RDKit
Open-source cheminformatics and machine learning.
Loading...
Searching...
No Matches
RDKit::UFF Namespace Reference

Namespaces

namespace  Tools
 

Typedefs

typedef std::vector< const ForceFields::UFF::AtomicParams * > AtomicParamVect
 

Functions

RDKIT_FORCEFIELDHELPERS_EXPORT std::pair< AtomicParamVect, boolgetAtomTypes (const ROMol &mol, const std::string &paramData="")
 
RDKIT_FORCEFIELDHELPERS_EXPORT bool getUFFBondStretchParams (const ROMol &mol, unsigned int idx1, unsigned int idx2, ForceFields::UFF::UFFBond &uffBondStretchParams)
 
RDKIT_FORCEFIELDHELPERS_EXPORT bool getUFFAngleBendParams (const ROMol &mol, unsigned int idx1, unsigned int idx2, unsigned int idx3, ForceFields::UFF::UFFAngle &uffAngleBendParams)
 
RDKIT_FORCEFIELDHELPERS_EXPORT bool getUFFTorsionParams (const ROMol &mol, unsigned int idx1, unsigned int idx2, unsigned int idx3, unsigned int idx4, ForceFields::UFF::UFFTor &uffTorsionParams)
 
RDKIT_FORCEFIELDHELPERS_EXPORT bool getUFFInversionParams (const ROMol &mol, unsigned int idx1, unsigned int idx2, unsigned int idx3, unsigned int idx4, ForceFields::UFF::UFFInv &uffInversionParams)
 
RDKIT_FORCEFIELDHELPERS_EXPORT bool getUFFVdWParams (const ROMol &mol, unsigned int idx1, unsigned int idx2, ForceFields::UFF::UFFVdW &uffVdWParams)
 
RDKIT_FORCEFIELDHELPERS_EXPORT ForceFields::ForceFieldconstructForceField (ROMol &mol, double vdwThresh=100.0, int confId=-1, bool ignoreInterfragInteractions=true)
 Builds and returns a UFF force field for a molecule.
 
RDKIT_FORCEFIELDHELPERS_EXPORT ForceFields::ForceFieldconstructForceField (ROMol &mol, const AtomicParamVect &params, double vdwThresh=100.0, int confId=-1, bool ignoreInterfragInteractions=true)
 Builds and returns a UFF force field for a molecule.
 
std::pair< int, doubleUFFOptimizeMolecule (ROMol &mol, int maxIters=1000, double vdwThresh=10.0, int confId=-1, bool ignoreInterfragInteractions=true)
 Convenience function for optimizing a molecule using UFF.
 
void UFFOptimizeMoleculeConfs (ROMol &mol, std::vector< std::pair< int, double > > &res, int numThreads=1, int maxIters=1000, double vdwThresh=10.0, bool ignoreInterfragInteractions=true)
 

Typedef Documentation

◆ AtomicParamVect

Function Documentation

◆ constructForceField() [1/2]

RDKIT_FORCEFIELDHELPERS_EXPORT ForceFields::ForceField * RDKit::UFF::constructForceField ( ROMol & mol,
const AtomicParamVect & params,
double vdwThresh = 100.0,
int confId = -1,
bool ignoreInterfragInteractions = true )

Builds and returns a UFF force field for a molecule.

Parameters
molthe molecule to use
paramsa vector with pointers to the ForceFields::UFF::AtomicParams structures to be used
vdwThreshthe threshold to be used in adding van der Waals terms to the force field. Any non-bonded contact whose current distance is greater than vdwThresh * the minimum value for that contact will not be included.
confIdthe optional conformer id, if this isn't provided, the molecule's default confId will be used.
ignoreInterfragInteractionsif true, nonbonded terms will not be added between fragments
Returns
the new force field. The client is responsible for free'ing this.

◆ constructForceField() [2/2]

RDKIT_FORCEFIELDHELPERS_EXPORT ForceFields::ForceField * RDKit::UFF::constructForceField ( ROMol & mol,
double vdwThresh = 100.0,
int confId = -1,
bool ignoreInterfragInteractions = true )

Builds and returns a UFF force field for a molecule.

Parameters
molthe molecule to use
vdwThreshthe threshold to be used in adding van der Waals terms to the force field. Any non-bonded contact whose current distance is greater than vdwThresh * the minimum value for that contact will not be included.
confIdthe optional conformer id, if this isn't provided, the molecule's default confId will be used.
ignoreInterfragInteractionsif true, nonbonded terms will not be added between fragments
Returns
the new force field. The client is responsible for free'ing this.

Referenced by UFFOptimizeMolecule(), and UFFOptimizeMoleculeConfs().

◆ getAtomTypes()

RDKIT_FORCEFIELDHELPERS_EXPORT std::pair< AtomicParamVect, bool > RDKit::UFF::getAtomTypes ( const ROMol & mol,
const std::string & paramData = "" )

◆ getUFFAngleBendParams()

RDKIT_FORCEFIELDHELPERS_EXPORT bool RDKit::UFF::getUFFAngleBendParams ( const ROMol & mol,
unsigned int idx1,
unsigned int idx2,
unsigned int idx3,
ForceFields::UFF::UFFAngle & uffAngleBendParams )

◆ getUFFBondStretchParams()

RDKIT_FORCEFIELDHELPERS_EXPORT bool RDKit::UFF::getUFFBondStretchParams ( const ROMol & mol,
unsigned int idx1,
unsigned int idx2,
ForceFields::UFF::UFFBond & uffBondStretchParams )

◆ getUFFInversionParams()

RDKIT_FORCEFIELDHELPERS_EXPORT bool RDKit::UFF::getUFFInversionParams ( const ROMol & mol,
unsigned int idx1,
unsigned int idx2,
unsigned int idx3,
unsigned int idx4,
ForceFields::UFF::UFFInv & uffInversionParams )

◆ getUFFTorsionParams()

RDKIT_FORCEFIELDHELPERS_EXPORT bool RDKit::UFF::getUFFTorsionParams ( const ROMol & mol,
unsigned int idx1,
unsigned int idx2,
unsigned int idx3,
unsigned int idx4,
ForceFields::UFF::UFFTor & uffTorsionParams )

◆ getUFFVdWParams()

RDKIT_FORCEFIELDHELPERS_EXPORT bool RDKit::UFF::getUFFVdWParams ( const ROMol & mol,
unsigned int idx1,
unsigned int idx2,
ForceFields::UFF::UFFVdW & uffVdWParams )

◆ UFFOptimizeMolecule()

std::pair< int, double > RDKit::UFF::UFFOptimizeMolecule ( ROMol & mol,
int maxIters = 1000,
double vdwThresh = 10.0,
int confId = -1,
bool ignoreInterfragInteractions = true )
inline

Convenience function for optimizing a molecule using UFF.

Definition at line 40 of file UFF.h.

References constructForceField(), RDKit::ForceFieldsHelper::OptimizeMolecule(), and RDKit::rdvalue_is().

◆ UFFOptimizeMoleculeConfs()

void RDKit::UFF::UFFOptimizeMoleculeConfs ( ROMol & mol,
std::vector< std::pair< int, double > > & res,
int numThreads = 1,
int maxIters = 1000,
double vdwThresh = 10.0,
bool ignoreInterfragInteractions = true )
inline

Convenience function for optimizing all of a molecule's conformations using UFF

Definition at line 70 of file UFF.h.

References constructForceField(), RDKit::ForceFieldsHelper::OptimizeMoleculeConfs(), and RDKit::rdvalue_is().