RDKit
Open-source cheminformatics and machine learning.
RDKit::UFF Namespace Reference

Namespaces

 Tools
 

Typedefs

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

Functions

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

Typedef Documentation

Definition at line 27 of file UFF/AtomTyper.h.

Function Documentation

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().

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.
std::pair<AtomicParamVect, bool> RDKit::UFF::getAtomTypes ( const ROMol mol,
const std::string &  paramData = "" 
)
bool RDKit::UFF::getUFFAngleBendParams ( const ROMol mol,
unsigned int  idx1,
unsigned int  idx2,
unsigned int  idx3,
ForceFields::UFF::UFFAngle uffAngleBendParams 
)
bool RDKit::UFF::getUFFBondStretchParams ( const ROMol mol,
unsigned int  idx1,
unsigned int  idx2,
ForceFields::UFF::UFFBond uffBondStretchParams 
)
bool RDKit::UFF::getUFFInversionParams ( const ROMol mol,
unsigned int  idx1,
unsigned int  idx2,
unsigned int  idx3,
unsigned int  idx4,
ForceFields::UFF::UFFInv uffInversionParams 
)
bool RDKit::UFF::getUFFTorsionParams ( const ROMol mol,
unsigned int  idx1,
unsigned int  idx2,
unsigned int  idx3,
unsigned int  idx4,
ForceFields::UFF::UFFTor uffTorsionParams 
)
bool RDKit::UFF::getUFFVdWParams ( const ROMol mol,
unsigned int  idx1,
unsigned int  idx2,
ForceFields::UFF::UFFVdW uffVdWParams 
)
std::pair<int, double> RDKit::UFF::UFFOptimizeMolecule ( ROMol mol,
int  maxIters = 1000,
double  vdwThresh = 10.0,
int  confId = -1,
bool  ignoreInterfragInteractions = true 
)
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 
)

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

Definition at line 90 of file UFF.h.

References RDKit::ROMol::beginConformers(), constructForceField(), RDKit::ROMol::endConformers(), RDKit::ROMol::getNumConformers(), RDKit::getNumThreadsToUse(), and UFFOptimizeMolecule().