chemaxon.marvin.calculations
Class GeometryPlugin

java.lang.Object
  chemaxon.marvin.plugin.CalculatorPlugin
      chemaxon.marvin.calculations.GeometryPlugin

All Implemented Interfaces:

chemaxon.license.Licensable

public class GeometryPlugin
extends CalculatorPlugin

Plugin class for geometrical properties calculations. Data types:

• "dreidingenergy"
• "distance"
• "angle"
• "dihedral"
• "hindrance",
• "minimalprojectionarea"
• "maximalprojectionarea"
• "minimalprojectionradius"
• "maximalprojectionradius"

API usage example:

    // read input molecule
    MolImporter mi = new MolImporter("test.mol");
    Molecule mol = mi.read();
    mi.close();

    // create plugin
    GeometryPlugin plugin = new GeometryPlugin();

    // set target molecule
    plugin.setMolecule(mol);
    
    // set parameters for calculation
    plugin.setCalculateForLEConformer("if2D");
    plugin.setCalculateEnergy(true); // sets the energy calculation
    plugin.setCalculateMoleculeProjections(true); // sets the calculation of molecule projections

    // run the calculation
    plugin.run();

    // get results
    double energy = plugin.getDreidingEnergy();
    double distance = plugin.getDistance(2,4);
    double angle = plugin.getAngle(4,2,6);
    int[] atoms = { 2, 1, 4, 6 };
    double dihedral = plugin.getDihedral(atoms);
    double hindrance = plugin.getStericHindrance(5); // steric hindrance of 5th atom
    double minimalProjectionArea = plugin.getMinimalProjectionArea();
    double maximalProjectionArea = plugin.getMaximalProjectionArea();
    double minimalProjectionRadius = plugin.getMinimalProjectionRadius();
    double maximalProjectionRadius = plugin.getMaximalProjectionRadius();

    // do something with the results ...
 

For concurrent plugin example applications using ChemAxon's concurrent framework, refer to the Concurrent plugin examples.

Since:

Marvin 4.1 02/21/2006

Version:

5.1, 07/28/2008

Author:

Zsolt Mohacsi

Field Summary

Fields inherited from class chemaxon.marvin.plugin.CalculatorPlugin

ATOM, BLUE, CALCRGB_OFF, COVALENT_HYDRATION_ERROR_REMARK, CRITICAL_ERROR_MSG, EPSILON, INCORRECT_AROMATIC_NITROGEN_REMARK, INSTABLE_TAUTOMERIC_FORM_REMARK, licenseEnvironment, MOLECULE, NAN, PLUGIN_CLASS_KEY, PLUGIN_DIR, RED

Constructor Summary

GeometryPlugin()
Constructor.

Method Summary

void	checkMolecule(Molecule mol) Checks the input molecule.
double	getAngle(int[] atoms) Returns the angle of 3 atoms.
double	getAngle(int atom1, int atom2, int atom3) Returns the angle of 3 atoms.
double	getDihedral(int[] atoms) Returns the dihedral of 4 atoms.
double	getDihedral(int atom1, int atom2, int atom3, int atom4) Returns the dihedral of 4 atoms.
double	getDistance(int[] atoms) Returns the distance of 2 atoms.
double	getDistance(int atom1, int atom2) Returns the distance of 2 atoms.
double	getDreidingEnergy() Returns the energy of the conformer in kcal/mol.
Molecule	getLowestEnergyConformer() Returns the lowest energy conformer of the molecule.
double	getMaximalProjectionArea() Returns the maximal projection area in Angstrom^2.
double	getMaximalProjectionRadius() Returns the radius of the circle surrounding the maximal projection in Angstrom.
double	getMinimalProjectionArea() Returns the minimal projection area in Angstrom^2.
double	getMinimalProjectionRadius() Returns the radius of the circle surrounding the minimal projection in Angstrom.
java.lang.String	getRemark() Returns the calculation remark: if no results (no result types) then returns remark, otherwise returns null.
java.lang.Object	getResult(java.lang.Object type, int index) Returns the result item for the specified key and index.
java.lang.Object	getResult(java.lang.Object type, java.lang.String arg) Returns the distance, angle or dihedral of 2, 3 or 4 atoms if type is set to "distance", "angle" or "diheral".
java.lang.String	getResultAsString(java.lang.Object type, int index, java.lang.Object result) Returns the specified result in String format.
int	getResultCount(java.lang.Object type) Returns the number of result items for the given result key.
int	getResultDomain(java.lang.Object type) Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
Molecule	getResultMolecule() Returns the result molecule for display.
Molecule[]	getResultMolecules() Returns the result molecules, molecular results are set in the first molecule, atomic results are set in subsequent molecules as atom labels.
java.lang.Object[]	getResultTypes() Returns the result types.
double	getStericHindrance(int atom) Calculates hindrance of an atom from covalent radii values and distances.
java.lang.String	getTypeString(java.lang.Object type) Returns a string representation of the given type.
java.lang.String	getWarningMessage() Returns a warning message if lowest energy conformer calculation was unsuccessful or aborted by user, null otherwise.
boolean	handlesMultiFragmentMolecules() Returns true if the plugin handles multifragment molecules, false otherwise.
boolean	isLicensed() Returns true if the plugin is licensed.
boolean	isMultiThreadedRunEnabled() For internal use only.
boolean	run() Runs the tool.
void	setCalculateEnergy(boolean e) Sets the calculation of dreiding energy.
void	setCalculateForLEConformer(java.lang.String condition) Sets the condition for lowest energy conformer calcuation before geometry calculations are processed.
void	setCalculateMoleculeProjections(boolean c) Sets the calculation of molecule projections.
protected void	setInputMolecule(Molecule mol) Sets the input molecule.
void	setOptimization(int opt) Sets the optimization criteria for lowest energy conformer calculation.
void	setParameters(java.util.Properties params) Sets the input parameters for the plugin.
void	setProgressMonitor(MProgressMonitor pmon) Sets a progress observer to be used to display progress status.
void	setRadiusScaleFactor(double sc) Sets the atomic radius scale factor.

Methods inherited from class chemaxon.marvin.plugin.CalculatorPlugin

checkType, containsCoordinateBond, containsMulticenterSgroup, containsPseudoAtom, containsSRUSgroup, create, createModifiedInputMolecule, createStandardizedMolecule, createStandardizedMolecule, dehydrogenize, format, format, format, format, getAtomCount, getAtomIndex, getCalcMolecule, getDisplayMolecule, getDocument, getDoublePrecision, getErrorMessage, getInputMolDim, getMainMolecule, getpH, getPluginResource, getResult, getResult, getResultAsRGB, getResultAsRGB, getResultAsString, getResultCount, getResultDomain, getResultMessage, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, getResultSource, isInputMoleculeAromatized, isMsCalc, isNegligibleResult, isOK, isRgrouped, loadClass, readAttribute, removeWhitespace, setDoublePrecision, setDoublePrecision, setDoublePrecision, setLicenseEnvironment, setMolecule, setMolecule, setMolecule, standardize, standardizeIonicGroups, standardizeNeutralGroups

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

GeometryPlugin

public GeometryPlugin()

Constructor. Creates the geometry analyser object.

Method Detail

isLicensed

public boolean isLicensed()

Description copied from class: CalculatorPlugin

Returns true if the plugin is licensed. Implement this only if you want to sell your plugin and protect it with a license key. The default implementation always returns true which means that the plugin is free: no license key is required. This method returns only information about the licensing, license checking has to be implemented separately.

Specified by:

isLicensed in interface chemaxon.license.Licensable

Overrides:

isLicensed in class CalculatorPlugin

Returns:

true if the plugin is licensed

setParameters

public void setParameters(java.util.Properties params)
                   throws PluginException

Sets the input parameters for the plugin. Parameters:

• type: result types, separated by ',', possible values:
  • "dreidingenergy",
  • "distance" (atomic)
  • "angle" (atomic)
  • "dihedral" (atomic)
  • "hindrance" (atomic)
  • "minimalprojectionarea"
  • "maximalprojectionarea"
  • "minimalprojectionradius"
  • "maximalprojectionradius"
  (default: all molecular types)
• atoms: <atom1-...-atomn> valid for type="distance" (n=2), "angle" (n=3) and "dihedral" (n=4) calculations only, sets the atoms used by cxcalc, for internal use only; API usage: call getDistance(int,int) or getDistance(int[]).

Overrides:

setParameters in class CalculatorPlugin

Parameters:

params - is the parameter table

Throws:

PluginException - on error

setProgressMonitor

public void setProgressMonitor(MProgressMonitor pmon)

Sets a progress observer to be used to display progress status. Short calculations may ignore the observer object. The default implementation does nothing.

Overrides:

setProgressMonitor in class CalculatorPlugin

Parameters:

pmon - is the progress observer object, may be null

handlesMultiFragmentMolecules

public boolean handlesMultiFragmentMolecules()

Returns true if the plugin handles multifragment molecules, false otherwise. In the latter case the plugin takes the fragment with more atoms if a multifragment molecule is given as input.

Overrides:

handlesMultiFragmentMolecules in class CalculatorPlugin

Returns:

true if the plugin handles multifragment molecules, false otherwise

checkMolecule

public void checkMolecule(Molecule mol)
                   throws PluginException

Checks the input molecule. Throws exception if the molecule is RxnMolecule or if the molecule contains R-groups.

Overrides:

checkMolecule in class CalculatorPlugin

Parameters:

mol - is the input molecule

Throws:

PluginException - with error message for the user if the molecule is refused

setInputMolecule

protected void setInputMolecule(Molecule mol)
                         throws PluginException

Sets the input molecule.

Specified by:

setInputMolecule in class CalculatorPlugin

Parameters:

mol - is the input molecule

Throws:

PluginException - on error

setCalculateEnergy

public void setCalculateEnergy(boolean e)

Sets the calculation of dreiding energy.

setCalculateForLEConformer

public void setCalculateForLEConformer(java.lang.String condition)

Sets the condition for lowest energy conformer calcuation before geometry calculations are processed. Possible values:

• "if2D" - if molecule is in 2D
• "never" - never, always use the input molecule for calculations
• "always" - always calculate with the lowest energy conformer

Parameters:

condition - is the condition for lowest energy conformer calculation

setOptimization

public void setOptimization(int opt)

Sets the optimization criteria for lowest energy conformer calculation.

Parameters:

opt - is the optimization limit for the calculation

getLowestEnergyConformer

public Molecule getLowestEnergyConformer()

Returns the lowest energy conformer of the molecule.

Returns:

the lowest energy conformer

getDreidingEnergy

public double getDreidingEnergy()

Returns the energy of the conformer in kcal/mol.

Returns:

the energy of the conformer

getDistance

public double getDistance(int atom1,
                          int atom2)

Returns the distance of 2 atoms.

Parameters:

atom1 - is the (1-based) index of the 1st atom

atom2 - is the (1-based) index of the 2nd atom

Returns:

the distance of 2 atoms

getDistance

public double getDistance(int[] atoms)
                   throws PluginException

Returns the distance of 2 atoms.

Parameters:

atoms - is the array containing (1-based) indexes of 2 atoms

Returns:

the distance of 2 atoms

Throws:

PluginException

getAngle

public double getAngle(int atom1,
                       int atom2,
                       int atom3)

Returns the angle of 3 atoms.

Parameters:

atom1 - is the (1-based) index of the 1st atom

atom2 - is the (1-based) index of the 2nd atom

atom3 - is the (1-based) index of the 3rd atom

Returns:

the angle of 3 atoms

getAngle

public double getAngle(int[] atoms)
                throws PluginException

Returns the angle of 3 atoms.

Parameters:

atoms - is the array containing (1-based) indexes of 3 atoms

Returns:

the angle of 3 atoms

Throws:

PluginException

getDihedral

public double getDihedral(int atom1,
                          int atom2,
                          int atom3,
                          int atom4)

Returns the dihedral of 4 atoms.

Parameters:

atom1 - is the (1-based) index of the 1st atom

atom2 - is the (1-based) index of the 2nd atom

atom3 - is the (1-based) index of the 3rd atom

atom4 - is the (1-based) index of the 4th atom

Returns:

the dihedral of 4 atoms

getDihedral

public double getDihedral(int[] atoms)
                   throws PluginException

Returns the dihedral of 4 atoms.

Parameters:

atoms - is the array containing (1-based) indexes of 4 atoms

Returns:

the dihedral of 4 atoms

Throws:

PluginException

getStericHindrance

public double getStericHindrance(int atom)

Calculates hindrance of an atom from covalent radii values and distances. The stericHindrance is related to the steric hindrance of the given atom.

Parameters:

atom - index of the atom

Returns:

the steric hindrance of the atom

setCalculateMoleculeProjections

public void setCalculateMoleculeProjections(boolean c)

Sets the calculation of molecule projections. Default: false

Parameters:

c - if true then molecule projection calculations are run.

See Also:

getMinimalProjectionArea(), getMaximalProjectionArea(), getMinimalProjectionRadius(), getMaximalProjectionRadius()

getMinimalProjectionArea

public double getMinimalProjectionArea()

Returns the minimal projection area in Angstrom^2.

Returns:

the minimal projection area

See Also:

setCalculateMoleculeProjections(boolean)

getMaximalProjectionArea

public double getMaximalProjectionArea()

Returns the maximal projection area in Angstrom^2.

Returns:

the maximal projection area

See Also:

setCalculateMoleculeProjections(boolean)

getMinimalProjectionRadius

public double getMinimalProjectionRadius()

Returns the radius of the circle surrounding the minimal projection in Angstrom.

Returns:

the radius of the circle surrounding the minimal projection

See Also:

setCalculateMoleculeProjections(boolean)

getMaximalProjectionRadius

public double getMaximalProjectionRadius()

Returns the radius of the circle surrounding the maximal projection in Angstrom.

Returns:

the radius of the circle surrounding the maximal projection

See Also:

setCalculateMoleculeProjections(boolean)

setRadiusScaleFactor

public void setRadiusScaleFactor(double sc)

Sets the atomic radius scale factor. The scale factor is used in molecule projection calculations. Default: 1.0

Parameters:

sc - is the scale factor

run

public boolean run()
            throws PluginException

Runs the tool.

Specified by:

run in class CalculatorPlugin

Returns:

true if the calculation was successful, false if unsuccesful

Throws:

PluginException - on error

See Also:

CalculatorPlugin.getErrorMessage()

getResult

public java.lang.Object getResult(java.lang.Object type,
                                  int index)
                           throws PluginException

Returns the result item for the specified key and index.

Overrides:

getResult in class CalculatorPlugin

Parameters:

type - is the result type

index - is the result index

Returns:

the result item for the specified key and index

Throws:

PluginException - if the result cannot be returned

See Also:

CalculatorPlugin.getResultTypes()

getResult

public java.lang.Object getResult(java.lang.Object type,
                                  java.lang.String arg)
                           throws PluginException

Returns the distance, angle or dihedral of 2, 3 or 4 atoms if type is set to "distance", "angle" or "diheral". For internal use only.

Overrides:

getResult in class CalculatorPlugin

Parameters:

type - is the result type ("distance", "angle" or "dihedral")

arg - is the atom string as atom1-atom2 (e.g. "2-3")

Returns:

the result item

Throws:

PluginException - on error

See Also:

CalculatorPlugin.getResultTypes()

getResultAsString

public java.lang.String getResultAsString(java.lang.Object type,
                                          int index,
                                          java.lang.Object result)
                                   throws PluginException

Returns the specified result in String format.

Overrides:

getResultAsString in class CalculatorPlugin

Parameters:

type - is the result type

index - is the result index

result - is the result item

Returns:

the specified result in String format

Throws:

PluginException - if an invalid result item is given

getResultCount

public int getResultCount(java.lang.Object type)

Returns the number of result items for the given result key.

Overrides:

getResultCount in class CalculatorPlugin

Parameters:

type - is the result type

Returns:

the number of result items

See Also:

getResultTypes()

getResultDomain

public int getResultDomain(java.lang.Object type)

Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.

Overrides:

getResultDomain in class CalculatorPlugin

Parameters:

type - is the result key

Returns:

the calculation domain

See Also:

getResultTypes()

getResultTypes

public java.lang.Object[] getResultTypes()

Returns the result types. Possible result types:

• "dreidingenergy",
• "distance" (atomic)
• "angle" (atomic)
• "dihedral" (atomic)
• "hindrance" (atomic)
• "minimalprojectionarea"
• "maximalprojectionarea"
• "minimalprojectionradius"
• "maximalprojectionradius"

Overrides:

getResultTypes in class CalculatorPlugin

Returns:

the result types

getTypeString

public java.lang.String getTypeString(java.lang.Object type)

Returns a string representation of the given type.

Overrides:

getTypeString in class CalculatorPlugin

Parameters:

type - is the type object

Returns:

the type string

getResultMolecule

public Molecule getResultMolecule()
                           throws PluginException

Returns the result molecule for display. Atomic results are stored in atom extra labels (MolAtom.getExtraLabel()). Molecular results are stored in molecule properties with keys being the result types (Molecule.getProperty(String)).

Overrides:

getResultMolecule in class CalculatorPlugin

Returns:

the result molecule

Throws:

PluginException - on error

getResultMolecules

public Molecule[] getResultMolecules()
                              throws PluginException

Returns the result molecules, molecular results are set in the first molecule, atomic results are set in subsequent molecules as atom labels.

Overrides:

getResultMolecules in class CalculatorPlugin

Returns:

the result molecules

Throws:

PluginException - on error

getRemark

public java.lang.String getRemark()

Returns the calculation remark: if no results (no result types) then returns remark, otherwise returns null.

Overrides:

getRemark in class CalculatorPlugin

Returns:

the calculation remark

getWarningMessage

public java.lang.String getWarningMessage()

Returns a warning message if lowest energy conformer calculation was unsuccessful or aborted by user, null otherwise.

Overrides:

getWarningMessage in class CalculatorPlugin

Returns:

a warning message if conformercalculation aborted

isMultiThreadedRunEnabled

public boolean isMultiThreadedRunEnabled()

For internal use only.

Overrides:

isMultiThreadedRunEnabled in class CalculatorPlugin

Returns:

true if multi-threaded run is enabled