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RDKit
Open-source cheminformatics and machine learning.
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Namespaces | |
Tools | |
Classes | |
class | MMFFAtomProperties |
class | MMFFMolProperties |
Typedefs | |
typedef boost::shared_ptr< MMFFAtomProperties > | MMFFAtomPropertiesPtr |
Enumerations | |
enum | { CONSTANT = 1, DISTANCE = 2 } |
enum | { MMFF_VERBOSITY_NONE = 0, MMFF_VERBOSITY_LOW = 1, MMFF_VERBOSITY_HIGH = 2 } |
Functions | |
RDKIT_FORCEFIELDHELPERS_EXPORT unsigned int | isAngleInRingOfSize3or4 (const ROMol &mol, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3) |
RDKIT_FORCEFIELDHELPERS_EXPORT unsigned int | isTorsionInRingOfSize4or5 (const ROMol &mol, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3, const unsigned int idx4) |
RDKIT_FORCEFIELDHELPERS_EXPORT bool | isRingAromatic (const ROMol &mol, const INT_VECT &ringIndxVect) |
RDKIT_FORCEFIELDHELPERS_EXPORT bool | isAtomInAromaticRingOfSize (const Atom *atom, const unsigned int ringSize) |
RDKIT_FORCEFIELDHELPERS_EXPORT bool | isAtomNOxide (const Atom *atom) |
RDKIT_FORCEFIELDHELPERS_EXPORT bool | areAtomsInSameAromaticRing (const ROMol &mol, const unsigned int idx1, const unsigned int idx2) |
RDKIT_FORCEFIELDHELPERS_EXPORT bool | areAtomsInSameRingOfSize (const ROMol &mol, const unsigned int ringSize, const unsigned int numAtoms,...) |
RDKIT_FORCEFIELDHELPERS_EXPORT unsigned int | sanitizeMMFFMol (RWMol &mol) |
RDKIT_FORCEFIELDHELPERS_EXPORT void | setMMFFAromaticity (RWMol &mol) |
RDKIT_FORCEFIELDHELPERS_EXPORT unsigned int | getMMFFStretchBendType (const unsigned int angleType, const unsigned int bondType1, const unsigned int bondType2) |
RDKIT_FORCEFIELDHELPERS_EXPORT unsigned int | getPeriodicTableRow (const int atomicNum) |
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFAngle * | getMMFFAngleBendEmpiricalRuleParams (const ROMol &mol, const ForceFields::MMFF::MMFFAngle *oldMMFFAngleParams, const ForceFields::MMFF::MMFFProp *mmffPropParamsCentralAtom, const ForceFields::MMFF::MMFFBond *mmffBondParams1, const ForceFields::MMFF::MMFFBond *mmffBondParams2, unsigned int idx1, unsigned int idx2, unsigned int idx3) |
RDKIT_FORCEFIELDHELPERS_EXPORT ForceFields::ForceField * | constructForceField (ROMol &mol, double nonBondedThresh=100.0, int confId=-1, bool ignoreInterfragInteractions=true) |
Builds and returns a MMFF force field for a molecule. More... | |
RDKIT_FORCEFIELDHELPERS_EXPORT ForceFields::ForceField * | constructForceField (ROMol &mol, MMFFMolProperties *mmffMolProperties, double nonBondedThresh=100.0, int confId=-1, bool ignoreInterfragInteractions=true) |
Builds and returns a MMFF force field for a molecule. More... | |
std::pair< int, double > | MMFFOptimizeMolecule (ROMol &mol, int maxIters=1000, std::string mmffVariant="MMFF94", double nonBondedThresh=10.0, int confId=-1, bool ignoreInterfragInteractions=true) |
Convenience function for optimizing a molecule using MMFF. More... | |
void | MMFFOptimizeMoleculeConfs (ROMol &mol, std::vector< std::pair< int, double >> &res, int numThreads=1, int maxIters=1000, std::string mmffVariant="MMFF94", double nonBondedThresh=10.0, bool ignoreInterfragInteractions=true) |
Convenience function for optimizing all of a molecule's conformations using. More... | |
typedef boost::shared_ptr<MMFFAtomProperties> RDKit::MMFF::MMFFAtomPropertiesPtr |
Definition at line 41 of file MMFF/AtomTyper.h.
anonymous enum |
Enumerator | |
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CONSTANT | |
DISTANCE |
Definition at line 42 of file MMFF/AtomTyper.h.
anonymous enum |
Enumerator | |
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MMFF_VERBOSITY_NONE | |
MMFF_VERBOSITY_LOW | |
MMFF_VERBOSITY_HIGH |
Definition at line 43 of file MMFF/AtomTyper.h.
RDKIT_FORCEFIELDHELPERS_EXPORT bool RDKit::MMFF::areAtomsInSameAromaticRing | ( | const ROMol & | mol, |
const unsigned int | idx1, | ||
const unsigned int | idx2 | ||
) |
Referenced by RDKit::MMFF::MMFFMolProperties::isValid().
RDKIT_FORCEFIELDHELPERS_EXPORT bool RDKit::MMFF::areAtomsInSameRingOfSize | ( | const ROMol & | mol, |
const unsigned int | ringSize, | ||
const unsigned int | numAtoms, | ||
... | |||
) |
Referenced by RDKit::MMFF::MMFFMolProperties::isValid().
RDKIT_FORCEFIELDHELPERS_EXPORT ForceFields::ForceField* RDKit::MMFF::constructForceField | ( | ROMol & | mol, |
double | nonBondedThresh = 100.0 , |
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int | confId = -1 , |
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bool | ignoreInterfragInteractions = true |
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Builds and returns a MMFF force field for a molecule.
mol | the molecule to use |
nonBondedThresh | the threshold to be used in adding non-bonded terms to the force field. Any non-bonded contact whose current distance is greater than nonBondedThresh * 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 MMFFOptimizeMolecule(), and MMFFOptimizeMoleculeConfs().
RDKIT_FORCEFIELDHELPERS_EXPORT ForceFields::ForceField* RDKit::MMFF::constructForceField | ( | ROMol & | mol, |
MMFFMolProperties * | mmffMolProperties, | ||
double | nonBondedThresh = 100.0 , |
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int | confId = -1 , |
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bool | ignoreInterfragInteractions = true |
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Builds and returns a MMFF force field for a molecule.
mol | the molecule to use |
mmffMolProperties | pointer to a MMFFMolProperties object |
nonBondedThresh | the threshold to be used in adding non-bonded terms to the force field. Any non-bonded contact whose current distance is greater than nonBondedThresh * 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 |
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFAngle* RDKit::MMFF::getMMFFAngleBendEmpiricalRuleParams | ( | const ROMol & | mol, |
const ForceFields::MMFF::MMFFAngle * | oldMMFFAngleParams, | ||
const ForceFields::MMFF::MMFFProp * | mmffPropParamsCentralAtom, | ||
const ForceFields::MMFF::MMFFBond * | mmffBondParams1, | ||
const ForceFields::MMFF::MMFFBond * | mmffBondParams2, | ||
unsigned int | idx1, | ||
unsigned int | idx2, | ||
unsigned int | idx3 | ||
) |
Referenced by RDKit::MMFF::MMFFMolProperties::isValid().
RDKIT_FORCEFIELDHELPERS_EXPORT unsigned int RDKit::MMFF::getMMFFStretchBendType | ( | const unsigned int | angleType, |
const unsigned int | bondType1, | ||
const unsigned int | bondType2 | ||
) |
Referenced by RDKit::MMFF::MMFFMolProperties::isValid().
RDKIT_FORCEFIELDHELPERS_EXPORT unsigned int RDKit::MMFF::getPeriodicTableRow | ( | const int | atomicNum | ) |
Referenced by RDKit::MMFF::MMFFMolProperties::isValid().
RDKIT_FORCEFIELDHELPERS_EXPORT unsigned int RDKit::MMFF::isAngleInRingOfSize3or4 | ( | const ROMol & | mol, |
const unsigned int | idx1, | ||
const unsigned int | idx2, | ||
const unsigned int | idx3 | ||
) |
Referenced by RDKit::MMFF::MMFFMolProperties::isValid().
RDKIT_FORCEFIELDHELPERS_EXPORT bool RDKit::MMFF::isAtomInAromaticRingOfSize | ( | const Atom * | atom, |
const unsigned int | ringSize | ||
) |
Referenced by RDKit::MMFF::MMFFMolProperties::isValid().
RDKIT_FORCEFIELDHELPERS_EXPORT bool RDKit::MMFF::isAtomNOxide | ( | const Atom * | atom | ) |
Referenced by RDKit::MMFF::MMFFMolProperties::isValid().
RDKIT_FORCEFIELDHELPERS_EXPORT bool RDKit::MMFF::isRingAromatic | ( | const ROMol & | mol, |
const INT_VECT & | ringIndxVect | ||
) |
Referenced by RDKit::MMFF::MMFFMolProperties::isValid().
RDKIT_FORCEFIELDHELPERS_EXPORT unsigned int RDKit::MMFF::isTorsionInRingOfSize4or5 | ( | const ROMol & | mol, |
const unsigned int | idx1, | ||
const unsigned int | idx2, | ||
const unsigned int | idx3, | ||
const unsigned int | idx4 | ||
) |
Referenced by RDKit::MMFF::MMFFMolProperties::isValid().
std::pair<int, double> RDKit::MMFF::MMFFOptimizeMolecule | ( | ROMol & | mol, |
int | maxIters = 1000 , |
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std::string | mmffVariant = "MMFF94" , |
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double | nonBondedThresh = 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 MMFF.
Definition at line 44 of file MMFF.h.
References RDKit::ROMol::beginConformers(), ForceFields::ForceField::calcEnergy(), constructForceField(), RDKit::ROMol::endConformers(), RDKit::ROMol::getNumAtoms(), ForceFields::ForceField::initialize(), RDKit::MMFF::MMFFMolProperties::isValid(), ForceFields::ForceField::minimize(), and ForceFields::ForceField::positions().
void RDKit::MMFF::MMFFOptimizeMoleculeConfs | ( | ROMol & | mol, |
std::vector< std::pair< int, double >> & | res, | ||
int | numThreads = 1 , |
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int | maxIters = 1000 , |
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std::string | mmffVariant = "MMFF94" , |
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double | nonBondedThresh = 10.0 , |
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bool | ignoreInterfragInteractions = true |
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) |
Convenience function for optimizing all of a molecule's conformations using.
Definition at line 105 of file MMFF.h.
References RDKit::ROMol::beginConformers(), ForceFields::ForceField::calcEnergy(), constructForceField(), RDKit::ROMol::endConformers(), RDKit::ROMol::getNumAtoms(), RDKit::ROMol::getNumConformers(), RDKit::getNumThreadsToUse(), ForceFields::ForceField::initialize(), RDKit::MMFF::MMFFMolProperties::isValid(), ForceFields::ForceField::minimize(), and ForceFields::ForceField::positions().
RDKIT_FORCEFIELDHELPERS_EXPORT unsigned int RDKit::MMFF::sanitizeMMFFMol | ( | RWMol & | mol | ) |
Referenced by RDKit::MMFF::MMFFMolProperties::isValid().
RDKIT_FORCEFIELDHELPERS_EXPORT void RDKit::MMFF::setMMFFAromaticity | ( | RWMol & | mol | ) |
Referenced by RDKit::MMFF::MMFFMolProperties::isValid().