Toolkit to perform ring closing conformational search. More...

Collaboration diagram for denoptim.molecularmodeling.RingClosureTool:

Classes
class	RingClosedMolComparator
	Compares the Molecule3DBuilder afters ring closing-biased conformational adaptation. More...

Public Member Functions
	RingClosureTool (MMBuilderParameters settings)
	Construct an empty RingClosureTool. More...

ArrayList< ChemicalObjectModel >	attemptAllRingClosures (ChemicalObjectModel mol) throws DENOPTIMException, TinkerException
	Performs one or more attempts to close rings by conformational adaptation. More...

ChemicalObjectModel	attemptRingClosure (ChemicalObjectModel chemObj, Set< ObjectPair > rcaCombination) throws DENOPTIMException, TinkerException
	Attempts to close rings by finding the conformation that allows to join heads and tails of atom specific chains. More...

void	closeRings (ChemicalObjectModel mol, Set< ObjectPair > rcaCombination)
	Makes new rings by connecting pairs of atoms that hold properly arranged RingClosingAttractors. More...

void	saturateRingClosingAttractor (ChemicalObjectModel mol) throws DENOPTIMException
	Looks for unused RingClosingAttractors and attach proper capping group saturating the free valency/bonding capability represented by free RingClosingAttractors. More...

Package Attributes
final String	fsep = System.getProperty("file.separator")
	File separator. More...

Private Member Functions
void	setTinkerTypes (TinkerMolecule tmol) throws DENOPTIMException
	Conversion to tinker IC may not always have the necessary atom types. More...

Private Attributes
int	itn = 0
	Iteration counter for making unique filenames. More...

MMBuilderParameters	settings
	Settings controlling the calculation. More...

Logger	logger
	Program.specific logger. More...

Detailed Description

Toolkit to perform ring closing conformational search.

This tool makes use of Tinker's PSSROT engine.

Author: Marco Foscato

Definition at line 58 of file RingClosureTool.java.

Constructor & Destructor Documentation

◆ RingClosureTool()

denoptim.molecularmodeling.RingClosureTool.RingClosureTool ( MMBuilderParameters settings )

Construct an empty RingClosureTool.

Definition at line 85 of file RingClosureTool.java.

References denoptim.programs.RunTimeParameters.getLogger(), and denoptim.molecularmodeling.RingClosureTool.settings.

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Member Function Documentation

◆ attemptAllRingClosures()

ArrayList< ChemicalObjectModel > denoptim.molecularmodeling.RingClosureTool.attemptAllRingClosures ( ChemicalObjectModel mol ) throws DENOPTIMException, TinkerException

Performs one or more attempts to close rings by conformational adaptation.

The number of attempts (i.e, different set of rings) and the list of definition of each attempt are defined into the object provided as input. If no ring closure is possible, returns an empty array.

Parameters

mol	the input molecular system

Returns: the list of generated molecules, if any.

Exceptions

DENOPTIMException
TinkerException

Definition at line 146 of file RingClosureTool.java.

References denoptim.molecularmodeling.RingClosureTool.attemptRingClosure(), denoptim.molecularmodeling.ChemicalObjectModel.deepcopy(), denoptim.molecularmodeling.ChemicalObjectModel.getIAtomContainer(), denoptim.molecularmodeling.ChemicalObjectModel.getNewRingClosures(), denoptim.molecularmodeling.ChemicalObjectModel.getRCACombinations(), denoptim.molecularmodeling.RingClosureTool.logger, and denoptim.constants.DENOPTIMConstants.MOLERRORTAG.

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

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◆ attemptRingClosure()

ChemicalObjectModel denoptim.molecularmodeling.RingClosureTool.attemptRingClosure	(	ChemicalObjectModel	chemObj,
		Set< ObjectPair >	rcaCombination
	)		throws DENOPTIMException, TinkerException

Attempts to close rings by finding the conformation that allows to join heads and tails of atom specific chains.

To this end a Potential Smoothing and Search conformational search in ROTational space (PSSROT) is performed under the effect of the Ring Closing potential, that defines which atoms (chain head/tails) attract each other. The PSSROT engine is provided by an ad hoc modified version of Tinker (call to external tool).

Parameters

chemObj	the definition of the system to work with. This system will be modified.
rcaCombination	the combination of RingClosingAttractors. This object defines which pairs of RingClosingAttractors will we try to join in this attempt.

Returns: a new molecular system with the freshly closed rings, if any, otherwise an empty molecule.

Exceptions

DENOPTIMException
TinkerException

Definition at line 268 of file RingClosureTool.java.

Referenced by denoptim.molecularmodeling.RingClosureTool.attemptAllRingClosures().

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◆ closeRings()

void denoptim.molecularmodeling.RingClosureTool.closeRings	(	ChemicalObjectModel	mol,
		Set< ObjectPair >	rcaCombination
	)

Makes new rings by connecting pairs of atoms that hold properly arranged RingClosingAttractors.

Parameters

mol	the molecular system
rcaCombination	the combination of RingClosingAttractors. This object defines which pairs of RingClosingAttractors will we try to join in this attempt.

Definition at line 363 of file RingClosureTool.java.

References denoptim.molecularmodeling.ChemicalObjectModel.addBond(), denoptim.programs.RunTimeParameters.containsParameters(), denoptim.graph.rings.RingClosingAttractor.getIAtom(), denoptim.programs.RunTimeParameters.getParameters(), denoptim.graph.rings.RingClosingAttractor.getRCBondType(), denoptim.graph.rings.RingClosureParameters.getRCDistTolerance(), denoptim.graph.rings.RingClosureParameters.getRCDotPrTolerance(), denoptim.graph.rings.RingClosingAttractor.getSrcAtom(), denoptim.graph.Edge.BondType.hasCDKAnalogue(), denoptim.graph.rings.RingClosure.isClosable(), denoptim.molecularmodeling.RingClosureTool.logger, denoptim.programs.RunTimeParameters.ParametersType.RC_PARAMS, denoptim.molecularmodeling.RingClosureTool.settings, and denoptim.graph.rings.RingClosingAttractor.setUsed().

Referenced by denoptim.molecularmodeling.RingClosureTool.attemptRingClosure().

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◆ saturateRingClosingAttractor()

void denoptim.molecularmodeling.RingClosureTool.saturateRingClosingAttractor ( ChemicalObjectModel mol ) throws DENOPTIMException

Looks for unused RingClosingAttractors and attach proper capping group saturating the free valency/bonding capability represented by free RingClosingAttractors.

TODO: make this method choose a proper capping group (if any) and use that to saturate the free AP Note that to do that the capping og the RingClosure-related APclasses must be reported in the CompatibilityMatrix. Thus, it is also necessary to make DenoptimGA prefer RingClosure-related APclasses over other capping groups

Parameters

mol	the molecule

Definition at line 444 of file RingClosureTool.java.

References denoptim.constants.DENOPTIMConstants.DUMMYATMSYMBOL, denoptim.integration.tinker.TinkerMolecule.getAtom(), denoptim.integration.tinker.TinkerAtom.getDistAngle(), denoptim.integration.tinker.TinkerAtom.setAtomString(), denoptim.integration.tinker.TinkerAtom.setDistAngle(), and denoptim.molecularmodeling.RingClosureTool.setTinkerTypes().

Referenced by denoptim.molecularmodeling.RingClosureTool.attemptRingClosure(), and denoptim.molecularmodeling.MultiMolecularModelBuilder.buildMulti3DStructure().

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◆ setTinkerTypes()

void denoptim.molecularmodeling.RingClosureTool.setTinkerTypes ( TinkerMolecule tmol ) throws DENOPTIMException

private

Conversion to tinker IC may not always have the necessary atom types.

In order to fix this, we add user defined atom types.

TODO: this method (from DENOPTIM3DMoleculeBuilder.java) should be made public and moved to a more sensible location (i.e., a class of utilities for tinker methods)

Parameters

tmol	The tinker IC representation

Exceptions

DENOPTIMException

Definition at line 104 of file RingClosureTool.java.

References denoptim.integration.tinker.TinkerAtom.getAtomString(), denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getTinkerMap(), denoptim.molecularmodeling.RingClosureTool.logger, denoptim.integration.tinker.TinkerAtom.setAtomType(), and denoptim.molecularmodeling.RingClosureTool.settings.

Referenced by denoptim.molecularmodeling.RingClosureTool.saturateRingClosingAttractor().

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Member Data Documentation

◆ fsep

final String denoptim.molecularmodeling.RingClosureTool.fsep = System.getProperty("file.separator")

package

File separator.

Definition at line 68 of file RingClosureTool.java.

◆ itn

int denoptim.molecularmodeling.RingClosureTool.itn = 0

private

Iteration counter for making unique filenames.

Definition at line 63 of file RingClosureTool.java.

Referenced by denoptim.molecularmodeling.RingClosureTool.attemptRingClosure().

◆ logger

Logger denoptim.molecularmodeling.RingClosureTool.logger

private

Program.specific logger.

Definition at line 78 of file RingClosureTool.java.

Referenced by denoptim.molecularmodeling.RingClosureTool.attemptAllRingClosures(), denoptim.molecularmodeling.RingClosureTool.attemptRingClosure(), denoptim.molecularmodeling.RingClosureTool.closeRings(), and denoptim.molecularmodeling.RingClosureTool.setTinkerTypes().

◆ settings

MMBuilderParameters denoptim.molecularmodeling.RingClosureTool.settings

private

Settings controlling the calculation.

Definition at line 73 of file RingClosureTool.java.

Referenced by denoptim.molecularmodeling.RingClosureTool.attemptRingClosure(), denoptim.molecularmodeling.RingClosureTool.closeRings(), denoptim.molecularmodeling.RingClosureTool.RingClosureTool(), and denoptim.molecularmodeling.RingClosureTool.setTinkerTypes().

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

/github/workspace/src/main/java/denoptim/molecularmodeling/RingClosureTool.java

Classes

Public Member Functions

Package Attributes

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ RingClosureTool()

Member Function Documentation

◆ attemptAllRingClosures()

◆ attemptRingClosure()

◆ closeRings()

◆ saturateRingClosingAttractor()

◆ setTinkerTypes()

Member Data Documentation

◆ fsep

◆ itn

◆ logger

◆ settings