYMER Field
ST_CROSSLINK Field
ST_DATA Field
ST_FORMULATION Field
ST_GENERIC Field
ST_GRAFT Field
ST_MER Field
ST_MIXTURE Field
ST_MODIFICATION Field
ST_MONOMER Field
ST_MULTICENTER Field
ST_MULTIPLE Field
ST_SRU Field
ST_SUPERATOM Field
XSTATE_C Field
XSTATE_NONE Field
XSTATE_X Field
XSTATE_XC Field
Sgroup Methods
add Method
addBracket Method
addChildSgroup Method
areChildSgroupsVisible Method
clearObjects Method
cloneSgroup Method
cloneStructure Method
containsAllAtomsOf Method
countAllAtoms Method
createMolecule Method
createMolecule Method
createMolecule Method (Molecule)
findCrossingBonds Method
findSmallestSgroupContaining Method
findSmallestSgroupOf Method
getAtom Method
getAtomArray Method
getAtomCount Method
getBracketCount Method
getBrackets Method
getChargeLocation Method
getChildSgroup Method
getChildSgroupCount Method
getConnectivity Method
getCrossingAtoms Method
getParentMolecule Method
getParentSgroup Method
getSgroupGraph Method
getSubscript Method
getSubType Method
getSuperscript Method
getTotalCharge Method
getType Method
getXState Method
hasAtom Method
hasBrackets Method
Implicit Operator
indexOf Method
indexOf Method (MolAtom)
indexOf Method (MolBond)
initBrackets Method
isBracketCrossingBond Method
isBracketVisible Method
isDescendantOf Method
isEmpty Method
isOrderedComponentSgroup Method
isPartSelected Method
isRemovable Method
isSelected Method
isTotalSelected Method
isVisible Method
removeAtom Method
removeBonds Method
removeChildSgroup Method
removeObject Method
replaceAtom Method
replaceAtom Method (MolAtom, MolAtom)
replaceAtom Method (MolAtom, MolAtom, Int32)
selectAllObjects Method
setAtom Method
setChargeLocation Method
setConnectivity Method
setGUIStateRecursively Method
setGUIStateRecursively Method (Boolean)
setGUIStateRecursively Method (Boolean, Int32)
setSgroupGraph Method
setSubscript Method
setSubType Method
setXState Method
setXState Method (Int32)
setXState Method (Int32, Int32)
sort Method
toString Method
toString Method
toString Method (Int32)
Smolecule Interface
Smolecule Members
Smolecule Fields
A_ALL Field
A_ASTEREO Field
A_ATOMMAP Field
A_BOND Field
A_CHARGE Field
A_CHIRALITY Field
A_EXPLH Field
A_HYBRIDIZATION Field
A_IMPLH Field
A_MASSNO Field
A_PARITY Field
A_RADICAL Field
A_RGROUP Field
A_VALENCE Field
RGROUP_MAX Field
Smolecule Methods
areNeighbors Method
gearch Method
getArrayFlags Method
getAtom1 Method
getAtom2 Method
getAtomMap Method
getAtomStereo Method
getAtomType Method
getBondFlags Method
getBondIndex Method
getBondType Method
getBondType Method (Int32)
getBondType Method (Int32, Int32)
getCharge Method
getChirality Method
getExplicitHcount Method
getHcount Method
getHybridizationState Method
getImplicitHcount Method
getImplicitHcount Method
getImplicitHcount Method (Int32)
getMassno Method
getNeighbor Method
getNeighborCount Method
getParity Method
getQPropAsInt Method
getRadical Method
getRgroupId Method
getValence Method
inAtomList Method
Smolecule.__Fields Class
Smolecule.__Fields Members
Smolecule.__Fields Fields
A_ALL Field
A_ASTEREO Field
A_ATOMMAP Field
A_BOND Field
A_CHARGE Field
A_CHIRALITY Field
A_EXPLH Field
A_HYBRIDIZATION Field
A_IMPLH Field
A_MASSNO Field
A_PARITY Field
A_RADICAL Field
A_RGROUP Field
A_VALENCE Field
RGROUP_MAX Field
StereoConstants Interface
StereoConstants Members
StereoConstants Fields
ANTI Field
ATOMSTEREO_EITHER Field
ATOMSTEREO_MASK Field
ATOMSTEREO_NONE Field
ATOMSTEREO_SPECIFIC Field
CHIRALITY_M Field
CHIRALITY_MASK Field
CHIRALITY_P Field
CHIRALITY_R Field
F:chemaxon.struc.StereoConstants.CHIRALITY_R
CHIRALITY_S Field
F:chemaxon.struc.StereoConstants.CHIRALITY_S
CHIRALITYSUPPORT_ALL Field
CHIRALITYSUPPORT_NONE Field
CHIRALITYSUPPORT_SELECTED Field
CIS Field
CTUMASK Field
CTUNKNOWN Field
CTUNSPEC Field
DBS_ALL Field
DBS_MARKED Field
DBS_NONE Field
ENDO Field
EXO Field
PARITY_ALLENE Field
PARITY_EITHER Field
PARITY_EVEN Field
PARITY_MASK Field
PARITY_ODD Field
PARITY_TETRAHEDRAL Field
PARITY_UNSPEC Field
STGRP_ABS Field
STGRP_AND Field
STGRP_NONE Field
STGRP_OR Field
SYN Field
TRANS Field
StereoConstants.__Fields Class
StereoConstants.__Fields Members
StereoConstants.__Fields Fields
ANTI Field
ATOMSTEREO_EITHER Field
ATOMSTEREO_MASK Field
ATOMSTEREO_NONE Field
ATOMSTEREO_SPECIFIC Field
CHIRALITY_M Field
CHIRALITY_MASK Field
CHIRALITY_P Field
CHIRALITY_R Field
F:chemaxon.struc.StereoConstants.__Fields.CHIRALITY_R
CHIRALITY_S Field
F:chemaxon.struc.StereoConstants.__Fields.CHIRALITY_S
CHIRALITYSUPPORT_ALL Field
CHIRALITYSUPPORT_NONE Field
CHIRALITYSUPPORT_SELECTED Field
CIS Field
CTUMASK Field
CTUNKNOWN Field
CTUNSPEC Field
DBS_ALL Field
DBS_MARKED Field
DBS_NONE Field
ENDO Field
EXO Field
PARITY_ALLENE Field
PARITY_EITHER Field
PARITY_EVEN Field
PARITY_MASK Field
PARITY_ODD Field
PARITY_TETRAHEDRAL Field
PARITY_UNSPEC Field
STGRP_ABS Field
STGRP_AND Field
STGRP_NONE Field
STGRP_OR Field
SYN Field
TRANS Field
WSmolecule Interface
WSmolecule Members
WSmolecule Methods
addAtom Method
addAtom Method (Int32)
addAtom Method (Smolecule, Int32)
addBond Method
newInstance Method
removeAtom Method
removeBond Method
reset Method
setAtomMap Method
setAtomStereo Method
setCharge Method
setHybridizationState Method
setImplicitHcount Method
setMassno Method
setRadical Method
setRgroupId Method
setValence Method
chemaxon.struc.graphics Namespace
MAtomSetPoint Class
MAtomSetPoint Members
MAtomSetPoint Constructor
MAtomSetPoint Constructor
MAtomSetPoint Constructor (MAtomSetPoint)
MAtomSetPoint Constructor (MolAtom[])
MAtomSetPoint Methods
checkValidity Method
clone Method
containsAtom Method
equals Method
equals Method (MAtomSetPoint)
equals Method (MPoint)
equals Method (Object)
finishCloning Method
getAtoms Method
getLocation Method
getPoint Method
getWeights Method
isTransformable Method
replaceAtom Method
setAtoms Method
setLocation Method
setWeights Method
transform Method
MBracket Class
MBracket Members
MBracket Constructor
MBracket Constructor
MBracket Constructor (MPoint, MPoint)
MBracket Constructor (MPoint, MPoint, )
MBracket Fields
T_BRACES Field
T_CHEVRONS Field
T_DOUBLE Field
T_ROUND Field
T_SINGLE Field
T_SQUARE Field
MBracket Methods
__<clinit> Method
addAttributeKeys Method
clone Method
copyProperties Method
enclosesPoint Method
getAttribute Method
getBracketOrientation Method
getType Method
getVisiblePointRef Method
getVisiblePointRefCount Method
hasBackground Method
setAttribute Method
setBracketOrientation Method
setType Method
transform Method
MChemicalStruct Class
MChemicalStruct Members
MChemicalStruct Constructor
MChemicalStruct Methods
calcCenter Method
clone Method
containsAtom Method
distanceFrom Method
distanceFrom Method (Double, Double, CTransform3D)
distanceFrom Method (MoleculeGraph, Double, Double, CTransform3D)
getMoleculeGraph Method
getPoint Method
getPointCount Method
hasSelection Method
hasSelection Method
hasSelection Method (MoleculeGraph)
isEmpty Method
setSelected Method
setSelected Method (Boolean)
setSelected Method (MoleculeGraph, Boolean)
transform Method
unselectContents Method
MEFlow Class
MEFlow Members
MEFlow Constructor
MEFlow Constructor
MEFlow Constructor (Int32)
MEFlow Constructor (MPoint, MPoint, Int32)
MEFlow Fields
E_SINK Field
E_SOURCE Field
MEFlow Methods
clone Method
getAtom Method
getAtoms Method
getBond Method
getMolObject Method
getNumElectrons Method
getPoint Method
getPointRefCount Method
getSink Method
getSinkAtom Method
getSinkAtoms Method
getSinkBond Method
getSource Method
getSourceAtom Method
getSourceAtoms Method
getSourceBond Method
getValidSinkAtomPairsForMolecule Method
getValidSinkAtomPairsForMolecule Method (Molecule, MolAtom)
getValidSinkAtomPairsForMolecule Method (Molecule, MolBond)
getValidSinkAtomsForMolecule Method
getValidSinkAtomsForMolecule Method (Molecule, MolAtom)
getValidSinkAtomsForMolecule Method (Molecule, MolBond)
getValidSinkBondsForMolecule Method
getValidSinkBondsForMolecule Method (Molecule, MolAtom)
getValidSinkBondsForMolecule Method (Molecule, MolBond)
getValidSourceAtomPairsForMolecule Method
getValidSourceAtomsForMolecule Method
getValidSourceBondsForMolecule Method
isAtom Method
isBond Method
isIncipBond Method
isValidSourceAndSinkForMolecule Method
isValidSourceForMolecule Method
sinkIsAtom Method
sinkIsBond Method
sinkIsIncipBond Method
sourceIsAtom Method
sourceIsBond Method
MEFlowBasePoint Class
MEFlowBasePoint Members
MEFlowBasePoint Constructor
MEFlowBasePoint Constructor
MEFlowBasePoint Constructor (MEFlowBasePoint)
MEFlowBasePoint Constructor (MolAtom, MPoint)
MEFlowBasePoint Methods
checkValidity Method
clone Method
containsAtom Method
equals Method
equals Method (MEFlowBasePoint)
equals Method (MPoint)
equals Method (Object)
finishCloning Method
getAtom Method
getLocation Method
getOtherEnd Method
getPoint Method
isTransformable Method
replaceAtom Method
setLocation Method
setStartEnd Method
transform Method
MEllipse Class
MEllipse Members
MEllipse Constructor
MEllipse Constructor
MEllipse Constructor (MPoint, MPoint)
MEllipse Constructor (MPoint, MPoint, )
MEllipse Methods
__<clinit> Method
clone Method
MFont Class
MFont Members
MFont Constructor
MFont Constructor (MFont)
MFont Constructor ()
MFont Constructor (String)
MFont Constructor (String, Int32, Double)
MFont Fields
BOLD Field
ITALIC Field
PLAIN Field
MFont Methods
__<clinit> Method
clone Method
cloneMFont Method
equals Method
getAWTFont Method
getFamily Method
getScaledAWTFont Method
getSizeDouble Method
getString Method
getStyle Method
Implicit Method
Implicit Operator
Implicit Operator
isBold Method
isItalic Method
sizeToString Method
MMidPoint Class
MMidPoint Members
MMidPoint Methods
addNotify Method
clone Method
equals Method
equals Method (MMidPoint)
equals Method (Object)
getLocation Method
getParentLine Method
getPositionInPolyline Method
isChildOf Method
isSelectableNow Method
removeNotify Method
setLocation Method
toString Method
transform Method
MMidPoint.Sticky Class
MMidPoint.Sticky Members
MMidPoint.Sticky Constructor
MMidPoint.Sticky Methods
clone Method
getLocation Method
MPolyline Class
MPolyline Members
MPolyline Constructor
MPolyline Constructor
MPolyline Constructor (MPolyline, MPoint)
MPolyline Constructor (MPoint, MPoint)
MPolyline Constructor (MPoint, MPoint, , )
MPolyline Fields
ARROW_BACK_FLAG Field
ARROW_HALF_LEFT Field
ARROW_HALF_MASK Field
ARROW_HALF_RIGHT Field
CLOSED_FLAG Field
DEFAULT_ARROW_HEAD_LENGTH Field
DEFAULT_ARROW_HEAD_WIDTH Field
DEFAULT_THICKNESS Field
HEAD Field
TAIL Field
THICKNESS_SET_FLAG Field
MPolyline Methods
addAttributeKeys Method
calcCenter Method
checkValidity Method
clone Method
containsAtom Method
copyProperties Method
distanceFrom Method
finishCloning Method
fixClonedPoints Method
fixMidPointClones Method
getArcAngle Method
getArcCenter Method
getArcRadius Method
getArcRadius Method (CTransform3D)
getArcRadius Method (DPoint3, DPoint3, Double)
getArrowFlags Method
getArrowLength Method
getArrowWidth Method
getAttribute Method
getFlags Method
getMidPointLocation Method
getPoint Method
getPointCount Method
getPointRef Method
getPointRefCount Method
getPoints Method
getSkip Method
getThickness Method
hasBackground Method
hasColor Method
hasFace Method
hasLineColor Method
hasOutline Method
isArrow Method
isEmpty Method
isThicknessSet Method
removeChild Method
replaceAtom Method
reverse Method
rotate Method
setArcAngle Method
setArrow Method
setArrowFlags Method
setArrowLength Method
setArrowWidth Method
setAttribute Method
setFlags Method
setPoints Method
setSkip Method
setThickness Method
transform Method
unselectContents Method
updateBoundingRect Method
MRectangle Class
MRectangle Members
MRectangle Constructor
MRectangle Constructor
MRectangle Constructor (MPoint, MPoint)
MRectangle Constructor (MPoint, MPoint, , )
MRectangle Fields
P_CENTER Field
P_E Field
P_N Field
P_NE Field
P_NW Field
P_S Field
P_SE Field
P_SW Field
P_W Field
T_NOROT Field
MRectangle Methods
__<clinit> Method
addAttributeKeys Method
calcCenter Method
clone Method
convertTransform Method
distanceFrom Method
fixClonedPoints Method
fixRectanglePointClones Method
getAttribute Method
getClip Method
getPointRef Method
getPointRefCount Method
getTCenter Method
getTOption Method
removeChild Method
setAttribute Method
setCorners Method
setTCenter Method
setTOption Method
transform Method
transformTo2D Method
MRectanglePoint Class
MRectanglePoint Members
MRectanglePoint Methods
addNotify Method
clone Method
equals Method
equals Method (MRectanglePoint)
equals Method (Object)
getParentRect Method
getPositionInRect Method
isChildOf Method
isSelectableNow Method
isTransformable Method
removeNotify Method
setLocation Method
toString Method
transform Method
MRectanglePoint.Sticky Class
MRectanglePoint.Sticky Members
MRectanglePoint.Sticky Constructor
MRectanglePoint.Sticky Methods
clone Method
getLocation Method
MRoundedRectangle Class
MRoundedRectangle Members
MRoundedRectangle Constructor
MRoundedRectangle Constructor
MRoundedRectangle Constructor (MPoint, MPoint)
MRoundedRectangle Constructor (MPoint, MPoint, )
MRoundedRectangle Constructor (MPoint, MPoint, Double, Double)
MRoundedRectangle Constructor (MPoint, MPoint, Double, Double, )
MRoundedRectangle Methods
__<clinit> Method
addAttributeKeys Method
clone Method
containsPoint Method
correctCornersRadius Method
getArcHeight Method
getArcWidth Method
getAttribute Method
getInnerPointRef Method
getPointRef Method
getPointRefCount Method
setArcHeight Method
setArcWidth Method
setAttribute Method
setCornersRadius Method
MTextAttributes Class
MTextAttributes Members
MTextAttributes Constructor
MTextAttributes Fields
A_ALL Field
A_BOLD Field
A_DX Field
A_DY Field
A_FONT Field
A_FONT_BITS Field
A_FONTFAMILY Field
A_FONTSIZE Field
A_FOREGROUND Field
A_ITALIC Field
A_SCALE Field
A_SUBLEVEL Field
DEFAULT Field
DEFAULT_SUPERSCRIPT_DELTAY Field
DEFAULT_SUPERSCRIPT_SCALE Field
DEFAULT_SUPERSCRIPT_SUBLEVEL Field
MTextAttributes Methods
__<clinit> Method
createCompatible Method
createNext Method
decode Method
encode Method
equals Method
equals Method (MTextAttributes)
equals Method (Object)
equalsNext Method
getBaseFont Method
getCompatibleAttributes Method
getDx Method
getDy Method
getFontFamily Method
getForeground Method
getScale Method
getSet Method
getSubLevel Method
Implicit Operator
isCompatible Method
isDefault Method
isFontDefault Method
isFontRegular Method
readExternal Method
toString Method
writeExternal Method
MTextBox Class
MTextBox Members
MTextBox Constructor
MTextBox Fields
ALIGN_BOTTOM Field
ALIGN_CENTER Field
ALIGN_LEFT Field
ALIGN_RIGHT Field
ALIGN_TOP Field
FONT_DEFAULT_SCALE Field
MTextBox Methods
__<clinit> Method
addAttributeKeys Method
addCdataAttributeKeys Method
addChar Method
addLine Method
addString Method
clearLines Method
clone Method
cursorDown Method
cursorToRowEnd Method
cursorToRowStart Method
cursorUp Method
deleteChar Method
deleteCharBackward Method
determinePosition Method
getActionMap Method
getAttribute Method
getBaseFont Method
getBaseFontFamily Method
getBaseFontStyle Method
getBreakingChars Method
getCurrentDefaultFontMetrics Method
getCurrentForeground Method
getCurrentHeight Method
getCurrentScriptCount Method
getCurrentSubLevel Method
getCurrentTextAttributes Method
getCurrentWidth Method
getCursorColumn Method
getCursorPos Method
getCursorRow Method
getFontScale Method
getHorizontalAlignment Method
getLine Method
getLineCount Method
getMinimumHeight Method
getPreBreakingChars Method
getPreviousNormalTextSectionIndex Method
getSelectedString Method
getSelectionEndColumn Method
getSelectionEndPos Method
getSelectionEndRow Method
getSelectionStartColumn Method
getSelectionStartPos Method
getSelectionStartRow Method
getText Method
getTextAttributesAtCursor Method
getTextDocument Method
getVerticalAlignment Method
hasBackground Method
hasColor Method
hasFace Method
hasRichText Method
hasSelection Method
isAutoHeight Method
isAutoSize Method
isCurrentFontDefault Method
isCurrentFontRegular Method
isEditable Method
isEmpty Method
isMinimumHeightSet Method
setActionMap Method
setAttribute Method
setAutoHeight Method
setAutoSize Method
setBaseFontFamily Method
setBaseFontStyle Method
setCurrentDefaultFontMetrics Method
setCurrentFont Method
setCurrentForeground Method
setCurrentHeight Method
setCurrentTextAttributes Method
setCurrentWidth Method
setCursorPos Method
setCursorRow Method
setFontScale Method
setHorizontalAlignment Method
setMinimumHeight Method
setMinimumHeightSet Method
setPoints Method
setRowAndColumn0 Method
setSelected Method
setText Method
setVerticalAlignment Method
transform Method
unselectContents Method
MTextDocument$Portion Class
MTextDocument$Portion Members
MTextDocument$Portion Methods
endsWith Method
getAscent Method
getDescent Method
getEndDx Method
getEndPos Method
getPlainText Method
getPortion Method
getStartPos Method
length Method
portionWidth Method
portionXAdvance Method
portionXAdvance Method (, MFont, )
portionXAdvance Method (, MFont, , Boolean)
toString Method
MTextDocument$Section Class
MTextDocument$Section Members
MTextDocument$Section Constructor
MTextDocument$Section Constructor (MTextDocument$Section)
MTextDocument$Section Constructor (Int32, String)
MTextDocument$Section Constructor (Int32, String, MTextAttributes)
MTextDocument$Section Methods
doubleStringWidth Method
getAttributes Method
getFontMetrics Method
getPosition Method
getString Method
length Method
substring Method
substring Method (Int32)
substring Method (Int32, Int32)
chemaxon.struc.prop Namespace
MBooleanProp Class
MBooleanProp Members
MBooleanProp Constructor
MBooleanProp Constructor (Boolean)
MBooleanProp Constructor (String)
MBooleanProp Methods
booleanValue Method
clone Method
cloneProp Method
convertToString Method
equals Method
getPropType Method
getPropValue Method
getPropXSDType Method
toString Method
MCollectionProp Class
MCollectionProp Members
MCollectionProp Constructor
MCollectionProp Methods
clone Method
cloneCollectionProp Method
cloneProp Method
contains Method
equals Method
getPropXSDType Method
replace Method
unorderedIterator Method
MDoubleArrayProp Class
MDoubleArrayProp Members
MDoubleArrayProp Constructor
MDoubleArrayProp Constructor (Double[])
MDoubleArrayProp Constructor (String, Int32, Int32)
MDoubleArrayProp Methods
clone Method
cloneProp Method
convertToString Method
equals Method
getDoubleArray Method
getPropArraySize Method
getPropType Method
getPropValue Method
getPropXSDType Method
toString Method
MDoubleProp Class
MDoubleProp Members
MDoubleProp Constructor
MDoubleProp Constructor (Double)
MDoubleProp Constructor (String)
MDoubleProp Methods
clone Method
cloneProp Method
convertToString Method
doubleValue Method
equals Method
getPropType Method
getPropValue Method
getPropXSDType Method
toString Method
MHashProp Class
MHashProp Members
MHashProp Constructor
MHashProp Methods
cloneCollectionProp Method
convertToString Method
equals Method
get Method
get Method (Int32)
get Method (String)
getKey Method
getMap Method
getPropArraySize Method
getPropType Method
getPropValue Method
put Method
replace Method
size Method
toString Method
unorderedIterator Method
MHCoords3DProp Class
MHCoords3DProp Members
MHCoords3DProp Constructor
MHCoords3DProp Constructor (String)
MHCoords3DProp Constructor (, MoleculeGraph)
MHCoords3DProp Constructor (, Int64)
MHCoords3DProp Methods
clone Method
cloneProp Method
convertToString Method
equals Method
getMap Method
getPoints Method
getPropType Method
getPropValue Method
getPropXSDType Method
toString Method
transform Method
MIntegerArrayProp Class
MIntegerArrayProp Members
MIntegerArrayProp Constructor
MIntegerArrayProp Constructor (Int32[])
MIntegerArrayProp Constructor (String, Int32, Int32)
MIntegerArrayProp Methods
clone Method
cloneProp Method
convertToString Method
equals Method
getIntArray Method
getPropArraySize Method
getPropType Method
getPropValue Method
getPropXSDType Method
toString Method
MIntegerProp Class
MIntegerProp Members
MIntegerProp Constructor
MIntegerProp Constructor (Int32)
MIntegerProp Constructor (String)
MIntegerProp Methods
clone Method
cloneProp Method
convertToString Method
equals Method
getPropType Method
getPropValue Method
getPropXSDType Method
intValue Method
toString Method
MListProp Class
MListProp Members
MListProp Constructor
MListProp Methods
add Method
cloneCollectionProp Method
convertToString Method
equals Method
get Method
getList Method
getPropArraySize Method
getPropType Method
getPropValue Method
remove Method
replace Method
set Method
size Method
toString Method
unorderedIterator Method
MMoleculeProp Class
MMoleculeProp Members
MMoleculeProp Constructor
MMoleculeProp Constructor (Molecule)
MMoleculeProp Constructor (String)
MMoleculeProp Methods
clone Method
cloneProp Method
convertToString Method
equals Method
getMolecule Method
getPropType Method
getPropValue Method
getPropXSDType Method
toString Method
MObjectProp Class
MObjectProp Members
MObjectProp Constructor
MObjectProp Constructor (Object)
MObjectProp Constructor (String)
MObjectProp Methods
clone Method
cloneProp Method
convertToString Method
equals Method
getPropType Method
getPropValue Method
getPropXSDType Method
toString Method
MStringProp Class
MStringProp Members
MStringProp Constructor
MStringProp Methods
clone Method
cloneProp Method
convertToString Method
equals Method
getPropType Method
getPropValue Method
getPropXSDType Method
stringValue Method
toString Method
chemaxon.struc.sgroup Namespace
DataSgroup Class
DataSgroup Members
DataSgroup Constructor
DataSgroup Constructor (Molecule)
DataSgroup Constructor (DataSgroup, Molecule, Sgroup)
DataSgroup Constructor (DataSgroup, Molecule, Sgroup, Int32[])
DataSgroup Fields
DT_FORMATTED Field
DT_NUMERIC Field
DT_TEXT Field
DT_UNSPEC Field
DT_URL Field
HIDDEN Field
DataSgroup Methods
__<clinit> Method
addDataLine Method
getAbsoluteXY Method
getContext Method
getContextId Method
getData Method
getDataLine Method
getDataLineCount Method
getDisplayedChars Method
getDisplayedLines Method
getFieldName Method
getFieldType Method
getLineOnScreen Method
getObjectsMiddle Method
getPlacementOrigin Method
getPos Method
getQueryCode Method
getQueryOp Method
getSubscript Method
getTag Method
getUnits Method
getX Method
getY Method
hasBrackets Method
isAbsolutePlacement Method
isDataDetached Method
isTotalSelected Method
isUnitDisplayed Method
setAbsolutePlacement Method
setAbsoluteXY Method
setAbsoluteXY Method (DPoint3)
setAbsoluteXY Method (Double, Double)
setContext Method
setContext Method (Int32)
setContext Method (String)
setData Method
setDataDetached Method
setDataLine Method
setDisplayedChars Method
setDisplayedLines Method
setFieldName Method
setFieldType Method
setFieldType Method (Int32)
setFieldType Method (String)
setPos Method
setQueryCode Method
setQueryOp Method
setTag Method
setUnitDisplayed Method
setUnits Method
setX Method
setY Method
Expandable Interface
Expandable Members
Expandable Fields
COORDS_UPDATE Field
DEFAULT_OPTIONS Field
FAST_COORDS Field
MDL_EXPAND Field
NONRECURSIVE_EXPAND Field
REVERSIBLE_EXPAND Field
Expandable Methods
contract Method
expand Method
isExpanded Method
Expandable.__Fields Class
Expandable.__Fields Members
Expandable.__Fields Fields
COORDS_UPDATE Field
DEFAULT_OPTIONS Field
FAST_COORDS Field
MDL_EXPAND Field
NONRECURSIVE_EXPAND Field
REVERSIBLE_EXPAND Field
MultipleSgroup Class
MultipleSgroup Members
MultipleSgroup Constructor
MultipleSgroup Methods
add Method
addRepeatingUnitAtom Method
contract Method
expand Method
getMultiplier Method
getRepeatingUnitAtom Method
getRepeatingUnitAtomCount Method
getRepeatingUnitAtoms Method
getSubscript Method
isAcceptableGraph Method
isBracketVisible Method
isContracted Method
isExpanded Method
isRepeatingUnitAtom Method
newInstance Method
removeRepeatingUnitAtom Method
replaceAtom Method
setAtom Method
setMultiplier Method
setRepeatingUnitAtom Method
setSubscript Method
toString Method
RepeatingUnitSgroup Class
RepeatingUnitSgroup Members
RepeatingUnitSgroup Constructor
RepeatingUnitSgroup Constructor (Molecule, Int32)
RepeatingUnitSgroup Constructor (Molecule, String, Int32)
RepeatingUnitSgroup Methods
addCrossingBonds Method
addStarAtoms Method
containsLadderTypePolymer Method
equalsHead Method
equalsTail Method
findCrossingBonds Method
getBondConnectionInfo Method
getBondCorrespondence Method
getHeadCrossingBonds Method
getOtherCrossingBond Method
getSuperscript Method
getTailCrossingBonds Method
isAcceptablePolymerGraph Method
isAcceptableRSRUGraph Method
isAcceptableSru Method
isCrossingBond Method
isFlipped Method
isStarAtom Method
mergeBrackets Method
removeStarAtoms Method
setBondCorrespondence Method
setFlipped Method
setHeadCrossingBonds Method
setTailCrossingBonds Method
swapHeadTail Method
SgroupAtom Class
SgroupAtom Members
SgroupAtom Constructor
SgroupAtom Fields
LABEL_AUTO Field
LABEL_DEFAULT Field
SgroupAtom Methods
__<clinit> Method
clone Method
cloneFromSgroupCopy Method
getAtomSymbol Method
getLabelCenter Method
getLeftName Method
getRightName Method
getSgroup Method
getSymbol Method
hasAlternativeName Method
set Method
setLabelCenter Method
setLeftName Method
setRightName Method
transform Method
SuperatomSgroup Class
SuperatomSgroup Members
SuperatomSgroup Constructor
SuperatomSgroup Constructor (Molecule)
SuperatomSgroup Constructor (Molecule, Boolean)
SuperatomSgroup Methods
areChildSgroupsVisible Method
contract Method
createMolecule Method
expand Method
expandOther Method
findAttachAtom Method
findCrossingBonds Method
getAttachAtoms Method
getCrossingAtoms Method
getExternalConnections Method
getFreeLegalAttachAtoms Method
getLegalAttachAtoms Method
getParentSgroupGraph Method
getSgroupGraph Method
getSuperAtom Method
hasAtom Method
hasBrackets Method
isBracketVisible Method
isContracted Method
isExpanded Method
isFreeLegalAttachAtom Method
isLegalAttachment Method
isTotalSelected Method
removeBond Method
replaceAtom Method
setAtom Method
setGUIStateRecursively Method
setSgroupGraph Method
sortXBonds Method
toString Method
updateAttachmentPoints Method
updateSgroupCrossings Method
chemaxon.util Namespace
Cancelable Interface
Cancelable Members
Cancelable Methods
cancel Method
isCanceled Method
ConnectionHandler Class
ConnectionHandler Members
ConnectionHandler Constructor
ConnectionHandler Constructor
ConnectionHandler Constructor (ConnectionHandler)
ConnectionHandler Constructor ()
ConnectionHandler Constructor (Boolean)
ConnectionHandler Constructor (ConnectionHandler, Boolean)
ConnectionHandler Constructor (, String)
ConnectionHandler Constructor (, String, Boolean)
ConnectionHandler Fields
DEFAULT_PROPERTY_TABLE Field
ConnectionHandler Methods
close Method
close_NE Method
connect Method
connect_NE Method
connectToDatabase Method
disconnect Method
getConnection Method
getDriver Method
getDriverName Method
getInstance Method
getLoginName Method
getPassword Method
getPropertyTable Method
getRememberPassword Method
getUrl Method
Implicit Operator
isCommitable Method
isConnected Method
loadValuesFromProperties Method
setConnected Method
setConnection Method
setDriver Method
setDriverName Method
setLoginName Method
setPassword Method
setPropertyTable Method
setRememberPassword Method
setUrl Method
storeValuesToProperties Method
toString Method
DatabaseTools Class
DatabaseTools Members
DatabaseTools Constructor
DatabaseTools Methods
getFieldNames Method
getFieldTypes Method
isConnectionAlive Method
isIntType Method
isRealType Method
isTextType Method
readBytes Method
readBytes Method (, Int32)
readBytes Method (, String)
readString Method
DotfileUtil Class
DotfileUtil Members
DotfileUtil Constructor
DotfileUtil Methods
__<clinit> Method
create Method
getDotDir Method
getDotDirName Method
getDotFile Method
getDotFileWithEnsuredPath Method
lastModified Method
main Method
open Method
setDotDirName Method
ErrorHandler Class
ErrorHandler Members
ErrorHandler Constructor
ErrorHandler Fields
CLASS_NOT_FOUND_ERROR Field
DATABASE_SEARCH_ERROR Field
ILLEGAL_ACCESS_ERROR Field
INSTANTIATION_ERROR Field
IO_ERROR Field
MAX_SEARCH_FREQUENCY_EXCEEDED_ERROR Field
MOL_FORMAT_ERROR Field
NO_ERROR Field
PROPERTY_NOT_SET_ERROR Field
SQL_ERROR Field
UNIDENTIFIED_ERROR Field
ErrorHandler Methods
checkError Method
checkException Method
getError Method
getErrorMessage Method
getException Method
getStackTrace Method
Implicit Operator
ErrorProcessor Interface
ErrorProcessor Members
ErrorProcessor Methods
processError Method
HitColoringAndAlignmentOptions Class
HitColoringAndAlignmentOptions Members
HitColoringAndAlignmentOptions Constructor
HitColoringAndAlignmentOptions Fields
ALIGNMENT_OFF Field
ALIGNMENT_PARTIAL_CLEAN Field
ALIGNMENT_ROTATE Field
alignmentMode Field
coloring Field
DISSIMILARITY Field
enumerateMarkush Field
hitColor Field
hitHomologyColor Field
MARKUSH_REDUCTION Field
MARKUSH_REDUCTION_HGEXPANSION Field
markushDisplayMode Field
nonHitColor Field
nonHitColor3D Field
ORIGINAL_MARKUSH Field
QUERY_LABEL Field
SIMILARITY Field
SIMILARITY_LABEL Field
SIMILARITY_OFF Field
similarityScoreDisplay Field
TARGET_LABEL Field
HitColoringAndAlignmentOptions Methods
clone Method
getHitHomologyColor Method
Implicit Operator
isDisplayLabelsAndBoxes Method
isQueryDisplay Method
isRemoveUnusedDefitions Method
setDisplayLabelsAndBoxes Method
setHitHomologyColor Method
setOptions Method
setQueryDisplay Method
setRemoveUnusedDefinitions Method
HitDisplayTool Class
HitDisplayTool Members
HitDisplayTool Constructor
HitDisplayTool Fields
HIT_ATOM_SET Field
HIT_BOND_SET Field
NON_HIT_ATOM_SET Field
NON_HIT_BOND_SET Field
HitDisplayTool Methods
getHit Method
getHitIndexes Method
getHits Method
getHits Method (Int32)
getHits Method (Molecule, Molecule, Int32)
getHits Method (Molecule, Byte[], Int32)
getNextHit Method
isLicensed Method
setLicenseEnvironment Method
setMoleculeMarkushSourceTarget Method
setTarget Method
HitDisplayUtil Class
HitDisplayUtil Members
HitDisplayUtil Constructor
HitDisplayUtil Fields
PROP_ALIGNHIT Field
SEQ_RESTORE Field
HitDisplayUtil Methods
color Method
color Method (Molecule, Molecule, HitColoringAndAlignmentOptions)
color Method (Molecule, Molecule, Int32[], HitColoringAndAlignmentOptions)
getScaffoldOrientatedHit Method
getScaffoldOrientatedHit Method (Molecule, Molecule)
getScaffoldOrientatedHit Method (Molecule, Molecule, Int32[])
HTMLTools Class
HTMLTools Members
HTMLTools Methods
convertForAppletParameter Method
convertForJavaScript Method
exceptionToPage Method
exceptionToString Method
getColor Method
getHTMLColorString Method
insertStringBeforeLineEnds Method
stringToPage Method
HTMLUtil Class
HTMLUtil Members
HTMLUtil Constructor
HTMLUtil Methods
convertBase64Gzip2Text Method
convertForJavaScript Method
replaceString Method
ImageExportUtil Class
ImageExportUtil Members
ImageExportUtil Methods
__<clinit> Method
createEMF Method
createImageExporterParameter Method
disableNewEmfGenerator Method
generateEMFToFile Method
mergeProperties Method
releaseNewEMFGenerator Method
startEMFGenerator Method
IntArray Class
IntArray Members
IntArray Constructor
IntArray Constructor
IntArray Constructor (Int32)
IntArray Fields
DEFAULT_BLOCK_SIZE Field
IntArray Methods
add Method
addAll Method
capacity Method
clear Method
contains Method
copyInto Method
fill Method
get Method
Implicit Method
Implicit Operator
Implicit Operator
indexOf Method
indexOf Method (Int32)
indexOf Method (Int32, Int32)
indexOfWithBinarySearch Method
isEmpty Method
lastIndexOf Method
lastIndexOf Method (Int32)
lastIndexOf Method (Int32, Int32)
main Method
set Method
setSize Method
setWithExpansion Method
size Method
sort Method
toArray Method
MolAligner Class
MolAligner Members
MolAligner Constructor
MolAligner Constructor
MolAligner Constructor (Molecule, Molecule)
MolAligner Methods
align Method
align Method
align Method (Int32[])
calculate Method
getError Method
setPatternMolecule Method
setTargetMolecule Method
MolFilter Interface
MolFilter Members
MolFilter Methods
accept Method
MolHandler Class
MolHandler Members
MolHandler Constructor
MolHandler Constructor
MolHandler Constructor (Molecule)
MolHandler Constructor (Byte[])
MolHandler Constructor (String)
MolHandler Constructor (Byte[], Boolean)
MolHandler Constructor (String, Boolean)
MolHandler Methods
__<clinit> Method
addHydrogens Method
addHydrogensToAromaticHeteroAtoms Method
align Method
aromatize Method
aromatize Method
aromatize Method (Int32)
calcMolFormula Method
calcMolWeight Method
calcMolWeightInDouble Method
clean Method
containsHydrogens Method
generateFingerprintInBytes Method
generateFingerprintInInts Method
getAtomCount Method
getFingerprintInBytes Method
getFingerprintInInts Method
getHeavyAtomCount Method
getImplicitHCount Method
getMolecule Method
getNonHitBondEndpoints Method
getNonHitBonds Method
getQueryMode Method
isDaylightFormat Method
isPlainH Method
main Method
readFromVMN Method
removeHydrogens Method
removeHydrogensFromCarbons Method
setMolecule Method
setMolecule Method (Molecule)
setMolecule Method (Byte[])
setMolecule Method (String)
setMolecule_BNE Method
setMolecule_SNE Method
setQueryMode Method
toBinFormat Method
toFormat Method
UploadThread Class
UploadThread Members
UploadThread Constructor
UploadThread Methods
__<clinit> Method
getData Method
getDefaultFileName Method
getError Method
getFile Method
getFileContent Method
getFileName Method
getFileSize Method
getParameter Method
getParameterNames Method
getPercent Method
getSuccess Method
isFinished Method
run Method
setFinished Method
setParams Method
setParams Method (String, Int32, )
setParams Method (String, Int32, , String)
setParams Method (String, Int32, , String, String)
chemaxon.util.concurrent Namespace
ConcurrentProcessor Interface
ConcurrentProcessor Members
ConcurrentProcessor Methods
cleanup Method
cleanup Method
cleanup Method (Int64)
setMaxOutputQueueSize Method
setWorkerThreadCount Method
start Method
InputProducer Interface
WorkUnit Interface
WorkUnit Members
WorkUnit Methods
setInput Method
WorkUnitFactory Interface
WorkUnitFactory Members
WorkUnitFactory Methods
createWorkUnit Method
chemaxon.util.concurrent.marvin Namespace
CompositeInputProducer Class
CompositeInputProducer Members
CompositeInputProducer Constructor
CompositeInputProducer Constructor
CompositeInputProducer Constructor (InputProducer[])
CompositeInputProducer Methods
getNext Method
hasNext Method
setInputProducers Method
CompositeWorkUnit Class
CompositeWorkUnit Members
CompositeWorkUnit Constructor
CompositeWorkUnit Constructor
CompositeWorkUnit Constructor (WorkUnit[])
CompositeWorkUnit Methods
call Method
setInput Method
setWorkUnits Method
CompositeWorkUnitFactory Class
CompositeWorkUnitFactory Members
CompositeWorkUnitFactory Constructor
CompositeWorkUnitFactory Methods
createWorkUnit Method
MolInputProducer Class
MolInputProducer Members
MolInputProducer Constructor
MolInputProducer Constructor
MolInputProducer Constructor (MolImporter)
MolInputProducer Constructor (MolImporter[])
MolInputProducer Methods
close Method
getNext Method
hasNext Method
ReusableInputProducer Class
ReusableInputProducer Members
ReusableInputProducer Constructor
ReusableInputProducer Methods
getNext Method
hasNext Method
reuse Method
chemaxon.util.concurrent.processors Namespace
ConcurrentProcessors Class
ConcurrentProcessors Members
ConcurrentProcessors Fields
IN_INPUT_ORDER Field
SINGLE_THREADED Field
UNORDERED Field
ConcurrentProcessors Methods
create Method
create Method (Int32, InputProducer)
create Method (Int32, InputProducer, WorkUnitFactory)
createPooledWu Method
chemaxon.util.iterator Namespace
IteratorFactory Class
IteratorFactory Members
IteratorFactory Constructor
IteratorFactory Constructor (Molecule)
IteratorFactory Constructor (Molecule, Int32, Int32)
IteratorFactory Fields
INCLUDE_ALL_ATOMS Field
INCLUDE_ALL_BONDS Field
INCLUDE_CHEMICAL_ATOMS Field
INCLUDE_CHEMICAL_ATOMS_ONLY Field
REPLACE_COORDINATE_BONDS Field
SKIP_COORDINATE_BONDS Field
SKIP_COVALENT_BONDS Field
SKIP_EXPLICIT_H Field
SKIP_LONE_PAIR Field
SKIP_MULTICENTER Field
SKIP_PSEUDO_ATOM Field
IteratorFactory Methods
createAtomIterator Method
createAtomNeighbourIterator Method
createBondIterator Method
createBondNeighbourIterator Method
createRgComponentIterator Method
createRxnComponentIterator Method
isExcludedAtom Method
isExcludedBond Method
numberOfAtoms Method
numberOfBonds Method
numberOfNeighbours Method
IteratorFactory.AtomIterator Class
IteratorFactory.AtomIterator Members
IteratorFactory.AtomIterator Constructor
IteratorFactory.AtomIterator Methods
<bridge>next Method
hasNext Method
next Method
nextAtom Method
remove Method
IteratorFactory.AtomNeighbourIterator Class
IteratorFactory.AtomNeighbourIterator Members
IteratorFactory.AtomNeighbourIterator Constructor
IteratorFactory.AtomNeighbourIterator Methods
<bridge>next Method
next Method
nextAtom Method
IteratorFactory.BondIterator Class
IteratorFactory.BondIterator Members
IteratorFactory.BondIterator Constructor
IteratorFactory.BondIterator Methods
<bridge>next Method
hasNext Method
next Method
nextBond Method
remove Method
IteratorFactory.BondNeighbourIterator Class
IteratorFactory.BondNeighbourIterator Members
IteratorFactory.BondNeighbourIterator Constructor
IteratorFactory.BondNeighbourIterator Methods
<bridge>next Method
next Method
nextBond Method
IteratorFactory.NeighbourIterator Class
IteratorFactory.NeighbourIterator Members
IteratorFactory.NeighbourIterator Constructor
IteratorFactory.NeighbourIterator Methods
hasNext Method
next Method
remove Method
IteratorFactory.RgComponentIterator Class
IteratorFactory.RgComponentIterator Members
IteratorFactory.RgComponentIterator Constructor
IteratorFactory.RgComponentIterator Methods
<bridge>next Method
hasNext Method
next Method
nextComponent Method
remove Method
IteratorFactory.RxnComponentIterator Class
IteratorFactory.RxnComponentIterator Members
IteratorFactory.RxnComponentIterator Constructor
IteratorFactory.RxnComponentIterator Methods
<bridge>next Method
hasNext Method
next Method
nextComponent Method
remove Method
MoleculeIterator Interface
MoleculeIterator Members
MoleculeIterator Methods
estimateProgress Method
getThrowable Method
hasNext Method
next Method
MoleculeIteratorFactory Class
MoleculeIteratorFactory Members
MoleculeIteratorFactory Constructor
MoleculeIteratorFactory Methods
createMoleculeIterator Method
createMoleculeIterator Method (Molecule[])
createMoleculeIterator Method ()
getMoleculeIterator Method
getMoleculeIterators Method
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