RDKit: RDKit::MMFF::MMFFMolProperties Class Reference

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RDKit::MMFF::MMFFMolProperties Class Reference

`#include <AtomTyper.h>`

## Public Member Functions
| MMFFMolProperties (ROMol &mol, const 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)

## Detailed Description

Definition at line 47 of file MMFF/AtomTyper.h.

## Constructor & Destructor Documentation

RDKit::MMFF::MMFFMolProperties::MMFFMolProperties | ( | ROMol & | mol,
|  | const std::string & | mmffVariant = `"MMFF94"`,
|  | boost::uint8_t | verbosity = `MMFF_VERBOSITY_NONE`,
|  | std::ostream & | oStream = `std::cout`
| ) |  |

RDKit::MMFF::MMFFMolProperties::~MMFFMolProperties | ( |  | ) |
| inline

Definition at line 52 of file MMFF/AtomTyper.h.

## Member Function Documentation

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
| ) |  |

bool RDKit::MMFF::MMFFMolProperties::getMMFFAngleTerm | ( |  | ) |
| inline

Definition at line 83 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
| ) |  |

boost::uint8_t RDKit::MMFF::MMFFMolProperties::getMMFFAtomType | ( | const unsigned int | idx | ) |
| inline

Definition at line 65 of file MMFF/AtomTyper.h.

References URANGE_CHECK.

const ForceFields::MMFF::MMFFBond* RDKit::MMFF::MMFFMolProperties::getMMFFBondStretchEmpiricalRuleParams | ( | const ROMol & | mol,
|  | const Bond * | bond
| ) |  |

bool RDKit::MMFF::MMFFMolProperties::getMMFFBondStretchParams | ( | const ROMol & | mol,
|  | const unsigned int | idx1,
|  | const unsigned int | idx2,
|  | unsigned int & | bondType,
|  | MMFFBond & | mmffBondStretchParams
| ) |  |

bool RDKit::MMFF::MMFFMolProperties::getMMFFBondTerm | ( |  | ) |
| inline

Definition at line 81 of file MMFF/AtomTyper.h.

unsigned int RDKit::MMFF::MMFFMolProperties::getMMFFBondType | ( | const Bond * | bond | ) |

double RDKit::MMFF::MMFFMolProperties::getMMFFDielectricConstant | ( |  | ) |
| inline

Definition at line 110 of file MMFF/AtomTyper.h.

boost::uint8_t RDKit::MMFF::MMFFMolProperties::getMMFFDielectricModel | ( |  | ) |
| inline

Definition at line 114 of file MMFF/AtomTyper.h.

bool RDKit::MMFF::MMFFMolProperties::getMMFFEleTerm | ( |  | ) |
| inline

Definition at line 95 of file MMFF/AtomTyper.h.

double RDKit::MMFF::MMFFMolProperties::getMMFFFormalCharge | ( | const unsigned int | idx | ) |
| inline

Definition at line 70 of file MMFF/AtomTyper.h.

References URANGE_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
| ) |  |

bool RDKit::MMFF::MMFFMolProperties::getMMFFOopTerm | ( |  | ) |
| inline

Definition at line 89 of file MMFF/AtomTyper.h.

std::ostream& RDKit::MMFF::MMFFMolProperties::getMMFFOStream | ( |  | ) |
| inline

Definition at line 120 of file MMFF/AtomTyper.h.

double RDKit::MMFF::MMFFMolProperties::getMMFFPartialCharge | ( | const unsigned int | idx | ) |
| inline

Definition at line 75 of file MMFF/AtomTyper.h.

References URANGE_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
| ) |  |

bool RDKit::MMFF::MMFFMolProperties::getMMFFStretchBendTerm | ( |  | ) |
| inline

Definition at line 87 of file MMFF/AtomTyper.h.

const ForceFields::MMFF::MMFFTor* RDKit::MMFF::MMFFMolProperties::getMMFFTorsionEmpiricalRuleParams | ( | const ROMol & | mol,
|  | unsigned int | idx2,
|  | unsigned int | idx3
| ) |  |

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
| ) |  |

bool RDKit::MMFF::MMFFMolProperties::getMMFFTorsionTerm | ( |  | ) |
| inline

Definition at line 91 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
| ) |  |

const std::string RDKit::MMFF::MMFFMolProperties::getMMFFVariant | ( |  | ) |
| inline

Definition at line 102 of file MMFF/AtomTyper.h.

bool RDKit::MMFF::MMFFMolProperties::getMMFFVdWParams | ( | const unsigned int | idx1,
|  | const unsigned int | idx2,
|  | MMFFVdWRijstarEps & | mmffVdWParams
| ) |  |

bool RDKit::MMFF::MMFFMolProperties::getMMFFVdWTerm | ( |  | ) |
| inline

Definition at line 93 of file MMFF/AtomTyper.h.

boost::uint8_t RDKit::MMFF::MMFFMolProperties::getMMFFVerbosity | ( |  | ) |
| inline

Definition at line 118 of file MMFF/AtomTyper.h.

bool RDKit::MMFF::MMFFMolProperties::isValid | ( |  | ) |
| inline

Definition at line 121 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::isRingAromatic(), RDKit::MMFF::isTorsionInRingOfSize4or5(), RDKit::MMFF::sanitizeMMFFMol(), RDKit::MMFF::setMMFFAromaticity(), and URANGE_CHECK.

Referenced by RDKit::MMFF::MMFFOptimizeMolecule(), and RDKit::MMFF::MMFFOptimizeMoleculeConfs().

void RDKit::MMFF::MMFFMolProperties::setMMFFAngleTerm | ( | const bool | state | ) |
| inline

Definition at line 82 of file MMFF/AtomTyper.h.

void RDKit::MMFF::MMFFMolProperties::setMMFFBondTerm | ( | const bool | state | ) |
| inline

Definition at line 80 of file MMFF/AtomTyper.h.

void RDKit::MMFF::MMFFMolProperties::setMMFFDielectricConstant | ( | const double | dielConst | ) |
| inline

Definition at line 105 of file MMFF/AtomTyper.h.

References PRECONDITION.

void RDKit::MMFF::MMFFMolProperties::setMMFFDielectricModel | ( | boost::uint8_t | dielModel | ) |
| inline

Definition at line 111 of file MMFF/AtomTyper.h.

void RDKit::MMFF::MMFFMolProperties::setMMFFEleTerm | ( | const bool | state | ) |
| inline

Definition at line 94 of file MMFF/AtomTyper.h.

void RDKit::MMFF::MMFFMolProperties::setMMFFOopTerm | ( | const bool | state | ) |
| inline

Definition at line 88 of file MMFF/AtomTyper.h.

void RDKit::MMFF::MMFFMolProperties::setMMFFOStream | ( | std::ostream * | oStream | ) |
| inline

Definition at line 119 of file MMFF/AtomTyper.h.

void RDKit::MMFF::MMFFMolProperties::setMMFFStretchBendTerm | ( | const bool | state | ) |
| inline

Definition at line 84 of file MMFF/AtomTyper.h.

void RDKit::MMFF::MMFFMolProperties::setMMFFTorsionTerm | ( | const bool | state | ) |
| inline

Definition at line 90 of file MMFF/AtomTyper.h.

void RDKit::MMFF::MMFFMolProperties::setMMFFVariant | ( | const std::string & | mmffVariant | ) |
| inline

Definition at line 96 of file MMFF/AtomTyper.h.

References PRECONDITION.

void RDKit::MMFF::MMFFMolProperties::setMMFFVdWTerm | ( | const bool | state | ) |
| inline

Definition at line 92 of file MMFF/AtomTyper.h.

void RDKit::MMFF::MMFFMolProperties::setMMFFVerbosity | ( | boost::uint8_t | verbosity | ) |
| inline

Definition at line 115 of file MMFF/AtomTyper.h.

The documentation for this class was generated from the following file:

- MMFF/AtomTyper.h