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RDKit
Open-source cheminformatics and machine learning.
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#include <AtomTyper.h>
Public Member Functions | |
MMFFMolProperties (ROMol &mol, std::string mmffVariant="MMFF94", boost::uint8_t verbosity=MMFF_VERBOSITY_NONE, std::ostream &oStream=std::cout) | |
~MMFFMolProperties () | |
unsigned int | getMMFFBondType (const Bond *bond) |
unsigned int | getMMFFAngleType (const ROMol &mol, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3) |
const std::pair< unsigned int, unsigned int > | getMMFFTorsionType (const ROMol &mol, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3, const unsigned int idx4) |
void | computeMMFFCharges (const ROMol &mol) |
const ForceFields::MMFF::MMFFTor * | getMMFFTorsionEmpiricalRuleParams (const ROMol &mol, unsigned int idx2, unsigned int idx3) |
const ForceFields::MMFF::MMFFBond * | getMMFFBondStretchEmpiricalRuleParams (const ROMol &mol, const Bond *bond) |
boost::uint8_t | getMMFFAtomType (const unsigned int idx) |
double | getMMFFFormalCharge (const unsigned int idx) |
double | getMMFFPartialCharge (const unsigned int idx) |
void | setMMFFBondTerm (const bool state) |
bool | getMMFFBondTerm () |
void | setMMFFAngleTerm (const bool state) |
bool | getMMFFAngleTerm () |
void | setMMFFStretchBendTerm (const bool state) |
bool | getMMFFStretchBendTerm () |
void | setMMFFOopTerm (const bool state) |
bool | getMMFFOopTerm () |
void | setMMFFTorsionTerm (const bool state) |
bool | getMMFFTorsionTerm () |
void | setMMFFVdWTerm (const bool state) |
bool | getMMFFVdWTerm () |
void | setMMFFEleTerm (const bool state) |
bool | getMMFFEleTerm () |
void | setMMFFVariant (const std::string mmffVariant) |
const std::string | getMMFFVariant () |
void | setMMFFDielectricConstant (const double dielConst) |
double | getMMFFDielectricConstant () |
void | setMMFFDielectricModel (boost::uint8_t dielModel) |
boost::uint8_t | getMMFFDielectricModel () |
void | setMMFFVerbosity (boost::uint8_t verbosity) |
boost::uint8_t | getMMFFVerbosity () |
void | setMMFFOStream (std::ostream *oStream) |
std::ostream & | getMMFFOStream () |
bool | isValid () |
bool | getMMFFBondStretchParams (const ROMol &mol, const unsigned int idx1, const unsigned int idx2, unsigned int &bondType, MMFFBond &mmffBondStretchParams) |
bool | getMMFFAngleBendParams (const ROMol &mol, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3, unsigned int &angleType, MMFFAngle &mmffAngleBendParams) |
bool | getMMFFStretchBendParams (const ROMol &mol, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3, unsigned int &stretchBendType, MMFFStbn &mmffStretchBendParams, MMFFBond mmffBondStretchParams[2], MMFFAngle &mmffAngleBendParams) |
bool | getMMFFTorsionParams (const ROMol &mol, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3, const unsigned int idx4, unsigned int &torsionType, MMFFTor &mmffTorsionParams) |
bool | getMMFFOopBendParams (const ROMol &mol, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3, const unsigned int idx4, MMFFOop &mmffOopBendParams) |
bool | getMMFFVdWParams (const unsigned int idx1, const unsigned int idx2, MMFFVdWRijstarEps &mmffVdWParams) |
Definition at line 52 of file MMFF/AtomTyper.h.
RDKit::MMFF::MMFFMolProperties::MMFFMolProperties | ( | ROMol & | mol, |
std::string | mmffVariant = "MMFF94" , |
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boost::uint8_t | verbosity = MMFF_VERBOSITY_NONE , |
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std::ostream & | oStream = std::cout |
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Definition at line 57 of file MMFF/AtomTyper.h.
void RDKit::MMFF::MMFFMolProperties::computeMMFFCharges | ( | const ROMol & | mol | ) |
bool RDKit::MMFF::MMFFMolProperties::getMMFFAngleBendParams | ( | const ROMol & | mol, |
const unsigned int | idx1, | ||
const unsigned int | idx2, | ||
const unsigned int | idx3, | ||
unsigned int & | angleType, | ||
MMFFAngle & | mmffAngleBendParams | ||
) |
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Definition at line 100 of file MMFF/AtomTyper.h.
unsigned int RDKit::MMFF::MMFFMolProperties::getMMFFAngleType | ( | const ROMol & | mol, |
const unsigned int | idx1, | ||
const unsigned int | idx2, | ||
const unsigned int | idx3 | ||
) |
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Definition at line 70 of file MMFF/AtomTyper.h.
References RANGE_CHECK.
const ForceFields::MMFF::MMFFBond* RDKit::MMFF::MMFFMolProperties::getMMFFBondStretchEmpiricalRuleParams | ( | const ROMol & | mol, |
const Bond * | bond | ||
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bool RDKit::MMFF::MMFFMolProperties::getMMFFBondStretchParams | ( | const ROMol & | mol, |
const unsigned int | idx1, | ||
const unsigned int | idx2, | ||
unsigned int & | bondType, | ||
MMFFBond & | mmffBondStretchParams | ||
) |
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Definition at line 92 of file MMFF/AtomTyper.h.
unsigned int RDKit::MMFF::MMFFMolProperties::getMMFFBondType | ( | const Bond * | bond | ) |
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Definition at line 161 of file MMFF/AtomTyper.h.
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Definition at line 169 of file MMFF/AtomTyper.h.
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Definition at line 140 of file MMFF/AtomTyper.h.
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Definition at line 76 of file MMFF/AtomTyper.h.
References RANGE_CHECK.
bool RDKit::MMFF::MMFFMolProperties::getMMFFOopBendParams | ( | const ROMol & | mol, |
const unsigned int | idx1, | ||
const unsigned int | idx2, | ||
const unsigned int | idx3, | ||
const unsigned int | idx4, | ||
MMFFOop & | mmffOopBendParams | ||
) |
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Definition at line 116 of file MMFF/AtomTyper.h.
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Definition at line 185 of file MMFF/AtomTyper.h.
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Definition at line 82 of file MMFF/AtomTyper.h.
References RANGE_CHECK.
bool RDKit::MMFF::MMFFMolProperties::getMMFFStretchBendParams | ( | const ROMol & | mol, |
const unsigned int | idx1, | ||
const unsigned int | idx2, | ||
const unsigned int | idx3, | ||
unsigned int & | stretchBendType, | ||
MMFFStbn & | mmffStretchBendParams, | ||
MMFFBond | mmffBondStretchParams[2], | ||
MMFFAngle & | mmffAngleBendParams | ||
) |
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Definition at line 108 of file MMFF/AtomTyper.h.
const ForceFields::MMFF::MMFFTor* RDKit::MMFF::MMFFMolProperties::getMMFFTorsionEmpiricalRuleParams | ( | const ROMol & | mol, |
unsigned int | idx2, | ||
unsigned int | idx3 | ||
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bool RDKit::MMFF::MMFFMolProperties::getMMFFTorsionParams | ( | const ROMol & | mol, |
const unsigned int | idx1, | ||
const unsigned int | idx2, | ||
const unsigned int | idx3, | ||
const unsigned int | idx4, | ||
unsigned int & | torsionType, | ||
MMFFTor & | mmffTorsionParams | ||
) |
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Definition at line 124 of file MMFF/AtomTyper.h.
const std::pair<unsigned int, unsigned int> RDKit::MMFF::MMFFMolProperties::getMMFFTorsionType | ( | const ROMol & | mol, |
const unsigned int | idx1, | ||
const unsigned int | idx2, | ||
const unsigned int | idx3, | ||
const unsigned int | idx4 | ||
) |
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Definition at line 151 of file MMFF/AtomTyper.h.
bool RDKit::MMFF::MMFFMolProperties::getMMFFVdWParams | ( | const unsigned int | idx1, |
const unsigned int | idx2, | ||
MMFFVdWRijstarEps & | mmffVdWParams | ||
) |
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Definition at line 132 of file MMFF/AtomTyper.h.
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Definition at line 177 of file MMFF/AtomTyper.h.
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Definition at line 189 of file MMFF/AtomTyper.h.
References RDKit::MMFF::areAtomsInSameAromaticRing(), RDKit::MMFF::areAtomsInSameRingOfSize(), RDKit::MMFF::getMMFFAngleBendEmpiricalRuleParams(), RDKit::MMFF::getMMFFStretchBendType(), RDKit::MMFF::getPeriodicTableRow(), RDKit::MMFF::isAngleInRingOfSize3or4(), RDKit::MMFF::isAtomInAromaticRingOfSize(), RDKit::MMFF::isAtomNOxide(), RDKit::MMFF::isTorsionInRingOfSize4or5(), RANGE_CHECK, RDKit::MMFF::sanitizeMMFFMol(), and RDKit::MMFF::setMMFFAromaticity().
Referenced by RDKit::MMFF::MMFFOptimizeMolecule(), and RDKit::MMFF::MMFFOptimizeMoleculeConfs().
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Definition at line 96 of file MMFF/AtomTyper.h.
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Definition at line 88 of file MMFF/AtomTyper.h.
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Definition at line 155 of file MMFF/AtomTyper.h.
References PRECONDITION.
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Definition at line 165 of file MMFF/AtomTyper.h.
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Definition at line 136 of file MMFF/AtomTyper.h.
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Definition at line 112 of file MMFF/AtomTyper.h.
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Definition at line 181 of file MMFF/AtomTyper.h.
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Definition at line 104 of file MMFF/AtomTyper.h.
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Definition at line 120 of file MMFF/AtomTyper.h.
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Definition at line 144 of file MMFF/AtomTyper.h.
References PRECONDITION.
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Definition at line 128 of file MMFF/AtomTyper.h.
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Definition at line 173 of file MMFF/AtomTyper.h.