GeometryPlugin (Marvin API documentation (c) 1998-2012 ChemAxon Ltd.)

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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
extends CalculatorPlugin

Plugin class for geometric properties calculations. Data types:

"dreidingenergy"
"distance"
"angle"
"dihedral"
"hindrance",
"minimalprojectionarea"
"maximalprojectionarea"
"minimalprojectionradius"
"maximalprojectionradius"
"volume",
"minz",
"maxz",

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:: 5.4, 08/30/2010
Author:: Zsolt Mohacsi, Adrian Kalaszi

Nested Class Summary

Nested classes/interfaces inherited from class chemaxon.marvin.plugin.CalculatorPlugin
`CalculatorPlugin.HydrogenData`

Field Summary

Fields inherited from class chemaxon.marvin.plugin.CalculatorPlugin
`ATOM, BLUE, CALCRGB_OFF, COVALENT_HYDRATION_ERROR_REMARK, CRITICAL_ERROR_MSG, EPSILON, explicitHydrogens, INCORRECT_AROMATIC_NITROGEN_REMARK, INSTABLE_TAUTOMERIC_FORM_REMARK, KEEP_HYDROGENS, keepHydrogens, licenseEnvironment, MOLECULE, MOLECULES, NAN, PLUGIN_CLASS_KEY, PLUGIN_DIR, RED, TRUE`

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`	`getMaxZ()`
`double`	`getMinimalProjectionArea()` Returns the minimal projection area in Angstrom^2.
`double`	`getMinimalProjectionRadius()` Returns the radius of the circle surrounding the minimal projection in Angstrom.
`double`	`getMinZ()`
`double`	`getMMFF94Energy()` Returns the MMFF94 energy of the structure in kcal/mol.
`java.lang.String`	`getProductName()` Returns the product identifier of the plugin as given by `LicenseManager`.
`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.
`double`	`getVolume()`
`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`	`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 calculation before geometry calculations are processed.
`void`	`setCalculateMMFF94Energy(boolean mmffe)` Sets the calculation of MMFF94 energy.
`void`	`setCalculateMoleculeProjections(boolean c)` Sets the calculation of molecule projections.
`void`	`setCalculateVolume(boolean calculateVolume)`
`protected void`	`setInputMolecule(Molecule mol)` Sets the input molecule.
`void`	`setLicenseEnvironment(java.lang.String env)` Sets license environment to be stored.
`void`	`setMMFF94Optimization(boolean opt)` Sets MMFF94 optimization.
`void`	`setOptimization(int opt)` Sets the optimization criteria for lowest energy conformer calculation.
`void`	`setOptimizeProjection(boolean optimize)`
`void`	`setParameters(java.util.Properties params)` Sets the input parameters for the plugin.
`void`	`setProgressMonitor(chemaxon.common.util.MProgressMonitor pmon)` Sets a progress observer to be used to display progress status.
`void`	`standardize(Molecule mol)` Expands sgroups.

Methods inherited from class chemaxon.marvin.plugin.CalculatorPlugin
arrangeHydrogenIncerments, canRepeat, checkLicense, checkType, containsCoordinateBond, containsMulticenterSgroup, containsPseudoAtom, containsSRUSgroup, create, createModifiedInputMolecule, createStandardizedMolecule, createStandardizedMolecule, dehydrogenize, format, format, format, format, getAtomCount, getAtomIndex, getCalcMolecule, getDisplayMolecule, getDocument, getDoublePrecision, getErrorMessage, getExplicitHydrogenData, getInputMolDim, getMainMolecule, getpH, getPluginResource, getQueryMoleculeErrorMessage, getResult, getResult, getResultAsRGB, getResultAsRGB, getResultAsString, getResultCount, getResultDomain, getResultMessage, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, getResultSource, isInputMoleculeAromatized, isLicensed, isMsCalc, isNegligibleResult, isOK, isRgrouped, loadClass, readAttribute, removeWhitespace, restoreExplicitHydrogens, setDoublePrecision, setDoublePrecision, setDoublePrecision, setKeepHydrogens, setMolecule, setMolecule, setMolecule, setMolecule, standardizeIonicGroups, standardizeNeutralGroups

Methods inherited from class chemaxon.marvin.plugin.CalculatorPlugin

arrangeHydrogenIncerments, canRepeat, checkLicense, checkType, containsCoordinateBond, containsMulticenterSgroup, containsPseudoAtom, containsSRUSgroup, create, createModifiedInputMolecule, createStandardizedMolecule, createStandardizedMolecule, dehydrogenize, format, format, format, format, getAtomCount, getAtomIndex, getCalcMolecule, getDisplayMolecule, getDocument, getDoublePrecision, getErrorMessage, getExplicitHydrogenData, getInputMolDim, getMainMolecule, getpH, getPluginResource, getQueryMoleculeErrorMessage, getResult, getResult, getResultAsRGB, getResultAsRGB, getResultAsString, getResultCount, getResultDomain, getResultMessage, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, getResultSource, isInputMoleculeAromatized, isLicensed, isMsCalc, isNegligibleResult, isOK, isRgrouped, loadClass, readAttribute, removeWhitespace, restoreExplicitHydrogens, setDoublePrecision, setDoublePrecision, setDoublePrecision, setKeepHydrogens, setMolecule, setMolecule, setMolecule, setMolecule, 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.

Method Detail

getProductName

public java.lang.String getProductName()

Returns the product identifier of the plugin as given by LicenseManager.

Specified by:: getProductName in class CalculatorPlugin

Returns:: The identifier LicenseManager.GEOMETRY_PLUGIN_GROUP

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",
- "mmff94energy",
- "distance" (atomic)
- "angle" (atomic)
- "dihedral" (atomic)
- "hindrance" (atomic)
- "minimalprojectionarea"
- "maximalprojectionarea"
- "minimalprojectionradius"
- "maximalprojectionradius"
- "volume",
- "minz",
- "maxz",
(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[]).
optimizeprojection: [true|false] sets projection optimization (default: false)

Overrides:: setParameters in class CalculatorPlugin

Parameters:: params - is the parameter table
Throws:: PluginException - on error

setProgressMonitor

public void setProgressMonitor(chemaxon.common.util.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

setCalculateVolume

public void setCalculateVolume(boolean calculateVolume)

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.

Parameters:: e - if true then dreiding energy is calculated

setCalculateMMFF94Energy

public void setCalculateMMFF94Energy(boolean mmffe)

Sets the calculation of MMFF94 energy.

Parameters:: mmffe - if true then MMFF94 energy is calculated
Since:: Marvin 5.4
See Also:: setMMFF94Optimization(boolean)

setMMFF94Optimization

public void setMMFF94Optimization(boolean opt)

Sets MMFF94 optimization.

Parameters:: opt - if true then MMFF94 optimization is performed
Since:: Marvin 5.4
See Also:: setCalculateMMFF94Energy(boolean)

setCalculateForLEConformer

public void setCalculateForLEConformer(java.lang.String condition)

Sets the condition for lowest energy conformer calculation 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

setLicenseEnvironment

public void setLicenseEnvironment(java.lang.String env)

Description copied from class: CalculatorPlugin

Sets license environment to be stored.

Specified by:: setLicenseEnvironment in interface chemaxon.license.Licensable
Overrides:: setLicenseEnvironment in class CalculatorPlugin

Parameters:: env - environment String to be stored and passed to the LicenseHandler in the isLicensed method

getDreidingEnergy

public double getDreidingEnergy()

Returns the energy of the conformer in kcal/mol.

Returns:: the energy of the conformer

getMMFF94Energy

public double getMMFF94Energy()

Returns the MMFF94 energy of the structure in kcal/mol.

Returns:: the MMFF94 energy of the conformer
Since:: Marvin 5.4

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 - if atoms are not set properly

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 - if atoms are not set properly

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 - if atoms are not set properly

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)

getVolume

public double getVolume()

setOptimizeProjection

public void setOptimizeProjection(boolean optimize)

run

public boolean run()
            throws PluginException

Runs the tool.

Specified by:: run in class CalculatorPlugin

Returns:: true if the calculation was successful, false if unsuccessful
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()

getMaxZ

public double getMaxZ()

getMinZ

public double getMinZ()

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",
"mmff94energy",
"distance" (atomic)
"angle" (atomic)
"dihedral" (atomic)
"hindrance" (atomic)
"minimalprojectionarea"
"maximalprojectionarea"
"minimalprojectionradius"
"maximalprojectionradius"
"volume",
"minz",
"maxz",

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 conformer calculation aborted

isMultiThreadedRunEnabled

public boolean isMultiThreadedRunEnabled()

For internal use only.

Overrides:: isMultiThreadedRunEnabled in class CalculatorPlugin

Returns:: true if multi-threaded run is enabled

standardize

public void standardize(Molecule mol)

Expands sgroups.

Overrides:: standardize in class CalculatorPlugin

Parameters:: mol - is the molecule to be standardized

Overview

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SUMMARY: NESTED | FIELD | CONSTR | METHOD

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chemaxon.marvin.calculations Class GeometryPlugin

GeometryPlugin

getProductName

setParameters

setProgressMonitor

setCalculateVolume

handlesMultiFragmentMolecules

checkMolecule

setInputMolecule

setCalculateEnergy

setCalculateMMFF94Energy

setMMFF94Optimization

setCalculateForLEConformer

setOptimization

getLowestEnergyConformer

setLicenseEnvironment

getDreidingEnergy

getMMFF94Energy

getDistance

getDistance

getAngle

getAngle

getDihedral

getDihedral

getStericHindrance

setCalculateMoleculeProjections

getMinimalProjectionArea

getMaximalProjectionArea

getMinimalProjectionRadius

getMaximalProjectionRadius

getVolume

setOptimizeProjection

run

getResult

getMaxZ

getMinZ

getResult

getResultAsString

getResultCount

getResultDomain

getResultTypes

getTypeString

getResultMolecule

getResultMolecules

getRemark

getWarningMessage

isMultiThreadedRunEnabled

standardize

chemaxon.marvin.calculations
Class GeometryPlugin