denoptim.molecularmodeling.MultiMolecularModelBuilder Class Reference

Collaboration diagram for denoptim.molecularmodeling.MultiMolecularModelBuilder:

Public Member Functions
	MultiMolecularModelBuilder (String molName, DGraph molGraph, MMBuilderParameters settings)
ArrayList< IAtomContainer >	buildMulti3DStructure () throws DENOPTIMException, TinkerException
	Given the graph representation of the molecular constitution, along with the 3D coordinates of the fragments and direction vectors, create 3D structures by merging internal coordinates. More...
ChemicalObjectModel	build3DTree () throws DENOPTIMException
	Generate 3D structure by assembling 3D fragments according to attachment point vector and following the tree-like structure of the graph. More...

Private Attributes
String	molName
DGraph	molGraph
MMBuilderParameters	settings
Logger	logger
	Program-specific logger. More...

Detailed Description

Author

Vishwesh Venkatraman

Marco Foscato

Definition at line 51 of file MultiMolecularModelBuilder.java.

Constructor & Destructor Documentation

MultiMolecularModelBuilder()

denoptim.molecularmodeling.MultiMolecularModelBuilder.MultiMolecularModelBuilder	(	String	molName,
		DGraph	molGraph,
		MMBuilderParameters	settings
	)

Definition at line 65 of file MultiMolecularModelBuilder.java.

References denoptim.programs.RunTimeParameters.getLogger(), denoptim.molecularmodeling.MultiMolecularModelBuilder.molGraph, denoptim.molecularmodeling.MultiMolecularModelBuilder.molName, and denoptim.molecularmodeling.MultiMolecularModelBuilder.settings.

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Member Function Documentation

build3DTree()

ChemicalObjectModel denoptim.molecularmodeling.MultiMolecularModelBuilder.build3DTree

(

)

throws DENOPTIMException

Generate 3D structure by assembling 3D fragments according to attachment point vector and following the tree-like structure of the graph.

Exceptions

DENOPTIMException

Definition at line 231 of file MultiMolecularModelBuilder.java.

References denoptim.molecularmodeling.ThreeDimTreeBuilder.convertGraphTo3DAtomContainer(), denoptim.utils.RotationalSpaceUtils.defineRotatableBonds(), denoptim.programs.RunTimeParameters.ParametersType.FS_PARAMS, denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getAtomOrderingScheme(), denoptim.integration.tinker.TinkerUtils.getICFromIAC(), denoptim.programs.RunTimeParameters.getLogger(), denoptim.utils.AtomOrganizer.getNewToOldOrder(), denoptim.utils.AtomOrganizer.getOldToNewOrder(), denoptim.programs.RunTimeParameters.getParameters(), denoptim.programs.RunTimeParameters.getRandomizer(), denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getTinkerMap(), denoptim.molecularmodeling.MultiMolecularModelBuilder.logger, denoptim.molecularmodeling.MultiMolecularModelBuilder.molGraph, denoptim.molecularmodeling.MultiMolecularModelBuilder.molName, denoptim.utils.AtomOrganizer.reorderStartingFrom(), denoptim.utils.AtomOrganizer.setScheme(), denoptim.molecularmodeling.MultiMolecularModelBuilder.settings, denoptim.integration.tinker.TinkerUtils.setTinkerTypes(), and denoptim.io.DenoptimIO.writeSDFFile().

Referenced by denoptim.molecularmodeling.MultiMolecularModelBuilder.buildMulti3DStructure().

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buildMulti3DStructure()

ArrayList< IAtomContainer > denoptim.molecularmodeling.MultiMolecularModelBuilder.buildMulti3DStructure

(

)

throws DENOPTIMException, TinkerException

Given the graph representation of the molecular constitution, along with the 3D coordinates of the fragments and direction vectors, create 3D structures by merging internal coordinates.

More than one structure can be obtained if the provided graph allows for isomerism for example by multiple possibility of ring formation or conformational isomerism (not implemented yet).

Exceptions

TinkerException

if Tinker fails

Definition at line 87 of file MultiMolecularModelBuilder.java.

References denoptim.graph.rings.RingClosureParameters.allowRingClosures(), denoptim.constants.DENOPTIMConstants.ATMPROPVERTEXID, denoptim.molecularmodeling.RingClosureTool.attemptAllRingClosures(), denoptim.molecularmodeling.MultiMolecularModelBuilder.build3DTree(), denoptim.programs.RunTimeParameters.containsParameters(), denoptim.molecularmodeling.ChemicalObjectModel.deepcopy(), denoptim.constants.DENOPTIMConstants.DUMMYATMSYMBOL, denoptim.molecularmodeling.ChemicalObjectModel.getGraph(), denoptim.molecularmodeling.ChemicalObjectModel.getIAtomContainer(), denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getInitPSSROTParams(), denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getKeepDummyFlag(), denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getKeyFileParams(), denoptim.programs.RunTimeParameters.getParameters(), denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getParamFile(), denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getPSSROTTool(), denoptim.molecularmodeling.ChemicalObjectModel.getRCACombinations(), denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getRestPSSROTParams(), denoptim.molecularmodeling.ChemicalObjectModel.getRotatableBonds(), denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getTaskID(), denoptim.graph.DGraph.getVertexList(), denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getWorkingDirectory(), denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getXYZINTTool(), denoptim.graph.DGraph.hasOrEmbedsRings(), denoptim.molecularmodeling.MultiMolecularModelBuilder.logger, denoptim.utils.AtomOrganizer.makeReorderedCopy(), denoptim.constants.DENOPTIMConstants.MOLERRORTAG, denoptim.molecularmodeling.MultiMolecularModelBuilder.molGraph, denoptim.integration.tinker.ConformationalSearchPSSROT.performPSSROT(), denoptim.programs.RunTimeParameters.ParametersType.RC_PARAMS, denoptim.utils.DummyAtomHandler.removeDummy(), denoptim.utils.DummyAtomHandler.removeDummyInHapto(), denoptim.graph.rings.RingClosureParameters.requireCompleteRingclosure, denoptim.molecularmodeling.RingClosureTool.saturateRingClosingAttractor(), denoptim.molecularmodeling.MultiMolecularModelBuilder.settings, and denoptim.graph.DGraph.toString().

Referenced by denoptim.programs.moldecularmodelbuilder.MolecularModelBuilder.runProgram().

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Member Data Documentation

logger

Logger denoptim.molecularmodeling.MultiMolecularModelBuilder.logger

private

Program-specific logger.

Definition at line 61 of file MultiMolecularModelBuilder.java.

Referenced by denoptim.molecularmodeling.MultiMolecularModelBuilder.build3DTree(), and denoptim.molecularmodeling.MultiMolecularModelBuilder.buildMulti3DStructure().

molGraph

DGraph denoptim.molecularmodeling.MultiMolecularModelBuilder.molGraph

private

Definition at line 54 of file MultiMolecularModelBuilder.java.

Referenced by denoptim.molecularmodeling.MultiMolecularModelBuilder.build3DTree(), denoptim.molecularmodeling.MultiMolecularModelBuilder.buildMulti3DStructure(), and denoptim.molecularmodeling.MultiMolecularModelBuilder.MultiMolecularModelBuilder().

molName

String denoptim.molecularmodeling.MultiMolecularModelBuilder.molName

private

Definition at line 53 of file MultiMolecularModelBuilder.java.

Referenced by denoptim.molecularmodeling.MultiMolecularModelBuilder.build3DTree(), and denoptim.molecularmodeling.MultiMolecularModelBuilder.MultiMolecularModelBuilder().

settings

MMBuilderParameters denoptim.molecularmodeling.MultiMolecularModelBuilder.settings

private

Definition at line 56 of file MultiMolecularModelBuilder.java.

Referenced by denoptim.molecularmodeling.MultiMolecularModelBuilder.build3DTree(), denoptim.molecularmodeling.MultiMolecularModelBuilder.buildMulti3DStructure(), and denoptim.molecularmodeling.MultiMolecularModelBuilder.MultiMolecularModelBuilder().

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The documentation for this class was generated from the following file:

• /github/workspace/src/main/java/denoptim/molecularmodeling/MultiMolecularModelBuilder.java