Tool box for definition and management of the rotational space, which is given by the list of rotatable bonds. More...

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Static Public Member Functions
static ArrayList< ObjectPair >	defineRotatableBonds (IAtomContainer mol, String defRotBndsFile, boolean addIterfragBonds, boolean excludeRings, Logger logger) throws DENOPTIMException
	Define the rotational space (a.k.a. More...

static ArrayList< ObjectPair >	getInterVertexBonds (IAtomContainer mol) throws DENOPTIMException
	Search for all bonds connecting atoms corresponding to two different vertices in the DENOPTIMGraph. More...

static Map< String, String >	getRotationalSpaceDefinition (String filename) throws DENOPTIMException
	Read a formatted file and return a map with all the SMARTS queries identifying rotatable bonds. More...

static void	processConstrainedRotatableBonds (IAtomContainer mol, ArrayList< ObjectPair > rotatableBonds, String defRotBndContrFile, Logger logger) throws DENOPTIMException
	Process the constrained rotatable bonds. More...

static TreeMap< String, RotBndConstraint >	getRotationalConstraintsDefinition (String filename) throws DENOPTIMException
	Reads the definition of constraints on the rotatable bonds. More...

Static Public Attributes
static final String	PROPERTY_RSU_ATMID = "RSU-ATMID"

static final String	PROPERTY_ROTDBDCSTR_DEF = "ROTDBDCSTR_DEF"

static final String	PROPERTY_ROTDBDCSTR_VALUE = "ROTDBDCSTR_VALUE"

Static Private Attributes
static final IChemObjectBuilder	builder

Detailed Description

Tool box for definition and management of the rotational space, which is given by the list of rotatable bonds.

Author: Marco Foscato

Definition at line 54 of file RotationalSpaceUtils.java.

Member Function Documentation

◆ defineRotatableBonds()

static ArrayList< ObjectPair > denoptim.utils.RotationalSpaceUtils.defineRotatableBonds	(	IAtomContainer	mol,
		String	defRotBndsFile,
		boolean	addIterfragBonds,
		boolean	excludeRings,
		Logger	logger
	)		throws DENOPTIMException

static

Define the rotational space (a.k.a.

torsional space) for a given molecule. The method identifies the rotatable bonds by using a provided set of SMARTS queries and can consider all fragment-fragment bonds (i.e., interfragment connections) while excluding cyclic bonds. The propety DENOPTIMConstants.BONDPROPROTATABLE is used to store the rotatability in the Bonds.

Parameters

mol	the molecular structure
defRotBndsFile	name of a text file with a list of SMARTS queries that defines which bonds are considered rotatable bonds. This can be an empty string, in which case, only inter-fragment connections will be rotatable.
addIterfragBonds	if `true` includes all inter-fragment connections
excludeRings	if `true` cyclic bonds will be excluded

Exceptions

DENOPTIMException

Definition at line 86 of file RotationalSpaceUtils.java.

References denoptim.constants.DENOPTIMConstants.BONDPROPROTATABLE, denoptim.utils.RotationalSpaceUtils.builder, denoptim.utils.RotationalSpaceUtils.getInterVertexBonds(), denoptim.utils.ManySMARTSQuery.getMatchesOfSMARTS(), denoptim.utils.ManySMARTSQuery.getMessage(), denoptim.utils.ManySMARTSQuery.getNumMatchesOfQuery(), denoptim.utils.RotationalSpaceUtils.getRotationalSpaceDefinition(), denoptim.utils.ManySMARTSQuery.hasProblems(), denoptim.utils.RotationalSpaceUtils.PROPERTY_RSU_ATMID, and denoptim.utils.MoleculeUtils.removeRCA().

Referenced by denoptim.molecularmodeling.MultiMolecularModelBuilder.build3DTree(), denoptim.graph.DGraph.makeAllGraphsWithDifferentRingSets(), and denoptim.ga.EAUtils.setupRings().

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◆ getInterVertexBonds()

static ArrayList< ObjectPair > denoptim.utils.RotationalSpaceUtils.getInterVertexBonds ( IAtomContainer mol ) throws DENOPTIMException

static

Search for all bonds connecting atoms corresponding to two different vertices in the DENOPTIMGraph.

Vertex membership is evaluated by comparing the DENOPTIMConstants.ATMPROPVERTEXID property of each Atom.

Parameters

mol	the molecule as IAtomContainer

Exceptions

DENOPTIMException

Definition at line 241 of file RotationalSpaceUtils.java.

References denoptim.constants.DENOPTIMConstants.ATMPROPVERTEXPATH.

Referenced by denoptim.utils.RotationalSpaceUtils.defineRotatableBonds().

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◆ getRotationalConstraintsDefinition()

static TreeMap< String, RotBndConstraint > denoptim.utils.RotationalSpaceUtils.getRotationalConstraintsDefinition ( String filename ) throws DENOPTIMException

static

Reads the definition of constraints on the rotatable bonds.

Parameters

filename the file to be read in.

Returns: the map with names and constraints

Exceptions

DENOPTIMException should anything go wrong with the reading of the file

Definition at line 505 of file RotationalSpaceUtils.java.

Referenced by denoptim.utils.RotationalSpaceUtils.processConstrainedRotatableBonds().

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◆ getRotationalSpaceDefinition()

static Map< String, String > denoptim.utils.RotationalSpaceUtils.getRotationalSpaceDefinition ( String filename ) throws DENOPTIMException

static

Read a formatted file and return a map with all the SMARTS queries identifying rotatable bonds.

Parameters

filename the name of the text file to read

Exceptions

DENOPTIMException

Definition at line 293 of file RotationalSpaceUtils.java.

Referenced by denoptim.utils.RotationalSpaceUtils.defineRotatableBonds().

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◆ processConstrainedRotatableBonds()

static void denoptim.utils.RotationalSpaceUtils.processConstrainedRotatableBonds	(	IAtomContainer	mol,
		ArrayList< ObjectPair >	rotatableBonds,
		String	defRotBndContrFile,
		Logger	logger
	)		throws DENOPTIMException

static

Process the constrained rotatable bonds.

This method will remove the rotatable bonds that are constrained and record the details of the constraint among the bond properties.

Parameters

mol	the molecule as IAtomContainer
rotatableBonds	the list of rotatable bonds
defRotBndContrFile	the file with the definition of the constrained rotatable bonds @params logger the logging tool

Exceptions

DENOPTIMException
Error	if the constraint is not defined by 4 atoms or if the attempt to match the constrained rotatable bonds returns an error

Definition at line 387 of file RotationalSpaceUtils.java.

References denoptim.constants.DENOPTIMConstants.BONDPROPROTATABLE, denoptim.utils.RotationalSpaceUtils.builder, denoptim.utils.MoleculeUtils.getAtomRef(), denoptim.utils.ManySMARTSQuery.getMatchesOfSMARTS(), denoptim.utils.ManySMARTSQuery.getNumMatchesOfQuery(), denoptim.utils.RotationalSpaceUtils.getRotationalConstraintsDefinition(), denoptim.utils.ManySMARTSQuery.hasProblems(), denoptim.utils.RotationalSpaceUtils.PROPERTY_ROTDBDCSTR_DEF, denoptim.utils.RotationalSpaceUtils.PROPERTY_ROTDBDCSTR_VALUE, denoptim.utils.RotationalSpaceUtils.PROPERTY_RSU_ATMID, and denoptim.utils.MoleculeUtils.removeRCA().

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

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Member Data Documentation

◆ builder

final IChemObjectBuilder denoptim.utils.RotationalSpaceUtils.builder

staticprivate

Initial value:

=

SilentChemObjectBuilder.getInstance()

Definition at line 56 of file RotationalSpaceUtils.java.

Referenced by denoptim.utils.RotationalSpaceUtils.defineRotatableBonds(), and denoptim.utils.RotationalSpaceUtils.processConstrainedRotatableBonds().

◆ PROPERTY_ROTDBDCSTR_DEF

final String denoptim.utils.RotationalSpaceUtils.PROPERTY_ROTDBDCSTR_DEF = "ROTDBDCSTR_DEF"

static

Definition at line 62 of file RotationalSpaceUtils.java.

Referenced by denoptim.integration.tinker.TinkerUtils.getICFromIAC(), and denoptim.utils.RotationalSpaceUtils.processConstrainedRotatableBonds().

◆ PROPERTY_ROTDBDCSTR_VALUE

final String denoptim.utils.RotationalSpaceUtils.PROPERTY_ROTDBDCSTR_VALUE = "ROTDBDCSTR_VALUE"

static

Definition at line 63 of file RotationalSpaceUtils.java.

Referenced by denoptim.integration.tinker.TinkerUtils.getICFromIAC(), and denoptim.utils.RotationalSpaceUtils.processConstrainedRotatableBonds().

◆ PROPERTY_RSU_ATMID

final String denoptim.utils.RotationalSpaceUtils.PROPERTY_RSU_ATMID = "RSU-ATMID"

static

Definition at line 59 of file RotationalSpaceUtils.java.

Referenced by denoptim.utils.RotationalSpaceUtils.defineRotatableBonds(), and denoptim.utils.RotationalSpaceUtils.processConstrainedRotatableBonds().

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

/github/workspace/src/main/java/denoptim/utils/RotationalSpaceUtils.java

Static Public Member Functions

Static Public Attributes

Static Private Attributes

Detailed Description

Member Function Documentation

◆ defineRotatableBonds()

◆ getInterVertexBonds()

◆ getRotationalConstraintsDefinition()

◆ getRotationalSpaceDefinition()

◆ processConstrainedRotatableBonds()

Member Data Documentation

◆ builder

◆ PROPERTY_ROTDBDCSTR_DEF

◆ PROPERTY_ROTDBDCSTR_VALUE

◆ PROPERTY_RSU_ATMID