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RDKit
Open-source cheminformatics and machine learning.
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13 #ifndef _RD_MMFFATOMTYPER_H__
14 #define _RD_MMFFATOMTYPER_H__
30 namespace DefaultParameters {
45 class RingMembershipSize;
50 : mmffAtomType(0), mmffFormalCharge(0.0), mmffPartialCharge(0.0){};
68 std::ostream &oStream = std::cout);
72 const unsigned int idx2,
73 const unsigned int idx3);
75 const ROMol &mol,
const unsigned int idx1,
const unsigned int idx2,
76 const unsigned int idx3,
const unsigned int idx4);
79 const ROMol &mol,
unsigned int idx2,
unsigned int idx3);
83 URANGE_CHECK(idx, this->d_MMFFAtomPropertiesPtrVect.size());
85 return this->d_MMFFAtomPropertiesPtrVect[idx]->mmffAtomType;
88 URANGE_CHECK(idx, this->d_MMFFAtomPropertiesPtrVect.size());
90 return this->d_MMFFAtomPropertiesPtrVect[idx]->mmffFormalCharge;
93 URANGE_CHECK(idx, this->d_MMFFAtomPropertiesPtrVect.size());
95 return this->d_MMFFAtomPropertiesPtrVect[idx]->mmffPartialCharge;
102 this->d_stretchBendTerm = state;
114 PRECONDITION((mmffVariant ==
"MMFF94") || (mmffVariant ==
"MMFF94s"),
117 this->d_mmffs = ((mmffVariant ==
"MMFF94s") ?
true :
false);
120 return (this->d_mmffs ?
"MMFF94s" :
"MMFF94");
123 PRECONDITION(dielConst > 0.0,
"bad dielectric constant");
125 this->d_dielConst = dielConst;
129 this->d_dielModel = dielModel;
133 this->d_verbosity = verbosity;
140 const unsigned int idx2,
unsigned int &bondType,
143 const unsigned int idx1,
144 const unsigned int idx2,
const unsigned int idx3,
145 unsigned int &angleType,
148 const unsigned int idx2,
149 const unsigned int idx3,
150 unsigned int &stretchBendType,
155 const unsigned int idx2,
const unsigned int idx3,
156 const unsigned int idx4,
unsigned int &torsionType,
159 const unsigned int idx2,
const unsigned int idx3,
160 const unsigned int idx4,
166 void setMMFFHeavyAtomType(
const RingMembershipSize &rmSize,
const Atom *atom);
167 void setMMFFHydrogenType(
const Atom *atom);
168 void setMMFFFormalCharge(
const unsigned int idx,
const double fChg) {
169 URANGE_CHECK(idx, this->d_MMFFAtomPropertiesPtrVect.size());
171 this->d_MMFFAtomPropertiesPtrVect[idx]->mmffFormalCharge = fChg;
173 void setMMFFPartialCharge(
const unsigned int idx,
const double pChg) {
174 URANGE_CHECK(idx, this->d_MMFFAtomPropertiesPtrVect.size());
176 this->d_MMFFAtomPropertiesPtrVect[idx]->mmffPartialCharge = pChg;
182 bool d_stretchBendTerm;
188 std::uint8_t d_dielModel;
190 std::uint8_t d_verbosity;
191 std::ostream *d_oStream;
192 std::vector<MMFFAtomPropertiesPtr> d_MMFFAtomPropertiesPtrVect;
195 const ROMol &mol,
const unsigned int idx1,
const unsigned int idx2,
196 const unsigned int idx3);
198 const ROMol &mol,
const unsigned int idx1,
const unsigned int idx2,
199 const unsigned int idx3,
const unsigned int idx4);
203 const Atom *atom,
const unsigned int ringSize);
206 const ROMol &mol,
const unsigned int idx1,
const unsigned int idx2);
208 const ROMol &mol,
const unsigned int ringSize,
const unsigned int numAtoms,
213 const unsigned int angleType,
const unsigned int bondType1,
214 const unsigned int bondType2);
216 const int atomicNum);
223 unsigned int idx2,
unsigned int idx3);
const std::string getMMFFVariant()
RDKIT_FORCEFIELDHELPERS_EXPORT bool isAtomNOxide(const Atom *atom)
RDKIT_FORCEFIELDHELPERS_EXPORT unsigned int getMMFFStretchBendType(const unsigned int angleType, const unsigned int bondType1, const unsigned int bondType2)
void setMMFFDielectricModel(std::uint8_t dielModel)
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFOopCollection * getMMFFOop(const bool isMMFFs)
RDKIT_FORCEFIELDHELPERS_EXPORT bool isAtomInAromaticRingOfSize(const Atom *atom, const unsigned int ringSize)
bool getMMFFStretchBendTerm()
std::vector< int > INT_VECT
MMFFMolProperties(ROMol &mol, const std::string &mmffVariant="MMFF94", std::uint8_t verbosity=MMFF_VERBOSITY_NONE, std::ostream &oStream=std::cout)
RDKIT_FORCEFIELDHELPERS_EXPORT unsigned int isAngleInRingOfSize3or4(const ROMol &mol, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3)
const ForceFields::MMFF::MMFFBond * getMMFFBondStretchEmpiricalRuleParams(const ROMol &mol, const Bond *bond)
RDKIT_FORCEFIELDHELPERS_EXPORT unsigned int getPeriodicTableRow(const int atomicNum)
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFTorCollection * getMMFFTor(const bool isMMFFs)
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFAromCollection * getMMFFArom()
class to store MMFF parameters for bond stretching
class for representing a bond
void setMMFFVerbosity(std::uint8_t verbosity)
RWMol is a molecule class that is intended to be edited.
std::uint8_t mmffAtomType
class to store MMFF parameters for out-of-plane bending
std::uint8_t getMMFFDielectricModel()
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 getMMFFTorsionTerm()
std::uint8_t getMMFFVerbosity()
unsigned int getMMFFAngleType(const ROMol &mol, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3)
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFPBCICollection * getMMFFPBCI()
bool getMMFFBondStretchParams(const ROMol &mol, const unsigned int idx1, const unsigned int idx2, unsigned int &bondType, MMFFBond &mmffBondStretchParams)
void setMMFFTorsionTerm(const bool state)
bool getMMFFAngleBendParams(const ROMol &mol, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3, unsigned int &angleType, MMFFAngle &mmffAngleBendParams)
The class for representing atoms.
std::ostream & getMMFFOStream()
void computeMMFFCharges(const ROMol &mol)
class to store MMFF parameters for stretch-bending
void setMMFFStretchBendTerm(const bool state)
std::uint8_t getMMFFAtomType(const unsigned int idx)
void setMMFFBondTerm(const bool state)
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFHerschbachLaurieCollection * getMMFFHerschbachLaurie()
RDKIT_FORCEFIELDHELPERS_EXPORT bool isRingAromatic(const ROMol &mol, const INT_VECT &ringIndxVect)
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFVdWCollection * getMMFFVdW()
const ForceFields::MMFF::MMFFTor * getMMFFTorsionEmpiricalRuleParams(const ROMol &mol, unsigned int idx2, unsigned int idx3)
class to store MMFF Properties
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFStbnCollection * getMMFFStbn()
class to store MMFF parameters for torsions
bool getMMFFVdWParams(const unsigned int idx1, const unsigned int idx2, MMFFVdWRijstarEps &mmffVdWParams)
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)
void setMMFFOopTerm(const bool state)
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFPropCollection * getMMFFProp()
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)
double getMMFFFormalCharge(const unsigned int idx)
class to store MMFF parameters for angle bending
double getMMFFPartialCharge(const unsigned int idx)
void setMMFFOStream(std::ostream *oStream)
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)
#define PRECONDITION(expr, mess)
unsigned int getMMFFBondType(const Bond *bond)
double getMMFFDielectricConstant()
#define URANGE_CHECK(x, hi)
#define RDKIT_FORCEFIELDHELPERS_EXPORT
void setMMFFEleTerm(const bool state)
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFDefCollection * getMMFFDef()
RDKIT_FORCEFIELDHELPERS_EXPORT unsigned int sanitizeMMFFMol(RWMol &mol)
RDKIT_FORCEFIELDHELPERS_EXPORT bool areAtomsInSameAromaticRing(const ROMol &mol, const unsigned int idx1, const unsigned int idx2)
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFAngleCollection * getMMFFAngle()
RDKIT_FORCEFIELDHELPERS_EXPORT const ForceFields::MMFF::MMFFDfsbCollection * getMMFFDfsb()
RDKIT_FORCEFIELDHELPERS_EXPORT void setMMFFAromaticity(RWMol &mol)
void setMMFFVdWTerm(const bool state)
void setMMFFVariant(const std::string &mmffVariant)
void setMMFFAngleTerm(const bool state)
bool getMMFFOopBendParams(const ROMol &mol, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3, const unsigned int idx4, MMFFOop &mmffOopBendParams)
void setMMFFDielectricConstant(const double dielConst)
RDKIT_FORCEFIELDHELPERS_EXPORT bool areAtomsInSameRingOfSize(const ROMol &mol, const unsigned int ringSize, const unsigned int numAtoms,...)
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)
boost::shared_ptr< MMFFAtomProperties > MMFFAtomPropertiesPtr