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RDKit
Open-source cheminformatics and machine learning.
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Namespaces | |
Tools | |
Typedefs | |
typedef std::vector< const ForceFields::UFF::AtomicParams * > | AtomicParamVect |
Functions | |
std::pair< AtomicParamVect, bool > | getAtomTypes (const ROMol &mol, const std::string ¶mData="") |
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::ForceField * | constructForceField (ROMol &mol, double vdwThresh=100.0, int confId=-1, bool ignoreInterfragInteractions=true) |
Builds and returns a UFF force field for a molecule. More... | |
ForceFields::ForceField * | constructForceField (ROMol &mol, const AtomicParamVect ¶ms, 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, unsigned int numThreads=1, int maxIters=1000, double vdwThresh=10.0, bool ignoreInterfragInteractions=true) |
Convenience function for optimizing all of a molecule's conformations using UFF. More... | |
typedef std::vector< const ForceFields::UFF::AtomicParams * > RDKit::UFF::AtomicParamVect |
Definition at line 27 of file UFF/AtomTyper.h.
ForceFields::ForceField* RDKit::UFF::constructForceField | ( | ROMol & | mol, |
double | vdwThresh = 100.0 , |
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int | confId = -1 , |
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bool | ignoreInterfragInteractions = true |
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Builds and returns a UFF force field for a molecule.
mol | the molecule to use |
vdwThresh | the 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. |
confId | the optional conformer id, if this isn't provided, the molecule's default confId will be used. |
ignoreInterfragInteractions | if true, nonbonded terms will not be added between fragments |
Referenced by UFFOptimizeMolecule(), and UFFOptimizeMoleculeConfs().
ForceFields::ForceField* RDKit::UFF::constructForceField | ( | ROMol & | mol, |
const AtomicParamVect & | params, | ||
double | vdwThresh = 100.0 , |
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int | confId = -1 , |
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bool | ignoreInterfragInteractions = true |
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Builds and returns a UFF force field for a molecule.
mol | the molecule to use |
params | a vector with pointers to the ForceFields::UFF::AtomicParams structures to be used |
vdwThresh | the 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. |
confId | the optional conformer id, if this isn't provided, the molecule's default confId will be used. |
ignoreInterfragInteractions | if true, nonbonded terms will not be added between fragments |
std::pair<AtomicParamVect,bool> RDKit::UFF::getAtomTypes | ( | const ROMol & | mol, |
const std::string & | paramData = "" |
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bool RDKit::UFF::getUFFAngleBendParams | ( | const ROMol & | mol, |
unsigned int | idx1, | ||
unsigned int | idx2, | ||
unsigned int | idx3, | ||
ForceFields::UFF::UFFAngle & | uffAngleBendParams | ||
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bool RDKit::UFF::getUFFBondStretchParams | ( | const ROMol & | mol, |
unsigned int | idx1, | ||
unsigned int | idx2, | ||
ForceFields::UFF::UFFBond & | uffBondStretchParams | ||
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bool RDKit::UFF::getUFFInversionParams | ( | const ROMol & | mol, |
unsigned int | idx1, | ||
unsigned int | idx2, | ||
unsigned int | idx3, | ||
unsigned int | idx4, | ||
ForceFields::UFF::UFFInv & | uffInversionParams | ||
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bool RDKit::UFF::getUFFTorsionParams | ( | const ROMol & | mol, |
unsigned int | idx1, | ||
unsigned int | idx2, | ||
unsigned int | idx3, | ||
unsigned int | idx4, | ||
ForceFields::UFF::UFFTor & | uffTorsionParams | ||
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bool RDKit::UFF::getUFFVdWParams | ( | const ROMol & | mol, |
unsigned int | idx1, | ||
unsigned int | idx2, | ||
ForceFields::UFF::UFFVdW & | uffVdWParams | ||
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std::pair<int,double> RDKit::UFF::UFFOptimizeMolecule | ( | ROMol & | mol, |
int | maxIters = 1000 , |
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double | vdwThresh = 10.0 , |
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int | confId = -1 , |
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bool | ignoreInterfragInteractions = true |
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Convenience function for optimizing a molecule using UFF.
Definition at line 39 of file UFF.h.
References RDKit::ROMol::beginConformers(), ForceFields::ForceField::calcEnergy(), constructForceField(), RDKit::ROMol::endConformers(), RDKit::ROMol::getNumAtoms(), ForceFields::ForceField::initialize(), ForceFields::ForceField::minimize(), and ForceFields::ForceField::positions().
Referenced by UFFOptimizeMoleculeConfs().
void RDKit::UFF::UFFOptimizeMoleculeConfs | ( | ROMol & | mol, |
std::vector< std::pair< int, double > > & | res, | ||
unsigned int | numThreads = 1 , |
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int | maxIters = 1000 , |
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double | vdwThresh = 10.0 , |
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bool | ignoreInterfragInteractions = true |
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Convenience function for optimizing all of a molecule's conformations using UFF.
Definition at line 89 of file UFF.h.
References RDKit::ROMol::beginConformers(), constructForceField(), RDKit::ROMol::endConformers(), RDKit::ROMol::getNumConformers(), and UFFOptimizeMolecule().