MMFF/AtomTyper.h
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//
// Copyright (C) 2013-2016 Paolo Tosco
//
// Copyright (C) 2004-2006 Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <RDGeneral/export.h>
#ifndef _RD_MMFFATOMTYPER_H__
#define _RD_MMFFATOMTYPER_H__
#include <vector>
#include <string>
#include <iostream>
#include <ForceField/MMFF/Params.h>
#include <cstdint>
namespace RDKit {
class ROMol;
class RWMol;
class Atom;
class Bond;
namespace MMFF {
namespace DefaultParameters {
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFPropCollection *
getMMFFProp();
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFAromCollection *
getMMFFArom();
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFDefCollection *
getMMFFDef();
RDKIT_FORCEFIELDHELPERS_EXPORT const
ForceFields::MMFF::MMFFHerschbachLaurieCollection *
getMMFFHerschbachLaurie();
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFPBCICollection *
getMMFFPBCI();
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFAngleCollection *
getMMFFAngle();
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFStbnCollection *
getMMFFStbn();
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFDfsbCollection *
getMMFFDfsb();
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFTorCollection *
getMMFFTor(const bool isMMFFs);
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFOopCollection *
getMMFFOop(const bool isMMFFs);
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFVdWCollection *
getMMFFVdW();
} // namespace DefaultParameters
class RingMembershipSize;
using namespace ForceFields::MMFF;
class RDKIT_FORCEFIELDHELPERS_EXPORT MMFFAtomProperties {
public:
MMFFAtomProperties() {}
~MMFFAtomProperties() = default;
std::uint8_t mmffAtomType{0};
double mmffFormalCharge{0.0};
double mmffPartialCharge{0.0};
};
typedef boost::shared_ptr<MMFFAtomProperties> MMFFAtomPropertiesPtr;
enum { CONSTANT = 1, DISTANCE = 2 };
enum {
MMFF_VERBOSITY_NONE = 0,
MMFF_VERBOSITY_LOW = 1,
MMFF_VERBOSITY_HIGH = 2
};
class RDKIT_FORCEFIELDHELPERS_EXPORT MMFFMolProperties {
public:
MMFFMolProperties(ROMol &mol, const std::string &mmffVariant = "MMFF94",
std::uint8_t verbosity = MMFF_VERBOSITY_NONE,
std::ostream &oStream = std::cout);
~MMFFMolProperties() = default;
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);
std::uint8_t getMMFFAtomType(const unsigned int idx) {
URANGE_CHECK(idx, this->d_MMFFAtomPropertiesPtrVect.size());
return this->d_MMFFAtomPropertiesPtrVect[idx]->mmffAtomType;
}
double getMMFFFormalCharge(const unsigned int idx) {
URANGE_CHECK(idx, this->d_MMFFAtomPropertiesPtrVect.size());
return this->d_MMFFAtomPropertiesPtrVect[idx]->mmffFormalCharge;
}
double getMMFFPartialCharge(const unsigned int idx) {
URANGE_CHECK(idx, this->d_MMFFAtomPropertiesPtrVect.size());
return this->d_MMFFAtomPropertiesPtrVect[idx]->mmffPartialCharge;
}
void setMMFFBondTerm(const bool state) { this->d_bondTerm = state; }
bool getMMFFBondTerm() { return this->d_bondTerm; }
void setMMFFAngleTerm(const bool state) { this->d_angleTerm = state; }
bool getMMFFAngleTerm() { return this->d_angleTerm; }
void setMMFFStretchBendTerm(const bool state) {
this->d_stretchBendTerm = state;
}
bool getMMFFStretchBendTerm() { return this->d_stretchBendTerm; }
void setMMFFOopTerm(const bool state) { this->d_oopTerm = state; }
bool getMMFFOopTerm() { return this->d_oopTerm; }
void setMMFFTorsionTerm(const bool state) { this->d_torsionTerm = state; }
bool getMMFFTorsionTerm() { return this->d_torsionTerm; }
void setMMFFVdWTerm(const bool state) { this->d_vdWTerm = state; }
bool getMMFFVdWTerm() { return this->d_vdWTerm; }
void setMMFFEleTerm(const bool state) { this->d_eleTerm = state; }
bool getMMFFEleTerm() { return this->d_eleTerm; }
void setMMFFVariant(const std::string &mmffVariant) {
PRECONDITION((mmffVariant == "MMFF94") || (mmffVariant == "MMFF94s"),
"bad MMFF variant");
this->d_mmffs = ((mmffVariant == "MMFF94s") ? true : false);
}
const std::string getMMFFVariant() {
return (this->d_mmffs ? "MMFF94s" : "MMFF94");
}
void setMMFFDielectricConstant(const double dielConst) {
PRECONDITION(dielConst > 0.0, "bad dielectric constant");
this->d_dielConst = dielConst;
}
double getMMFFDielectricConstant() { return this->d_dielConst; }
void setMMFFDielectricModel(std::uint8_t dielModel) {
this->d_dielModel = dielModel;
}
std::uint8_t getMMFFDielectricModel() { return this->d_dielModel; }
void setMMFFVerbosity(std::uint8_t verbosity) {
this->d_verbosity = verbosity;
}
std::uint8_t getMMFFVerbosity() { return this->d_verbosity; }
void setMMFFOStream(std::ostream *oStream) { this->d_oStream = oStream; }
std::ostream &getMMFFOStream() { return *(this->d_oStream); }
bool isValid() { return d_valid; }
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);
private:
void setMMFFHeavyAtomType(const RingMembershipSize &rmSize, const Atom *atom);
void setMMFFHydrogenType(const Atom *atom);
void setMMFFFormalCharge(const unsigned int idx, const double fChg) {
URANGE_CHECK(idx, this->d_MMFFAtomPropertiesPtrVect.size());
this->d_MMFFAtomPropertiesPtrVect[idx]->mmffFormalCharge = fChg;
}
void setMMFFPartialCharge(const unsigned int idx, const double pChg) {
URANGE_CHECK(idx, this->d_MMFFAtomPropertiesPtrVect.size());
this->d_MMFFAtomPropertiesPtrVect[idx]->mmffPartialCharge = pChg;
}
bool d_valid;
bool d_mmffs;
bool d_bondTerm;
bool d_angleTerm;
bool d_stretchBendTerm;
bool d_oopTerm;
bool d_torsionTerm;
bool d_vdWTerm;
bool d_eleTerm;
double d_dielConst; //!< the dielectric constant
std::uint8_t d_dielModel; //!< the dielectric model (1 = constant, 2 =
// distance-dependent)
std::uint8_t d_verbosity;
std::ostream *d_oStream;
std::vector<MMFFAtomPropertiesPtr> d_MMFFAtomPropertiesPtrVect;
};
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);
} // namespace MMFF
} // namespace RDKit
#endif
URANGE_CHECK
#define URANGE_CHECK(x, hi)
Definition: Invariant.h:142
PRECONDITION
#define PRECONDITION(expr, mess)
Definition: Invariant.h:109
Params.h
ForceFields::MMFF::MMFFAngleCollection
Definition: MMFF/Params.h:556
ForceFields::MMFF::MMFFAngle
class to store MMFF parameters for angle bending
Definition: MMFF/Params.h:112
ForceFields::MMFF::MMFFAromCollection
Definition: MMFF/Params.h:158
ForceFields::MMFF::MMFFBond
class to store MMFF parameters for bond stretching
Definition: MMFF/Params.h:88
ForceFields::MMFF::MMFFDefCollection
Definition: MMFF/Params.h:175
ForceFields::MMFF::MMFFDfsbCollection
Definition: MMFF/Params.h:770
ForceFields::MMFF::MMFFHerschbachLaurieCollection
Definition: MMFF/Params.h:465
ForceFields::MMFF::MMFFOopCollection
Definition: MMFF/Params.h:816
ForceFields::MMFF::MMFFOop
class to store MMFF parameters for out-of-plane bending
Definition: MMFF/Params.h:126
ForceFields::MMFF::MMFFPBCICollection
Definition: MMFF/Params.h:236
ForceFields::MMFF::MMFFPropCollection
Definition: MMFF/Params.h:203
ForceFields::MMFF::MMFFProp
class to store MMFF Properties
Definition: MMFF/Params.h:61
ForceFields::MMFF::MMFFStbnCollection
Definition: MMFF/Params.h:670
ForceFields::MMFF::MMFFStbn
class to store MMFF parameters for stretch-bending
Definition: MMFF/Params.h:119
ForceFields::MMFF::MMFFTorCollection
Definition: MMFF/Params.h:926
ForceFields::MMFF::MMFFTor
class to store MMFF parameters for torsions
Definition: MMFF/Params.h:132
ForceFields::MMFF::MMFFVdWCollection
Definition: MMFF/Params.h:1095
ForceFields::MMFF::MMFFVdWRijstarEps
Definition: MMFF/Params.h:150
RDKit::Atom
The class for representing atoms.
Definition: Atom.h:68
RDKit::Bond
class for representing a bond
Definition: Bond.h:46
RDKit::MMFF::MMFFAtomProperties
Definition: MMFF/AtomTyper.h:58
RDKit::MMFF::MMFFAtomProperties::~MMFFAtomProperties
~MMFFAtomProperties()=default
RDKit::MMFF::MMFFAtomProperties::MMFFAtomProperties
MMFFAtomProperties()
Definition: MMFF/AtomTyper.h:60
RDKit::MMFF::MMFFMolProperties
Definition: MMFF/AtomTyper.h:74
RDKit::MMFF::MMFFMolProperties::getMMFFStretchBendParams
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)
RDKit::MMFF::MMFFMolProperties::setMMFFStretchBendTerm
void setMMFFStretchBendTerm(const bool state)
Definition: MMFF/AtomTyper.h:111
RDKit::MMFF::MMFFMolProperties::getMMFFDielectricModel
std::uint8_t getMMFFDielectricModel()
Definition: MMFF/AtomTyper.h:141
RDKit::MMFF::MMFFMolProperties::setMMFFOopTerm
void setMMFFOopTerm(const bool state)
Definition: MMFF/AtomTyper.h:115
RDKit::MMFF::MMFFMolProperties::isValid
bool isValid()
Definition: MMFF/AtomTyper.h:148
RDKit::MMFF::MMFFMolProperties::getMMFFVdWParams
bool getMMFFVdWParams(const unsigned int idx1, const unsigned int idx2, MMFFVdWRijstarEps &mmffVdWParams)
RDKit::MMFF::MMFFMolProperties::setMMFFVariant
void setMMFFVariant(const std::string &mmffVariant)
Definition: MMFF/AtomTyper.h:123
RDKit::MMFF::MMFFMolProperties::getMMFFEleTerm
bool getMMFFEleTerm()
Definition: MMFF/AtomTyper.h:122
RDKit::MMFF::MMFFMolProperties::getMMFFTorsionType
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)
RDKit::MMFF::MMFFMolProperties::getMMFFBondStretchEmpiricalRuleParams
const ForceFields::MMFF::MMFFBond * getMMFFBondStretchEmpiricalRuleParams(const ROMol &mol, const Bond *bond)
RDKit::MMFF::MMFFMolProperties::setMMFFDielectricModel
void setMMFFDielectricModel(std::uint8_t dielModel)
Definition: MMFF/AtomTyper.h:138
RDKit::MMFF::MMFFMolProperties::getMMFFBondStretchParams
bool getMMFFBondStretchParams(const ROMol &mol, const unsigned int idx1, const unsigned int idx2, unsigned int &bondType, MMFFBond &mmffBondStretchParams)
RDKit::MMFF::MMFFMolProperties::getMMFFVerbosity
std::uint8_t getMMFFVerbosity()
Definition: MMFF/AtomTyper.h:145
RDKit::MMFF::MMFFMolProperties::getMMFFDielectricConstant
double getMMFFDielectricConstant()
Definition: MMFF/AtomTyper.h:137
RDKit::MMFF::MMFFMolProperties::getMMFFAngleBendParams
bool getMMFFAngleBendParams(const ROMol &mol, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3, unsigned int &angleType, MMFFAngle &mmffAngleBendParams)
RDKit::MMFF::MMFFMolProperties::getMMFFAngleType
unsigned int getMMFFAngleType(const ROMol &mol, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3)
RDKit::MMFF::MMFFMolProperties::getMMFFVdWTerm
bool getMMFFVdWTerm()
Definition: MMFF/AtomTyper.h:120
RDKit::MMFF::MMFFMolProperties::getMMFFOopTerm
bool getMMFFOopTerm()
Definition: MMFF/AtomTyper.h:116
RDKit::MMFF::MMFFMolProperties::getMMFFAtomType
std::uint8_t getMMFFAtomType(const unsigned int idx)
Definition: MMFF/AtomTyper.h:92
RDKit::MMFF::MMFFMolProperties::getMMFFBondType
unsigned int getMMFFBondType(const Bond *bond)
RDKit::MMFF::MMFFMolProperties::setMMFFBondTerm
void setMMFFBondTerm(const bool state)
Definition: MMFF/AtomTyper.h:107
RDKit::MMFF::MMFFMolProperties::setMMFFVerbosity
void setMMFFVerbosity(std::uint8_t verbosity)
Definition: MMFF/AtomTyper.h:142
RDKit::MMFF::MMFFMolProperties::computeMMFFCharges
void computeMMFFCharges(const ROMol &mol)
RDKit::MMFF::MMFFMolProperties::getMMFFTorsionEmpiricalRuleParams
const ForceFields::MMFF::MMFFTor * getMMFFTorsionEmpiricalRuleParams(const ROMol &mol, unsigned int idx2, unsigned int idx3)
RDKit::MMFF::MMFFMolProperties::setMMFFTorsionTerm
void setMMFFTorsionTerm(const bool state)
Definition: MMFF/AtomTyper.h:117
RDKit::MMFF::MMFFMolProperties::getMMFFTorsionTerm
bool getMMFFTorsionTerm()
Definition: MMFF/AtomTyper.h:118
RDKit::MMFF::MMFFMolProperties::setMMFFEleTerm
void setMMFFEleTerm(const bool state)
Definition: MMFF/AtomTyper.h:121
RDKit::MMFF::MMFFMolProperties::setMMFFDielectricConstant
void setMMFFDielectricConstant(const double dielConst)
Definition: MMFF/AtomTyper.h:132
RDKit::MMFF::MMFFMolProperties::getMMFFStretchBendTerm
bool getMMFFStretchBendTerm()
Definition: MMFF/AtomTyper.h:114
RDKit::MMFF::MMFFMolProperties::setMMFFVdWTerm
void setMMFFVdWTerm(const bool state)
Definition: MMFF/AtomTyper.h:119
RDKit::MMFF::MMFFMolProperties::getMMFFOStream
std::ostream & getMMFFOStream()
Definition: MMFF/AtomTyper.h:147
RDKit::MMFF::MMFFMolProperties::getMMFFOopBendParams
bool getMMFFOopBendParams(const ROMol &mol, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3, const unsigned int idx4, MMFFOop &mmffOopBendParams)
RDKit::MMFF::MMFFMolProperties::getMMFFVariant
const std::string getMMFFVariant()
Definition: MMFF/AtomTyper.h:129
RDKit::MMFF::MMFFMolProperties::getMMFFPartialCharge
double getMMFFPartialCharge(const unsigned int idx)
Definition: MMFF/AtomTyper.h:102
RDKit::MMFF::MMFFMolProperties::getMMFFBondTerm
bool getMMFFBondTerm()
Definition: MMFF/AtomTyper.h:108
RDKit::MMFF::MMFFMolProperties::getMMFFFormalCharge
double getMMFFFormalCharge(const unsigned int idx)
Definition: MMFF/AtomTyper.h:97
RDKit::MMFF::MMFFMolProperties::setMMFFAngleTerm
void setMMFFAngleTerm(const bool state)
Definition: MMFF/AtomTyper.h:109
RDKit::MMFF::MMFFMolProperties::~MMFFMolProperties
~MMFFMolProperties()=default
RDKit::MMFF::MMFFMolProperties::MMFFMolProperties
MMFFMolProperties(ROMol &mol, const std::string &mmffVariant="MMFF94", std::uint8_t verbosity=MMFF_VERBOSITY_NONE, std::ostream &oStream=std::cout)
RDKit::MMFF::MMFFMolProperties::setMMFFOStream
void setMMFFOStream(std::ostream *oStream)
Definition: MMFF/AtomTyper.h:146
RDKit::MMFF::MMFFMolProperties::getMMFFAngleTerm
bool getMMFFAngleTerm()
Definition: MMFF/AtomTyper.h:110
RDKit::MMFF::MMFFMolProperties::getMMFFTorsionParams
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)
RDKit::ROMol
Definition: ROMol.h:178
RDKit::RWMol
RWMol is a molecule class that is intended to be edited.
Definition: RWMol.h:32
export.h
RDKIT_FORCEFIELDHELPERS_EXPORT
#define RDKIT_FORCEFIELDHELPERS_EXPORT
Definition: export.h:185
ForceFields::MMFF
Definition: MMFF/AngleBend.h:20
RDKit::MMFF::DefaultParameters::getMMFFHerschbachLaurie
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFHerschbachLaurieCollection * getMMFFHerschbachLaurie()
RDKit::MMFF::DefaultParameters::getMMFFVdW
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFVdWCollection * getMMFFVdW()
RDKit::MMFF::DefaultParameters::getMMFFDfsb
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFDfsbCollection * getMMFFDfsb()
RDKit::MMFF::DefaultParameters::getMMFFDef
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFDefCollection * getMMFFDef()
RDKit::MMFF::DefaultParameters::getMMFFProp
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFPropCollection * getMMFFProp()
RDKit::MMFF::DefaultParameters::getMMFFStbn
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFStbnCollection * getMMFFStbn()
RDKit::MMFF::DefaultParameters::getMMFFAngle
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFAngleCollection * getMMFFAngle()
RDKit::MMFF::DefaultParameters::getMMFFTor
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFTorCollection * getMMFFTor(const bool isMMFFs)
RDKit::MMFF::DefaultParameters::getMMFFArom
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFAromCollection * getMMFFArom()
RDKit::MMFF::DefaultParameters::getMMFFPBCI
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFPBCICollection * getMMFFPBCI()
RDKit::MMFF::DefaultParameters::getMMFFOop
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFOopCollection * getMMFFOop(const bool isMMFFs)
RDKit::MMFF::MMFF_VERBOSITY_NONE
@ MMFF_VERBOSITY_NONE
Definition: MMFF/AtomTyper.h:70
RDKit::MMFF::MMFF_VERBOSITY_HIGH
@ MMFF_VERBOSITY_HIGH
Definition: MMFF/AtomTyper.h:72
RDKit::MMFF::MMFF_VERBOSITY_LOW
@ MMFF_VERBOSITY_LOW
Definition: MMFF/AtomTyper.h:71
RDKit::MMFF::getPeriodicTableRow
RDKIT_FORCEFIELDHELPERS_EXPORT unsigned int getPeriodicTableRow(const int atomicNum)
RDKit::MMFF::sanitizeMMFFMol
RDKIT_FORCEFIELDHELPERS_EXPORT unsigned int sanitizeMMFFMol(RWMol &mol)
RDKit::MMFF::areAtomsInSameAromaticRing
RDKIT_FORCEFIELDHELPERS_EXPORT bool areAtomsInSameAromaticRing(const ROMol &mol, const unsigned int idx1, const unsigned int idx2)
RDKit::MMFF::MMFFAtomPropertiesPtr
boost::shared_ptr< MMFFAtomProperties > MMFFAtomPropertiesPtr
Definition: MMFF/AtomTyper.h:67
RDKit::MMFF::getMMFFAngleBendEmpiricalRuleParams
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::MMFF::getMMFFStretchBendType
RDKIT_FORCEFIELDHELPERS_EXPORT unsigned int getMMFFStretchBendType(const unsigned int angleType, const unsigned int bondType1, const unsigned int bondType2)
RDKit::MMFF::setMMFFAromaticity
RDKIT_FORCEFIELDHELPERS_EXPORT void setMMFFAromaticity(RWMol &mol)
RDKit::MMFF::isRingAromatic
RDKIT_FORCEFIELDHELPERS_EXPORT bool isRingAromatic(const ROMol &mol, const INT_VECT &ringIndxVect)
RDKit::MMFF::isAtomInAromaticRingOfSize
RDKIT_FORCEFIELDHELPERS_EXPORT bool isAtomInAromaticRingOfSize(const Atom *atom, const unsigned int ringSize)
RDKit::MMFF::isAngleInRingOfSize3or4
RDKIT_FORCEFIELDHELPERS_EXPORT unsigned int isAngleInRingOfSize3or4(const ROMol &mol, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3)
RDKit::MMFF::CONSTANT
@ CONSTANT
Definition: MMFF/AtomTyper.h:68
RDKit::MMFF::DISTANCE
@ DISTANCE
Definition: MMFF/AtomTyper.h:68
RDKit::MMFF::areAtomsInSameRingOfSize
RDKIT_FORCEFIELDHELPERS_EXPORT bool areAtomsInSameRingOfSize(const ROMol &mol, const unsigned int ringSize, const unsigned int numAtoms,...)
RDKit::MMFF::isAtomNOxide
RDKIT_FORCEFIELDHELPERS_EXPORT bool isAtomNOxide(const Atom *atom)
RDKit::MMFF::isTorsionInRingOfSize4or5
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
Std stuff.
Definition: Abbreviations.h:18
RDKit::INT_VECT
std::vector< int > INT_VECT
Definition: types.h:274