Molecule (JChem API documentation (c)1998-2008 ChemAxon Ltd.)

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chemaxon.struc
Class Molecule

java.lang.Object
  chemaxon.struc.CGraph
      chemaxon.struc.MoleculeGraph
          chemaxon.struc.Molecule

All Implemented Interfaces:: MTransformable, chemaxon.struc.ReadableMolecule, StereoConstants, java.io.Serializable, java.lang.Cloneable

Direct Known Subclasses:: RgMolecule, RxnMolecule

public class Molecule
extends MoleculeGraph
extends MoleculeGraph

Molecule class. A MoleculeGraph that may also contain S-groups.

Version:: 5.1.2, 09/11/2008
Author:: Peter Csizmadia, Andras Volford, Szabolcs Csepregi, Erika Biro
See Also:: Serialized Form

Field Summary
`static int`	`DEFAULT_UNGROUP` Do not ungroup and do not expand S-group's children.
`static int`	`RECURSIVE_UNGROUP` Ungroup and expand (if possible) the child S-groups.
`static int`	`RMCLEANUP_FROMSGROUPS` Remove atoms from S-groups.
`static int`	`RMCLEANUP_SGROUPATOMS` Remove S-groups of removed superatoms.
`protected static int`	`RMSG_DEFAULT` Remove S-group's children and remove S-group from its parent.
`protected static int`	`RMSG_KEEP_CHILDREN` Do not remove S-group's children.
`protected static int`	`RMSG_KEEP_MULTICENTER` Do not remove central atom of multicenter S-groups.
`protected static int`	`RMSG_KEEP_PARENT` Do not remove S-group from its parent.

Fields inherited from class chemaxon.struc.MoleculeGraph
`AROM_BASIC, AROM_CHEMAXON, AROM_DAYLIGHT, AROM_GENERAL, CACHE_REMOVE_AROMATAMODULE, CACHE_REMOVE_GRINVMODULE, CACHE_REMOVE_PARITYMODULE, CACHE_REMOVE_SSSRMODULE, DIM_MASK, GRINV_DONT_STORE, GRINV_NOHYDROGEN, GRINV_OLDSTEREO, GRINV_STEREO, GRINV_USEMAPS, GRINV_VALUE_OPTIONS, INVALID_LINKNODE_MESSAGE, MIN_RING_SIZE_FOR_TRANS_DB, OMIT_POSTCLEAN, orix, oriy, oriz, propertyContainer, RMCLEANUP_MOBJECT, RMCLEANUP_PARENTDOC, RMCLEANUP_STEREO, useOnlyFirstAtomInStereoCalculation`

Fields inherited from class chemaxon.struc.MoleculeGraph

AROM_BASIC, AROM_CHEMAXON, AROM_DAYLIGHT, AROM_GENERAL, CACHE_REMOVE_AROMATAMODULE, CACHE_REMOVE_GRINVMODULE, CACHE_REMOVE_PARITYMODULE, CACHE_REMOVE_SSSRMODULE, DIM_MASK, GRINV_DONT_STORE, GRINV_NOHYDROGEN, GRINV_OLDSTEREO, GRINV_STEREO, GRINV_USEMAPS, GRINV_VALUE_OPTIONS, INVALID_LINKNODE_MESSAGE, MIN_RING_SIZE_FOR_TRANS_DB, OMIT_POSTCLEAN, orix, oriy, oriz, propertyContainer, RMCLEANUP_MOBJECT, RMCLEANUP_PARENTDOC, RMCLEANUP_STEREO, useOnlyFirstAtomInStereoCalculation

Fields inherited from class chemaxon.struc.CGraph
`btab, CACHE_REMOVE_ALL, CACHE_REMOVE_CACHEMEMORY, cacheMemory, cssr, ctab, edgeCount, edges, fragIds, grinv, grinvCC, grinvOptions, INITIAL_CAPACITY, nFrags, nGrinv, nodeCount, nodes, parentGraph, RMCLEANUP_ALL, RMCLEANUP_EDGES, RMCLEANUP_FIXCOMPONENT, RMCLEANUP_NONE, sssr, sssr2idx, sssrl2idx, superGraph`

Fields inherited from interface chemaxon.struc.ReadableMolecule
`HS_S, HS_SP, HS_SP2, HS_SP3, HS_UNKNOWN`

Fields inherited from interface chemaxon.struc.StereoConstants
`ATOMSTEREO_EITHER, ATOMSTEREO_MASK, ATOMSTEREO_NONE, ATOMSTEREO_SPECIFIC, CHIRALITY_MASK, CHIRALITY_R, CHIRALITY_S, CHIRALITYSUPPORT_ALL, CHIRALITYSUPPORT_NONE, CHIRALITYSUPPORT_SELECTED, CIS, CTUMASK, CTUNKNOWN, CTUNSPEC, DBS_ALL, DBS_MARKED, DBS_NONE, PARITY_EITHER, PARITY_EVEN, PARITY_MASK, PARITY_ODD, PARITY_UNSPEC, STGRP_ABS, STGRP_AND, STGRP_NONE, STGRP_OR, TRANS`

Constructor Summary
`Molecule()` Construct a molecule.
`Molecule(Molecule p, int na, int nb)` Construct a molecule or fragment with the specified number of atoms and bonds.
`Molecule(Molecule p, MolAtom a)` Construct a graph consisting of a single vertex (atom).
`Molecule(Molecule p, MolBond b)` Construct a graph consisting of a single edge (bond).

Method Summary
`protected void`	`addNode0(CNode node)` Adds a node.
`protected void`	`addSgroup(Sgroup sg, boolean setparent)` Adds an S-group to this object and its parent.
`protected void`	`addSgroupClones(Molecule origparentm, Molecule origm, Molecule newm)` Adds the S-groups of a child molecule clone to the new parent molecule clone.
`protected void`	`addSgroupsOf(Molecule m)` Adds S-groups to this object and its parent.
`void`	`aromatize(int method)` Aromatize molecule.
`double`	`bondlength()` Calculate the regular bond length for the unified structure.
`boolean`	`canBeReactionComponent()` Tests whether an object of this class can be a reaction component.
`void`	`checkConsistency()` Checks the internal consistency of the structure.
`protected void`	`checkSgroupConsistency()` Checks the internal consisitency of S-groups.
`boolean`	`clean(int dim, java.lang.String opts, MProgressMonitor pmon)` Calculates atom coordinates.
`protected void`	`cleanSgroups(int dim, java.lang.String opts)` Clean S-groups.
`void`	`clear()` Clears the molecule.
`void`	`clearExtraLabels()` Clears extra atom labels.
`void`	`clearForImport(java.lang.String format)` Initializes molecule for import.
`void`	`clearProperties()` Clears RDfile/SDfile properties.
`java.lang.Object`	`clone()` Makes an identical copy of the molecule.
`void`	`clonecopy(CGraph g)` Makes another molecule identical to this one.
`void`	`clonecopy(int[] iatoms, MoleculeGraph g)` Copies the specified atoms and bonds of this graph to another one.
`protected void`	`clonecopyWithoutSgroups(Molecule m)` Copies the all the contents except the S-groups into another molecule object.
`void`	`clonelesscopy(CGraph g)` Copies to selection.
`Molecule`	`cloneMolecule()` Makes an identical copy of the molecule.
`Molecule`	`cloneMoleculeWithDocument()` Makes an identical copy of the molecule and its document.
`boolean`	`contains(CNode node)` Checks if the graph contains the specified node.
`protected void`	`contractExpandedSgroups()`
`boolean`	`contractSgroups()` Contracts all S-groups.
`Molecule[]`	`convertToFrags()` Converts this molecule to its disconnected fragments.
`int`	`countExpandableContractableSgroups()` Counts the expandable and contractable S-groups.
`int`	`countOrderedComponentSgroups()` Counts the ordered component S-groups.
`boolean`	`dearomatize()` Dearomatize molecule.
`void`	`draw(java.awt.Graphics g, java.lang.String opts)` Deprecated. As of release 4.1.6, replaced by chemaxon.marvin.util.MPainterUtil.draw(Molecule,Graphics,String)
`void`	`endReuse(int n)` End reusing atoms.
`boolean`	`expandSgroups()` Expands all S-groups.
`boolean`	`expandSgroups(int opts)` Expands all S-groups.
`byte[]`	`exportToBinFormat(java.lang.String fmt)` Creates a binary representation of the molecule.
`java.lang.String`	`exportToFormat(java.lang.String fmt)` Creates a string representation of the molecule.
`java.lang.Object`	`exportToObject(java.lang.String fmt)` Creates a String, byte[] array or Image representation of the molecule.
`protected void`	`fillSelectionMolecule(SelectionMolecule s)` Adds all atoms and bonds to the specified molecule.
`Sgroup[]`	`findAllSgroupContaining(MolAtom a)` Finds the smallest S-groups containing the specified node.
`chemaxon.struc.sgroup.MulticenterSgroup`	`findContainingMulticenterSgroup(MolAtom atom)` Gets the containing multicenter S-group of a multicenter atom.
`Sgroup`	`findContractableSgroup()` Finds an expanded residue.
`Sgroup`	`findExpandableSgroup()` Finds a contracted residue.
`SelectionMolecule[]`	`findFrags()` Determines the disconnected fragments and puts them into an array.
`CGraph[]`	`findFrags(java.lang.Class cl)` Determines the disconnected fragments and puts them into an array.
`Sgroup`	`findSgroupContaining(MolAtom a)` Finds the largest S-group that contains the specified node.
`Sgroup`	`findSgroupOf(MolAtom a)` Finds the smallest S-group related to the specified node.
`Sgroup`	`findSmallestSgroupContaining(MolAtom a)` Finds the smallest S-group that contains the specified node.
`protected boolean`	`fixSelfReferringProperty(MProp prop)` Fix a property containing reference to the molecule.
`java.lang.String`	`getComment()` Gets the comment.
`long`	`getEndPosition()` Gets the end position of this molecule in the input file.
`protected SelectionMolecule`	`getGraphUnionAsSelection()` Gets a selection molecule containing all the atoms and bonds.
`MolImageSize`	`getImageSize(java.lang.String fmt)` Gets size information of an image created with the specified format string.
`java.lang.String`	`getInputFormat()` Gets the input file format.
`protected Molecule`	`getMostSimplifiedMolecule()` Gets the simplified molecule object even if there is a parent document with other objects.
`java.lang.String`	`getName()` Gets the molecule name.
`java.lang.String`	`getProperty(java.lang.String key)` Gets an RDfile/SDfile property.
`int`	`getPropertyCount()` Gets the total number of RDfile/SDfile properties.
`java.lang.String`	`getPropertyKey(int i)` Gets an RDfile/SDfile property key.
`java.util.Enumeration`	`getPropertyKeys()` Deprecated. as of Marvin 4.1, replaced by `properties()`.`getKeys()`
`java.lang.Object`	`getPropertyObject(java.lang.String key)` Gets an RDfile/SDfile property object.
`Sgroup`	`getSgroup(int i)` Gets an S-group.
`Sgroup[]`	`getSgroupArray()` Gets the array of S-groups.
`int`	`getSgroupCount()` Gets the number of S-groups.
`MolAtom[]`	`getSgroupLigands()` Gets the S-group's ligands if the structure represents an S-group.
`Molecule`	`getSimplifiedMolecule()` Gets the simplified molecule object.
`Sgroup[]`	`getSortedSgroups()` Gets the sorted S-groups in parent-child order.
`long`	`getStartPosition()` Gets the starting position of this molecule in the input file.
`double[]`	`getVisibleCoords(MolAtom ma)` Returns the coordinates of the given atom (contained in the molecule).
`int`	`indexOf(Sgroup sg)` Gets the array index of an S-group.
`boolean`	`isEmpty()` Tests whether the molecule is empty.
`boolean`	`isExpandable(int opts)` Tests if the molecule is expandable with the specified options.
`boolean`	`isGUIContracted()` Tests if the molecule has a GUI-contracted S-group or not.
`protected boolean`	`isPeptideChain(Molecule mol)`
`boolean`	`isReaction()` Checks if the structure represents a reaction or not.
`boolean`	`isSgroup()` Checks if the structure represents an S-group or not.
`protected void`	`makeBiopolymerSnake(Molecule mol)` If there is a chain with all the members being SuperatomSgroups, the method arranges them into a "snake" form to fit into the canvas (intead of being linear).
`protected void`	`makeItSimilar(CGraph g)` Copies some properties of this molecule to the other one specified as argument.
`void`	`mergeNodes(CNode that, CNode node)` Merges bonds of an atom with another atom, then add the atom to the molecule.
`CGraph`	`newInstance()` Creates a new Molecule object.
`SelectionMolecule`	`newSelectionMolecule()` Creates a new SelectionMolecule object appropriate for storing selection from this molecule.
`boolean`	`partialClean(int dim, int[] fixed, java.lang.String opts)` Calculates atom coordinates by using fixed atoms.
`protected void`	`postClean()` Operations performed after cleaning.
`protected void`	`regenFragIds()` Searches the disconnected fragments.
`void`	`removeAll()` Removes all the nodes and edges.
`void`	`removeAllEdges()` Removes all edges.
`protected void`	`removeAllSgroups()` Removes all S-groups.
`protected void`	`removeEdge(CEdge edge, int cleanupFlags)` Removes an edge by reference.
`protected void`	`removeEdge(int i, int cleanupFlags)` Removes an edge.
`void`	`removeNode(CNode node, int cleanupFlags)` Removes a node and its edges.
`void`	`removeNode(int i, int cleanupFlags)` Remove a node and its edges.
`protected void`	`removeSgroupFromList(Sgroup sg)` Removes an S-group from the sgroupVector.
`protected void`	`removeSgroupsOf(Molecule m)` Removes S-groups from this object and its parent.
`protected void`	`removeSgroupsOf(Molecule m, int rmflags)` Removes S-groups that are contained in a given molecule but not contained in another molecule.
`protected void`	`reparentSgroups(Molecule p)` Change parents of all S-groups in this molecule.
`static java.lang.String`	`residueSymbolOf(int id)` Gets the name of a residue.
`static int`	`residueTypeOf(java.lang.String name)` Gets the residue identifier for a residue name.
`MolAtom`	`reuseAtom(int z, int i)` Reuse an atom or create a new one.
`void`	`setComment(java.lang.String s)` Sets the comment.
`void`	`setDim(int d)` Sets the dimension.
`void`	`setEndPosition(long off)` Sets the end position of this molecule in the input file.
`void`	`setGUIContracted(boolean v)` Contracts some S-groups to use in GUI or expands for any other use.
`void`	`setInputFormat(java.lang.String format)` Sets the input file format.
`void`	`setName(java.lang.String s)` Sets the molecule name.
`protected void`	`setNode0(int i, CNode node)` Sets the node at the specified index.
`void`	`setProperty(java.lang.String key, java.lang.String value)` Sets an RDfile/SDfile property.
`void`	`setPropertyObject(java.lang.String key, java.lang.Object value)` Sets an RDfile/SDfile property object.
`void`	`setSgroupParent(MolAtom a, Sgroup sg, boolean set)` Sets or unsets an S-group as a parent of an atom.
`void`	`setStartPosition(long off)` Sets the starting position of this molecule in the input file.
`void`	`sortSgroupXBonds()` Sorts superatom S-group crossing bonds in attachment point number order.
`byte[]`	`toBinFormat(java.lang.String fmt)` Creates a binary representation of the molecule.
`java.lang.String`	`toFormat(java.lang.String fmt)` Creates a string representation of the molecule.
`java.lang.Object`	`toObject(java.lang.String fmt)` Creates a String, byte[] array or Image representation of the molecule.
`void`	`transform(CTransform3D t, boolean incg)` Apply a transformation matrix to the atomic coordinates and Data Sgroup coordinates.
`boolean`	`ungroupSgroup(int i)` Ungroups the specified S-group and expands it if it is an Expandable S-group.
`boolean`	`ungroupSgroup(int i, int opts)` Ungroups the specified S-group and expands it if it is an Expandable S-group.
`boolean`	`ungroupSgroup(Sgroup sg)` Expand and ungroup the specified S-group.
`boolean`	`ungroupSgroup(Sgroup sg, int opts)` Expand and ungroup the specified S-group.
`boolean`	`ungroupSgroups()` Expand and ungroup all S-groups.

Methods inherited from class chemaxon.struc.MoleculeGraph
addAtomsAndBondsTo, addExplicitHydrogens, addExplicitHydrogens, addExplicitLonePairs, adjustMultiChiralFlag, aromatize, aromatize, arrangeComponents, calcCenter, calcCenter, calcDehydrogenizedGrinv, calcHeight, calcHybridization, calcOutRect, calcOutRect, calcOutRectCenter, calcOutRectCenter, calcWidth, canBeCT, canBeCT, clean, clearCachedInfo, clonecopyCGraphWithoutSgroups, contains, createBHtab, createCHtab, createDehydrogenizedReadOnlyGraph, findAtomClone, fuse0, getAromaticAndAliphaticRings, getAromrings, getAromrings, getAtom, getAtomArray, getAtomCount, getBond, getBondArray, getBondCount, getCharge, getChirality, getDesiredLength, getDesiredLength, getDim, getDocument, getDocumentForChild, getEdgeArray, getEdgeVector, getExactMass, getExplicitHcount, getExplicitLonePairCount, getFlags, getFormula, getGraphUnion, getGrinv, getGrinv, getGrinv, getGrinvOptions, getHybridizationState, getImplicitHcount, getLocalChirality, getLocalParity, getLocation, getLonePairCount, getMass, getMassno, getNeighbor, getNeighborCount, getNodeVector, getNonAromrings, getNonAromrings, getParentDocument, getParity, getPoints, getRadical, getSSSRBondSet, getSSSRBondSetInLong, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getSubGraphCount, getSubGraphs, getSubGraphs, getTotalCharge, hasAtomSet, hasBondSet, hasExplicitLonePairs, hasExtraLabelSet, hasImplicitH, hasSelfReferringProperty, hasValenceError, hydrogenize, implicitizeHydrogens, implicitizeHydrogens, implicitizeHydrogens, isAbsStereo, isAtom, isBond, isMultiChiral, isOnlyFirstAtomInStereoCalculation, isQuery, isRingBond, isSelfReference, isSimilarTo, isValidLinkNode, moveTo, partialClean, properties, qpropCheck, removeExplicitLonePairs, restoreCache, revalidateCoordDependentProps, saveCache, setAbsStereo, setAtomSetSeqs, setBondSetSeqs, setChirality, setEdge, setFlags, setGrinvOptions, setLinkNodeDefaultOuters, setLocalParity, setLocation, setParity, setParity, setParity, setSetSeqs, stereoClean, sumConservedQuantities, toString, transform, updateDim, useOnlyFirstAtomInStereoCalculation, valenceCheck, valenceCheck

Methods inherited from class chemaxon.struc.MoleculeGraph

addAtomsAndBondsTo, addExplicitHydrogens, addExplicitHydrogens, addExplicitLonePairs, adjustMultiChiralFlag, aromatize, aromatize, arrangeComponents, calcCenter, calcCenter, calcDehydrogenizedGrinv, calcHeight, calcHybridization, calcOutRect, calcOutRect, calcOutRectCenter, calcOutRectCenter, calcWidth, canBeCT, canBeCT, clean, clearCachedInfo, clonecopyCGraphWithoutSgroups, contains, createBHtab, createCHtab, createDehydrogenizedReadOnlyGraph, findAtomClone, fuse0, getAromaticAndAliphaticRings, getAromrings, getAromrings, getAtom, getAtomArray, getAtomCount, getBond, getBondArray, getBondCount, getCharge, getChirality, getDesiredLength, getDesiredLength, getDim, getDocument, getDocumentForChild, getEdgeArray, getEdgeVector, getExactMass, getExplicitHcount, getExplicitLonePairCount, getFlags, getFormula, getGraphUnion, getGrinv, getGrinv, getGrinv, getGrinvOptions, getHybridizationState, getImplicitHcount, getLocalChirality, getLocalParity, getLocation, getLonePairCount, getMass, getMassno, getNeighbor, getNeighborCount, getNodeVector, getNonAromrings, getNonAromrings, getParentDocument, getParity, getPoints, getRadical, getSSSRBondSet, getSSSRBondSetInLong, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getSubGraphCount, getSubGraphs, getSubGraphs, getTotalCharge, hasAtomSet, hasBondSet, hasExplicitLonePairs, hasExtraLabelSet, hasImplicitH, hasSelfReferringProperty, hasValenceError, hydrogenize, implicitizeHydrogens, implicitizeHydrogens, implicitizeHydrogens, isAbsStereo, isAtom, isBond, isMultiChiral, isOnlyFirstAtomInStereoCalculation, isQuery, isRingBond, isSelfReference, isSimilarTo, isValidLinkNode, moveTo, partialClean, properties, qpropCheck, removeExplicitLonePairs, restoreCache, revalidateCoordDependentProps, saveCache, setAbsStereo, setAtomSetSeqs, setBondSetSeqs, setChirality, setEdge, setFlags, setGrinvOptions, setLinkNodeDefaultOuters, setLocalParity, setLocation, setParity, setParity, setParity, setSetSeqs, stereoClean, sumConservedQuantities, toString, transform, updateDim, useOnlyFirstAtomInStereoCalculation, valenceCheck, valenceCheck

Methods inherited from class chemaxon.struc.CGraph
add, add, addEdge0, addEdgeWithoutChangingIt, addNodeWithoutChangingIt, checkEdgeConsistency, contains, findBasicFrags, findComponentIds, findComponentIds, findEdge, findFrag, findFragById, findInArray, findNode, fuse, fuse, fuse0, getBtab, getCSSR, getCtab, getEdge, getEdgeCount, getEdgeList, getForefather, getFragCount, getFragIds, getGrinv, getGrinvCC, getLock, getNode, getNodeCount, getParent, getSmallestRingSizeForIdx, getSSSR, getSSSREdges, getSSSRIdxesForAtoms, incGrinvCC, incGrinvCCOnly, indexOf, indexOf, insertEdge, insertEdgeInOrder, insertNode, insertNullEdges, insertNullNodes, isGrinvCCValid, isolate, isolate, isRealNodeParent, isRing, isSymmetric, mergeFrags, pack, regenCtabs, regenEdges, removeEdge, removeEdge, removeIsolatedEdges, removeIsolatedNodes, removeNode, removeNode, replaceEdge, resetCtab, resetGrinvInParents, setGrinvCC, setNode, sortEdgesAccordingTo

Methods inherited from class chemaxon.struc.CGraph

add, add, addEdge0, addEdgeWithoutChangingIt, addNodeWithoutChangingIt, checkEdgeConsistency, contains, findBasicFrags, findComponentIds, findComponentIds, findEdge, findFrag, findFragById, findInArray, findNode, fuse, fuse, fuse0, getBtab, getCSSR, getCtab, getEdge, getEdgeCount, getEdgeList, getForefather, getFragCount, getFragIds, getGrinv, getGrinvCC, getLock, getNode, getNodeCount, getParent, getSmallestRingSizeForIdx, getSSSR, getSSSREdges, getSSSRIdxesForAtoms, incGrinvCC, incGrinvCCOnly, indexOf, indexOf, insertEdge, insertEdgeInOrder, insertNode, insertNullEdges, insertNullNodes, isGrinvCCValid, isolate, isolate, isRealNodeParent, isRing, isSymmetric, mergeFrags, pack, regenCtabs, regenEdges, removeEdge, removeEdge, removeIsolatedEdges, removeIsolatedNodes, removeNode, removeNode, replaceEdge, resetCtab, resetGrinvInParents, setGrinvCC, setNode, sortEdgesAccordingTo

Methods inherited from class java.lang.Object
`equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait`

Field Detail

RMCLEANUP_SGROUPATOMS

public static final int RMCLEANUP_SGROUPATOMS

Remove S-groups of removed superatoms.

Since:: Marvin 4.1, 07/27/2006
See Also:: removeNode(CNode, int), removeNode(int, int), CGraph.RMCLEANUP_ALL, Constant Field Values

RMCLEANUP_FROMSGROUPS

public static final int RMCLEANUP_FROMSGROUPS

Remove atoms from S-groups.

Since:: Marvin 4.1, 07/27/2006
See Also:: removeNode(CNode, int), removeNode(int, int), CGraph.RMCLEANUP_ALL, Constant Field Values

RMSG_DEFAULT

protected static final int RMSG_DEFAULT

Remove S-group's children and remove S-group from its parent.

Since:: Marvin 5.0, 03/27/2007
See Also:: Constant Field Values

RMSG_KEEP_CHILDREN

protected static final int RMSG_KEEP_CHILDREN

Do not remove S-group's children.

Since:: Marvin 5.0, 03/27/2007
See Also:: Constant Field Values

RMSG_KEEP_PARENT

protected static final int RMSG_KEEP_PARENT

Do not remove S-group from its parent.

Since:: Marvin 5.0, 03/27/2007
See Also:: Constant Field Values

RMSG_KEEP_MULTICENTER

protected static final int RMSG_KEEP_MULTICENTER

Do not remove central atom of multicenter S-groups.

Since:: Marvin 5.0, 10/22/2007
See Also:: Constant Field Values

RECURSIVE_UNGROUP

public static final int RECURSIVE_UNGROUP

Ungroup and expand (if possible) the child S-groups.

Since:: Marvin 5.1, 06/05/2008
See Also:: Constant Field Values

DEFAULT_UNGROUP

public static final int DEFAULT_UNGROUP

Do not ungroup and do not expand S-group's children.

Since:: Marvin 5.1, 06/05/2008
See Also:: Constant Field Values

Constructor Detail

Molecule

public Molecule(Molecule p,
                int na,
                int nb)

Construct a molecule or fragment with the specified number of atoms and bonds.

Parameters:: p - the molecule that contains the created fragment; na - no reallocation needed until the number of atoms is less than this value; nb - no reallocation needed until the number of bonds is less than this value

Molecule

public Molecule(Molecule p,
                MolAtom a)

Construct a graph consisting of a single vertex (atom).

Parameters:: p - the parent structure; a - the atom

Molecule

public Molecule(Molecule p,
                MolBond b)

Construct a graph consisting of a single edge (bond).

Parameters:: p - the parent structure; b - the bond

Molecule

public Molecule()

Construct a molecule.

Method Detail

setDim

public void setDim(int d)

Sets the dimension.

Overrides:: setDim in class MoleculeGraph

Parameters:: d - 0, 2, or 3
See Also:: MoleculeGraph.getFlags()

clear

public void clear()

Clears the molecule.

Overrides:: clear in class MoleculeGraph

See Also:: MoleculeGraph.clearForImport(java.lang.String), CGraph.nodes

clearForImport

public void clearForImport(java.lang.String format)

Initializes molecule for import.

Overrides:: clearForImport in class MoleculeGraph

Parameters:: format - input file format
Since:: Marvin 2.7
See Also:: CGraph.edges, MoleculeGraph.orix, MoleculeGraph.oriy, MoleculeGraph.oriz, MoleculeGraph.setFlags(int)

getStartPosition

public long getStartPosition()

Gets the starting position of this molecule in the input file.

Returns:: the starting position

setStartPosition

public void setStartPosition(long off)

Sets the starting position of this molecule in the input file.

Parameters:: off - the starting position

getEndPosition

public long getEndPosition()

Gets the end position of this molecule in the input file.

Returns:: the end position

setEndPosition

public void setEndPosition(long off)

Sets the end position of this molecule in the input file.

Parameters:: off - the end position

getName

public java.lang.String getName()

Gets the molecule name.

Specified by:: getName in interface chemaxon.struc.ReadableMolecule
Overrides:: getName in class MoleculeGraph

Returns:: the molecule name or an empty string
Since:: Marvin 2.7

setName

public void setName(java.lang.String s)

Sets the molecule name.

Parameters:: s - the molecule name, empty string or null (null is equivalent to empty string)
Since:: Marvin 2.7

getComment

public final java.lang.String getComment()

Gets the comment.

Returns:: the comment or empty string
Since:: Marvin 2.9

setComment

public final void setComment(java.lang.String s)

Sets the comment.

Parameters:: s - the comment, empty string or null (null is equivalent to empty string)
Since:: Marvin 2.9

getInputFormat

public final java.lang.String getInputFormat()

Gets the input file format. Set by the import module if the molecule is from a file.

Returns:: "mol", "csmol", "sdf", "cssdf", "rdf", "csrdf", "smiles", "sybyl", "mol2", "pdb", "xyz" or "cube" or "inchi"
Since:: Marvin 2.7

setInputFormat

public void setInputFormat(java.lang.String format)

Sets the input file format.

Parameters:: format - the input format
Since:: Marvin 2.7
See Also:: getInputFormat()

clearProperties

public void clearProperties()

Clears RDfile/SDfile properties.

getPropertyCount

public int getPropertyCount()

Gets the total number of RDfile/SDfile properties.

Returns:: number of properties
Since:: Marvin 2.7

getPropertyKeys

public java.util.Enumeration getPropertyKeys()

Deprecated. as of Marvin 4.1, replaced by properties().getKeys()

getPropertyKey

public java.lang.String getPropertyKey(int i)

Gets an RDfile/SDfile property key.

Parameters:: i - property index
Returns:: the property name
Since:: Marvin 2.7

getProperty

public java.lang.String getProperty(java.lang.String key)

Gets an RDfile/SDfile property.

Parameters:: key - property name
Returns:: the value of the property, or null if the key is not found

getPropertyObject

public java.lang.Object getPropertyObject(java.lang.String key)

Gets an RDfile/SDfile property object.

Parameters:: key - property name
Returns:: the value of the property, or null if the key is not found
Since:: Marvin 3.1.2

setProperty

public void setProperty(java.lang.String key,
                        java.lang.String value)

Sets an RDfile/SDfile property. Setting null value removes the property.

Parameters:: key - the property name; value - the value or null

setPropertyObject

public void setPropertyObject(java.lang.String key,
                              java.lang.Object value)

Sets an RDfile/SDfile property object. Setting null value removes the property.

Parameters:: key - the property name; value - the value or null
Since:: Marvin 3.1.2

residueTypeOf

public static int residueTypeOf(java.lang.String name)

Gets the residue identifier for a residue name.

Parameters:: name - residue name
Returns:: the residue type

residueSymbolOf

public static java.lang.String residueSymbolOf(int id)

Gets the name of a residue.

Parameters:: id - the residue identifier
Returns:: the residue symbol

setNode0

protected void setNode0(int i,
                        CNode node)

Sets the node at the specified index. Overridden because Sgroups must be set correctly in RgMolecule.clone() and RxnMolecule.clone().

Overrides:: setNode0 in class MoleculeGraph

Parameters:: i - the atom index; node - the atom

removeNode

public void removeNode(CNode node,
                       int cleanupFlags)

Removes a node and its edges. This method is for internal use only. Use CGraph.removeNode(CNode) instead unless you are sure what you are doing.

Overrides:: removeNode in class MoleculeGraph

Parameters:: node - the node; cleanupFlags - extra clean-up methods
Since:: Marvin 3.1
See Also:: CGraph.RMCLEANUP_NONE, CGraph.RMCLEANUP_ALL, CGraph.RMCLEANUP_EDGES, MoleculeGraph.RMCLEANUP_STEREO

removeNode

public void removeNode(int i,
                       int cleanupFlags)

Remove a node and its edges. This method is for internal use only. Use CGraph.removeNode(CNode) instead unless you are sure what you are doing.

Overrides:: removeNode in class MoleculeGraph

Parameters:: i - the node index; cleanupFlags - extra clean-up methods
Since:: Marvin 3.1
See Also:: CGraph.RMCLEANUP_NONE, CGraph.RMCLEANUP_ALL, CGraph.RMCLEANUP_EDGES, MoleculeGraph.RMCLEANUP_STEREO

removeEdge

protected void removeEdge(CEdge edge,
                          int cleanupFlags)

Removes an edge by reference.

Overrides:: removeEdge in class CGraph

Parameters:: edge - the edge; cleanupFlags - extra clean-up methods
Since:: Marvin 3.1
See Also:: CGraph.RMCLEANUP_NONE, CGraph.RMCLEANUP_ALL, CGraph.RMCLEANUP_EDGES, MoleculeGraph.RMCLEANUP_STEREO

removeEdge

protected void removeEdge(int i,
                          int cleanupFlags)

Removes an edge.

Overrides:: removeEdge in class MoleculeGraph

Parameters:: i - the edge index; cleanupFlags - extra clean-up methods
Since:: Marvin 3.1
See Also:: CGraph.RMCLEANUP_NONE, CGraph.RMCLEANUP_ALL, CGraph.RMCLEANUP_EDGES, MoleculeGraph.RMCLEANUP_STEREO

removeAllEdges

public void removeAllEdges()

Removes all edges.

Overrides:: removeAllEdges in class CGraph

removeAll

public void removeAll()

Removes all the nodes and edges.

Overrides:: removeAll in class CGraph

isEmpty

public boolean isEmpty()

Tests whether the molecule is empty.

Overrides:: isEmpty in class CGraph

Returns:: true if the graph does not contain any nodes, edges or non-empty S-groups, false otherwise
Since:: Marvin 4.1.1, 09/06/2006

clean

public boolean clean(int dim,
                     java.lang.String opts,
                     MProgressMonitor pmon)

Calculates atom coordinates.

Overrides:: clean in class MoleculeGraph

Parameters:: dim - dimensions; opts - cleaning options or null; pmon - progress observer object or null
Returns:: true for success, false if an error occured
Throws:: java.lang.SecurityException - cannot load module because of a security problem (firewall)
See Also:: MoleculeGraph.clean(int, java.lang.String)

cleanSgroups

protected void cleanSgroups(int dim,
                            java.lang.String opts)

Clean S-groups.

Parameters:: dim - dimensions; opts - cleaning options or null
Since:: Marvin 4.1, 07/31/2006

contractExpandedSgroups

protected void contractExpandedSgroups()

isPeptideChain

protected boolean isPeptideChain(Molecule mol)

postClean

protected void postClean()

Operations performed after cleaning. Creates a peptide snake if needed

Since:: Marvin 4.1, 07/31/2006

makeBiopolymerSnake

protected void makeBiopolymerSnake(Molecule mol)

If there is a chain with all the members being SuperatomSgroups, the method arranges them into a "snake" form to fit into the canvas (intead of being linear). We are assuming that it is already checked that all the entries are SuperatomSgroups.

aromatize

public void aromatize(int method)

Aromatize molecule.

Overrides:: aromatize in class MoleculeGraph

Parameters:: method - specifies the algorithm for aromatization.
Throws:: java.lang.SecurityException - cannot load module because of a security problem (firewall)
See Also:: MoleculeGraph.AROM_BASIC, MoleculeGraph.AROM_GENERAL, Document about aromatization

dearomatize

public boolean dearomatize()

Dearomatize molecule.

Overrides:: dearomatize in class MoleculeGraph

Returns:: true if success, else false.
Throws:: java.lang.SecurityException - cannot load module because of a security problem (firewall)

clonecopy

public void clonecopy(CGraph g)

Makes another molecule identical to this one.

Overrides:: clonecopy in class MoleculeGraph

Parameters:: g - the target molecule

fixSelfReferringProperty

protected boolean fixSelfReferringProperty(MProp prop)

Fix a property containing reference to the molecule. Called from clonelesscopy().

Overrides:: fixSelfReferringProperty in class MoleculeGraph

Parameters:: prop - the property
Since:: Marvin 4.1.6, 02/14/2007
See Also:: MoleculeGraph.clonecopy(CGraph)

addSgroupClones

protected final void addSgroupClones(Molecule origparentm,
                                     Molecule origm,
                                     Molecule newm)

Adds the S-groups of a child molecule clone to the new parent molecule clone.

Parameters:: origparentm - the original parent molecule; origm - the original child molecule; newm - the new child molecule (clone of the original)
Since:: Marvin 3.4

clonecopy

public void clonecopy(int[] iatoms,
                      MoleculeGraph g)

Copies the specified atoms and bonds of this graph to another one.

Overrides:: clonecopy in class MoleculeGraph

Parameters:: iatoms - array of node indices to copy or null; g - the target graph
Since:: Marvin 5.0.2, 03/11/2008

clonecopyWithoutSgroups

protected void clonecopyWithoutSgroups(Molecule m)

Copies the all the contents except the S-groups into another molecule object.

Parameters:: m - the target molecule
Since:: Marvin 3.4

clonelesscopy

public void clonelesscopy(CGraph g)

Copies to selection. Makes another molecule identical to this one, but does not clone atoms, bonds, and the properties.

Overrides:: clonelesscopy in class MoleculeGraph

Parameters:: g - the target molecule object (the selection)

cloneMoleculeWithDocument

public Molecule cloneMoleculeWithDocument()

Makes an identical copy of the molecule and its document. Copies non-molecular data: graphics objects, electron flows, text boxes.

Returns:: the copy
Since:: Marvin 4.1, 01/16/2006

cloneMolecule

public Molecule cloneMolecule()

Makes an identical copy of the molecule.

Returns:: the copy
Since:: Marvin 3.5.1, 11/20/2004

clone

public final java.lang.Object clone()

Makes an identical copy of the molecule.

Overrides:: clone in class MoleculeGraph

Returns:: the copy

getImageSize

public MolImageSize getImageSize(java.lang.String fmt)

Gets size information of an image created with the specified format string. Examples:

 MolImageSize g1 = mol.getImageSize("image:scale24");
     // (g1.width, g2.width) is the bounding box size for an image created
     // with scaling factor 24
 MolImageSize g2 = mol.getImageSize("image:w100h100");
     // g2.scale is the maximum scaling factor for 100x100 image

Parameters:: fmt - format string that contains the image export options
Returns:: an object containing the image size and the scaling factor
Throws:: java.lang.IllegalArgumentException - Invalid format string.; java.lang.SecurityException - Export module cannot be loaded because of security reasons (firewall).
Since:: Marvin 2.9.11
See Also:: toBinFormat(java.lang.String), toObject(java.lang.String)

toFormat

public final java.lang.String toFormat(java.lang.String fmt)

Creates a string representation of the molecule. The format descriptor string can also contain export options. Format and options are separated by a colon, multiple options can be separated by commas. See the text formats and their options on the File Formats in Marvin page. Examples:

 s1 = mol.toFormat("mol");
 s2 = mol.toFormat("smiles:a-H"); // aromatize and remove Hydrogens

Parameters:: fmt - the format descriptor string
Returns:: string representation of the molecule in the specified format
Throws:: java.lang.IllegalArgumentException - Invalid format string.; java.lang.SecurityException - Export module cannot be loaded because of security reasons (firewall).
See Also:: toObject(java.lang.String)

exportToFormat

public final java.lang.String exportToFormat(java.lang.String fmt)
                                      throws MolExportException

Creates a string representation of the molecule. Similar to toFormat(String), the only difference is that export exceptions are not converted to IllegalArgumentException.

Parameters:: fmt - the format descriptor string
Returns:: string representation of the molecule in the specified format
Throws:: MolExportException - Export error; java.lang.IllegalArgumentException - Invalid format string.; java.lang.SecurityException - Export module cannot be loaded because of security reasons (firewall).
Since:: Marvin 4.0, 07/01/2005
See Also:: toFormat(String)

toBinFormat

public final byte[] toBinFormat(java.lang.String fmt)

Creates a binary representation of the molecule. Works with all the text formats that are supported by the toFormat method, and also with the binary image formats (jpeg, msbmp, png, ppm). When creating an image, display options can also be specified in the format descriptor

chemaxon.struc Class Molecule

RMCLEANUP_SGROUPATOMS

RMCLEANUP_FROMSGROUPS

RMSG_DEFAULT

RMSG_KEEP_CHILDREN

RMSG_KEEP_PARENT

RMSG_KEEP_MULTICENTER

RECURSIVE_UNGROUP

DEFAULT_UNGROUP

Molecule

Molecule

Molecule

Molecule

setDim

clear

clearForImport

getStartPosition

setStartPosition

getEndPosition

setEndPosition

getName

setName

getComment

setComment

getInputFormat

setInputFormat

clearProperties

getPropertyCount

getPropertyKeys

getPropertyKey

getProperty

getPropertyObject

setProperty

setPropertyObject

residueTypeOf

residueSymbolOf

setNode0

removeNode

removeNode

removeEdge

removeEdge

removeAllEdges

removeAll

isEmpty

clean

cleanSgroups

contractExpandedSgroups

isPeptideChain

postClean

makeBiopolymerSnake

aromatize

dearomatize

clonecopy

fixSelfReferringProperty

addSgroupClones

clonecopy

clonecopyWithoutSgroups

clonelesscopy

cloneMoleculeWithDocument

cloneMolecule

clone

getImageSize

toFormat

exportToFormat

toBinFormat

chemaxon.struc
Class Molecule