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DENOPTIM
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denoptim.utils.RotationalSpaceUtils Class Reference

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 (also torsional space) for a given molecule. 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 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 52 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 (also 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
molthe molecular structure
defRotBndsFilename 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.
addIterfragBondsif true includes all inter-fragment connections
excludeRingsif true cyclic bonds will be excluded
Exceptions
DENOPTIMException

Definition at line 78 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(), 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
molthe molecule as IAtomContainer
Exceptions
DENOPTIMException

Definition at line 230 of file RotationalSpaceUtils.java.

References denoptim.constants.DENOPTIMConstants.ATMPROPVERTEXPATH.

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

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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
filenamethe name of the text file to read
Exceptions
DENOPTIMException

Definition at line 282 of file RotationalSpaceUtils.java.

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

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Member Data Documentation

◆ builder

final IChemObjectBuilder denoptim.utils.RotationalSpaceUtils.builder
staticprivate
Initial value:
=
SilentChemObjectBuilder.getInstance()

Definition at line 54 of file RotationalSpaceUtils.java.

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

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