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Add Getter functions to MMFF property python interface (#9254)

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This commit is contained in:
Kevin Boyd
2026-04-30 11:06:31 -04:00
committed by GitHub
parent 251353a217
commit 232e4ffc84
5 changed files with 159 additions and 74 deletions
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69
Code/ForceField/Wrap/ForceField.cpp
View File

@@ -204,7 +204,8 @@ python::tuple PyForceField::minimizeTrajectory(unsigned int snapshotFreq,
}
PyObject *PyMMFFMolProperties::getMMFFBondStretchParams(
const RDKit::ROMol &mol, const unsigned int idx1, const unsigned int idx2) {
const RDKit::ROMol &mol, const unsigned int idx1,
const unsigned int idx2) const {
PyObject *res = nullptr;
unsigned int bondType;
ForceFields::MMFF::MMFFBond mmffBondStretchParams;
@@ -218,10 +219,9 @@ PyObject *PyMMFFMolProperties::getMMFFBondStretchParams(
return res;
};
PyObject *PyMMFFMolProperties::getMMFFAngleBendParams(const RDKit::ROMol &mol,
const unsigned int idx1,
const unsigned int idx2,
const unsigned int idx3) {
PyObject *PyMMFFMolProperties::getMMFFAngleBendParams(
const RDKit::ROMol &mol, const unsigned int idx1, const unsigned int idx2,
const unsigned int idx3) const {
PyObject *res = nullptr;
unsigned int angleType;
ForceFields::MMFF::MMFFAngle mmffAngleBendParams;
@@ -237,7 +237,7 @@ PyObject *PyMMFFMolProperties::getMMFFAngleBendParams(const RDKit::ROMol &mol,
PyObject *PyMMFFMolProperties::getMMFFStretchBendParams(
const RDKit::ROMol &mol, const unsigned int idx1, const unsigned int idx2,
const unsigned int idx3) {
const unsigned int idx3) const {
PyObject *res = nullptr;
unsigned int stretchBendType;
ForceFields::MMFF::MMFFStbn mmffStretchBendParams;
@@ -254,11 +254,9 @@ PyObject *PyMMFFMolProperties::getMMFFStretchBendParams(
return res;
};
PyObject *PyMMFFMolProperties::getMMFFTorsionParams(const RDKit::ROMol &mol,
const unsigned int idx1,
const unsigned int idx2,
const unsigned int idx3,
const unsigned int idx4) {
PyObject *PyMMFFMolProperties::getMMFFTorsionParams(
const RDKit::ROMol &mol, const unsigned int idx1, const unsigned int idx2,
const unsigned int idx3, const unsigned int idx4) const {
PyObject *res = nullptr;
unsigned int torType;
ForceFields::MMFF::MMFFTor mmffTorsionParams;
@@ -273,11 +271,9 @@ PyObject *PyMMFFMolProperties::getMMFFTorsionParams(const RDKit::ROMol &mol,
return res;
};
PyObject *PyMMFFMolProperties::getMMFFOopBendParams(const RDKit::ROMol &mol,
const unsigned int idx1,
const unsigned int idx2,
const unsigned int idx3,
const unsigned int idx4) {
PyObject *PyMMFFMolProperties::getMMFFOopBendParams(
const RDKit::ROMol &mol, const unsigned int idx1, const unsigned int idx2,
const unsigned int idx3, const unsigned int idx4) const {
PyObject *res = nullptr;
ForceFields::MMFF::MMFFOop mmffOopBendParams;
if (mmffMolProperties->getMMFFOopBendParams(mol, idx1, idx2, idx3, idx4,
@@ -288,7 +284,7 @@ PyObject *PyMMFFMolProperties::getMMFFOopBendParams(const RDKit::ROMol &mol,
};
PyObject *PyMMFFMolProperties::getMMFFVdWParams(const unsigned int idx1,
const unsigned int idx2) {
const unsigned int idx2) const {
PyObject *res = nullptr;
ForceFields::MMFF::MMFFVdWRijstarEps mmffVdWParams;
if (mmffMolProperties->getMMFFVdWParams(idx1, idx2, mmffVdWParams)) {
@@ -309,7 +305,7 @@ BOOST_PYTHON_MODULE(rdForceField) {
python::class_<PyForceField>("ForceField", "A force field", python::no_init)
.def("CalcEnergy",
(double (PyForceField::*)(const python::object &) const) &
(double(PyForceField::*)(const python::object &) const) &
PyForceField::calcEnergyWithPos,
((python::arg("self"), python::arg("pos") = python::object())),
"Returns the energy (in kcal/mol) of the current arrangement\n"
@@ -483,43 +479,80 @@ BOOST_PYTHON_MODULE(rdForceField) {
"Sets the DielModel MMFF property (1: constant; 2: "
"distance-dependent; "
"defaults to constant)")
.def("GetMMFFDielectricModel",
&PyMMFFMolProperties::getMMFFDielectricModel, python::arg("self"),
"Returns the currently configured MMFF dielectric model "
"(1: constant; 2: distance-dependent).")
.def("SetMMFFDielectricConstant",
&PyMMFFMolProperties::setMMFFDielectricConstant,
(python::arg("self"), python::arg("dielConst") = 1.0),
"Sets the DielConst MMFF property (defaults to 1.0)")
.def("GetMMFFDielectricConstant",
&PyMMFFMolProperties::getMMFFDielectricConstant, python::arg("self"),
"Returns the currently configured MMFF dielectric constant.")
.def("SetMMFFBondTerm", &PyMMFFMolProperties::setMMFFBondTerm,
(python::arg("self"), python::arg("state") = true),
"Sets the bond term to be included in the MMFF equation (defaults "
"to True)")
.def("GetMMFFBondTerm", &PyMMFFMolProperties::getMMFFBondTerm,
python::arg("self"),
"Returns whether the bond term is included in the MMFF equation.")
.def("SetMMFFAngleTerm", &PyMMFFMolProperties::setMMFFAngleTerm,
(python::arg("self"), python::arg("state") = true),
"Sets the angle term to be included in the MMFF equation (defaults "
"to True)")
.def("GetMMFFAngleTerm", &PyMMFFMolProperties::getMMFFAngleTerm,
python::arg("self"),
"Returns whether the angle term is included in the MMFF equation.")
.def("SetMMFFStretchBendTerm",
&PyMMFFMolProperties::setMMFFStretchBendTerm,
(python::arg("self"), python::arg("state") = true),
"Sets the stretch-bend term to be included in the MMFF equation "
"(defaults to True)")
.def("GetMMFFStretchBendTerm",
&PyMMFFMolProperties::getMMFFStretchBendTerm, python::arg("self"),
"Returns whether the stretch-bend term is included in the MMFF "
"equation.")
.def("SetMMFFOopTerm", &PyMMFFMolProperties::setMMFFOopTerm,
(python::arg("self"), python::arg("state") = true),
"Sets the out-of-plane bend term to be included in the MMFF "
"equation (defaults to True)")
.def("GetMMFFOopTerm", &PyMMFFMolProperties::getMMFFOopTerm,
python::arg("self"),
"Returns whether the out-of-plane bend term is included in the "
"MMFF equation.")
.def("SetMMFFTorsionTerm", &PyMMFFMolProperties::setMMFFTorsionTerm,
(python::arg("self"), python::arg("state") = true),
"Sets the torsional term to be included in the MMFF equation "
"(defaults to True)")
.def("GetMMFFTorsionTerm", &PyMMFFMolProperties::getMMFFTorsionTerm,
python::arg("self"),
"Returns whether the torsional term is included in the MMFF "
"equation.")
.def("SetMMFFVdWTerm", &PyMMFFMolProperties::setMMFFVdWTerm,
(python::arg("self"), python::arg("state") = true),
"Sets the Van der Waals term to be included in the MMFF equation "
"(defaults to True)")
.def("GetMMFFVdWTerm", &PyMMFFMolProperties::getMMFFVdWTerm,
python::arg("self"),
"Returns whether the Van der Waals term is included in the MMFF "
"equation.")
.def("SetMMFFEleTerm", &PyMMFFMolProperties::setMMFFEleTerm,
(python::arg("self"), python::arg("state") = true),
"Sets the electrostatic term to be included in the MMFF equation "
"(defaults to True)")
.def("GetMMFFEleTerm", &PyMMFFMolProperties::getMMFFEleTerm,
python::arg("self"),
"Returns whether the electrostatic term is included in the MMFF "
"equation.")
.def("SetMMFFVariant", &PyMMFFMolProperties::setMMFFVariant,
(python::arg("self"), python::arg("mmffVariant") = "MMFF94"),
"Sets the MMFF variant to be used (\"MMFF94\" or \"MMFF94s\"; "
"defaults to \"MMFF94\")")
.def("GetMMFFVariant", &PyMMFFMolProperties::getMMFFVariant,
python::arg("self"),
"Returns the currently configured MMFF variant "
"(\"MMFF94\" or \"MMFF94s\").")
.def("SetMMFFVerbosity", &PyMMFFMolProperties::setMMFFVerbosity,
(python::arg("self"), python::arg("verbosity") = 0),
"Sets the MMFF verbosity (0: none; 1: low; 2: high; defaults to 0)");

41
Code/ForceField/Wrap/PyForceField.h
View File

@@ -89,67 +89,90 @@ class PyMMFFMolProperties {
: mmffMolProperties(mp) {}
~PyMMFFMolProperties() = default;
unsigned int getMMFFAtomType(unsigned int idx) {
unsigned int getMMFFAtomType(unsigned int idx) const {
return (unsigned int)(mmffMolProperties->getMMFFAtomType(idx));
}
double getMMFFFormalCharge(unsigned int idx) {
double getMMFFFormalCharge(unsigned int idx) const {
return mmffMolProperties->getMMFFFormalCharge(idx);
}
double getMMFFPartialCharge(unsigned int idx) {
double getMMFFPartialCharge(unsigned int idx) const {
return mmffMolProperties->getMMFFPartialCharge(idx);
}
PyObject *getMMFFBondStretchParams(const RDKit::ROMol &mol,
const unsigned int idx1,
const unsigned int idx2);
const unsigned int idx2) const;
PyObject *getMMFFAngleBendParams(const RDKit::ROMol &mol,
const unsigned int idx1,
const unsigned int idx2,
const unsigned int idx3);
const unsigned int idx3) const;
PyObject *getMMFFStretchBendParams(const RDKit::ROMol &mol,
const unsigned int idx1,
const unsigned int idx2,
const unsigned int idx3);
const unsigned int idx3) const;
PyObject *getMMFFTorsionParams(const RDKit::ROMol &mol,
const unsigned int idx1,
const unsigned int idx2,
const unsigned int idx3,
const unsigned int idx4);
const unsigned int idx4) const;
PyObject *getMMFFOopBendParams(const RDKit::ROMol &mol,
const unsigned int idx1,
const unsigned int idx2,
const unsigned int idx3,
const unsigned int idx4);
PyObject *getMMFFVdWParams(const unsigned int idx1, const unsigned int idx2);
const unsigned int idx4) const;
PyObject *getMMFFVdWParams(const unsigned int idx1,
const unsigned int idx2) const;
void setMMFFDielectricModel(std::uint8_t dielModel) {
mmffMolProperties->setMMFFDielectricModel(dielModel);
}
std::uint8_t getMMFFDielectricModel() const {
return mmffMolProperties->getMMFFDielectricModel();
}
void setMMFFDielectricConstant(double dielConst) {
mmffMolProperties->setMMFFDielectricConstant(dielConst);
}
double getMMFFDielectricConstant() const {
return mmffMolProperties->getMMFFDielectricConstant();
}
void setMMFFBondTerm(bool state) {
mmffMolProperties->setMMFFBondTerm(state);
}
bool getMMFFBondTerm() const { return mmffMolProperties->getMMFFBondTerm(); }
void setMMFFAngleTerm(const bool state) {
mmffMolProperties->setMMFFAngleTerm(state);
}
bool getMMFFAngleTerm() const {
return mmffMolProperties->getMMFFAngleTerm();
}
void setMMFFStretchBendTerm(const bool state) {
mmffMolProperties->setMMFFStretchBendTerm(state);
}
bool getMMFFStretchBendTerm() const {
return mmffMolProperties->getMMFFStretchBendTerm();
}
void setMMFFOopTerm(const bool state) {
mmffMolProperties->setMMFFOopTerm(state);
}
bool getMMFFOopTerm() const { return mmffMolProperties->getMMFFOopTerm(); }
void setMMFFTorsionTerm(const bool state) {
mmffMolProperties->setMMFFTorsionTerm(state);
}
bool getMMFFTorsionTerm() const {
return mmffMolProperties->getMMFFTorsionTerm();
}
void setMMFFVdWTerm(const bool state) {
mmffMolProperties->setMMFFVdWTerm(state);
}
bool getMMFFVdWTerm() const { return mmffMolProperties->getMMFFVdWTerm(); }
void setMMFFEleTerm(const bool state) {
mmffMolProperties->setMMFFEleTerm(state);
}
bool getMMFFEleTerm() const { return mmffMolProperties->getMMFFEleTerm(); }
void setMMFFVariant(const std::string &mmffVariant) {
mmffMolProperties->setMMFFVariant(mmffVariant);
}
std::string getMMFFVariant() const {
return mmffMolProperties->getMMFFVariant();
}
void setMMFFVerbosity(unsigned int verbosity) {
mmffMolProperties->setMMFFVerbosity(verbosity);
}

38
Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp
View File

@@ -2412,7 +2412,7 @@ MMFFMolProperties::MMFFMolProperties(ROMol &mol, const std::string &mmffVariant,
unsigned int MMFFMolProperties::getMMFFAngleType(const ROMol &mol,
const unsigned int idx1,
const unsigned int idx2,
const unsigned int idx3) {
const unsigned int idx3) const {
PRECONDITION(this->isValid(), "missing atom types - invalid force-field");
// ftp://ftp.wiley.com/public/journals/jcc/suppmat/17/553/MMFF-III_AppendixA.html
@@ -2454,7 +2454,7 @@ unsigned int MMFFMolProperties::getMMFFAngleType(const ROMol &mol,
}
// returns the MMFF bond type of the bond
unsigned int MMFFMolProperties::getMMFFBondType(const Bond *bond) {
unsigned int MMFFMolProperties::getMMFFBondType(const Bond *bond) const {
PRECONDITION(this->isValid(), "missing atom types - invalid force-field");
PRECONDITION(bond, "invalid bond");
@@ -2529,7 +2529,7 @@ const std::pair<unsigned int, unsigned int>
MMFFMolProperties::getMMFFTorsionType(const ROMol &mol, const unsigned int idx1,
const unsigned int idx2,
const unsigned int idx3,
const unsigned int idx4) {
const unsigned int idx4) const {
PRECONDITION(this->isValid(), "missing atom types - invalid force-field");
const Bond *bondJK = mol.getBondBetweenAtoms(idx2, idx3);
@@ -2575,7 +2575,7 @@ MMFFMolProperties::getMMFFTorsionType(const ROMol &mol, const unsigned int idx1,
// pointer to a MMFFBond object must be freed by the caller
const ForceFields::MMFF::MMFFBond *
MMFFMolProperties::getMMFFBondStretchEmpiricalRuleParams(const ROMol &,
const Bond *bond) {
const Bond *bond) const {
PRECONDITION(this->isValid(), "missing atom types - invalid force-field");
const MMFFBond *mmffBndkParams;
@@ -2879,7 +2879,7 @@ const ForceFields::MMFF::MMFFAngle *getMMFFAngleBendEmpiricalRuleParams(
const ForceFields::MMFF::MMFFTor *
MMFFMolProperties::getMMFFTorsionEmpiricalRuleParams(const ROMol &mol,
unsigned int idx2,
unsigned int idx3) {
unsigned int idx3) const {
PRECONDITION(this->isValid(), "missing atom types - invalid force-field");
const MMFFPropCollection *mmffProp = DefaultParameters::getMMFFProp();
@@ -3489,7 +3489,7 @@ void MMFFMolProperties::computeMMFFCharges(const ROMol &mol) {
bool MMFFMolProperties::getMMFFBondStretchParams(
const ROMol &mol, const unsigned int idx1, const unsigned int idx2,
unsigned int &bondType, MMFFBond &mmffBondStretchParams) {
unsigned int &bondType, MMFFBond &mmffBondStretchParams) const {
const MMFFBondCollection *mmffBond = DefaultParameters::getMMFFBond();
bool res = false;
if (isValid()) {
@@ -3517,12 +3517,10 @@ bool MMFFMolProperties::getMMFFBondStretchParams(
return res;
}
bool MMFFMolProperties::getMMFFAngleBendParams(const ROMol &mol,
const unsigned int idx1,
const unsigned int idx2,
const unsigned int idx3,
unsigned int &angleType,
MMFFAngle &mmffAngleBendParams) {
bool MMFFMolProperties::getMMFFAngleBendParams(
const ROMol &mol, const unsigned int idx1, const unsigned int idx2,
const unsigned int idx3, unsigned int &angleType,
MMFFAngle &mmffAngleBendParams) const {
bool res = false;
if (isValid() && mol.getBondBetweenAtoms(idx1, idx2) &&
mol.getBondBetweenAtoms(idx2, idx3)) {
@@ -3569,7 +3567,7 @@ bool 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) {
MMFFAngle &mmffAngleBendParams) const {
bool res = false;
if (isValid()) {
const MMFFPropCollection *mmffProp = DefaultParameters::getMMFFProp();
@@ -3629,7 +3627,7 @@ bool MMFFMolProperties::getMMFFStretchBendParams(
bool 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) {
MMFFTor &mmffTorsionParams) const {
bool res = false;
if (isValid() && mol.getBondBetweenAtoms(idx1, idx2) &&
mol.getBondBetweenAtoms(idx2, idx3) &&
@@ -3669,12 +3667,10 @@ bool MMFFMolProperties::getMMFFTorsionParams(
return res;
}
bool MMFFMolProperties::getMMFFOopBendParams(const ROMol &mol,
const unsigned int idx1,
const unsigned int idx2,
const unsigned int idx3,
const unsigned int idx4,
MMFFOop &mmffOopBendParams) {
bool MMFFMolProperties::getMMFFOopBendParams(
const ROMol &mol, const unsigned int idx1, const unsigned int idx2,
const unsigned int idx3, const unsigned int idx4,
MMFFOop &mmffOopBendParams) const {
bool res = false;
if (isValid() && mol.getBondBetweenAtoms(idx1, idx2) &&
mol.getBondBetweenAtoms(idx2, idx3) &&
@@ -3702,7 +3698,7 @@ bool MMFFMolProperties::getMMFFOopBendParams(const ROMol &mol,
bool MMFFMolProperties::getMMFFVdWParams(const unsigned int idx1,
const unsigned int idx2,
MMFFVdWRijstarEps &mmffVdWParams) {
MMFFVdWRijstarEps &mmffVdWParams) const {
bool res = false;
if (isValid()) {
const MMFFVdWCollection *mmffVdW = DefaultParameters::getMMFFVdW();

52
Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h
View File

@@ -79,56 +79,56 @@ class RDKIT_FORCEFIELDHELPERS_EXPORT MMFFMolProperties {
std::uint8_t verbosity = MMFF_VERBOSITY_NONE,
std::ostream &oStream = std::cout);
~MMFFMolProperties() = default;
unsigned int getMMFFBondType(const Bond *bond);
unsigned int getMMFFBondType(const Bond *bond) const;
unsigned int getMMFFAngleType(const ROMol &mol, const unsigned int idx1,
const unsigned int idx2,
const unsigned int idx3);
const unsigned int idx3) const;
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);
const unsigned int idx3, const unsigned int idx4) const;
void computeMMFFCharges(const ROMol &mol);
const ForceFields::MMFF::MMFFTor *getMMFFTorsionEmpiricalRuleParams(
const ROMol &mol, unsigned int idx2, unsigned int idx3);
const ROMol &mol, unsigned int idx2, unsigned int idx3) const;
const ForceFields::MMFF::MMFFBond *getMMFFBondStretchEmpiricalRuleParams(
const ROMol &mol, const Bond *bond);
std::uint8_t getMMFFAtomType(const unsigned int idx) {
const ROMol &mol, const Bond *bond) const;
std::uint8_t getMMFFAtomType(const unsigned int idx) const {
URANGE_CHECK(idx, this->d_MMFFAtomPropertiesPtrVect.size());
return this->d_MMFFAtomPropertiesPtrVect[idx]->mmffAtomType;
}
double getMMFFFormalCharge(const unsigned int idx) {
double getMMFFFormalCharge(const unsigned int idx) const {
URANGE_CHECK(idx, this->d_MMFFAtomPropertiesPtrVect.size());
return this->d_MMFFAtomPropertiesPtrVect[idx]->mmffFormalCharge;
}
double getMMFFPartialCharge(const unsigned int idx) {
double getMMFFPartialCharge(const unsigned int idx) const {
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; }
bool getMMFFBondTerm() const { return this->d_bondTerm; }
void setMMFFAngleTerm(const bool state) { this->d_angleTerm = state; }
bool getMMFFAngleTerm() { return this->d_angleTerm; }
bool getMMFFAngleTerm() const { return this->d_angleTerm; }
void setMMFFStretchBendTerm(const bool state) {
this->d_stretchBendTerm = state;
}
bool getMMFFStretchBendTerm() { return this->d_stretchBendTerm; }
bool getMMFFStretchBendTerm() const { return this->d_stretchBendTerm; }
void setMMFFOopTerm(const bool state) { this->d_oopTerm = state; }
bool getMMFFOopTerm() { return this->d_oopTerm; }
bool getMMFFOopTerm() const { return this->d_oopTerm; }
void setMMFFTorsionTerm(const bool state) { this->d_torsionTerm = state; }
bool getMMFFTorsionTerm() { return this->d_torsionTerm; }
bool getMMFFTorsionTerm() const { return this->d_torsionTerm; }
void setMMFFVdWTerm(const bool state) { this->d_vdWTerm = state; }
bool getMMFFVdWTerm() { return this->d_vdWTerm; }
bool getMMFFVdWTerm() const { return this->d_vdWTerm; }
void setMMFFEleTerm(const bool state) { this->d_eleTerm = state; }
bool getMMFFEleTerm() { return this->d_eleTerm; }
bool getMMFFEleTerm() const { return this->d_eleTerm; }
void setMMFFVariant(const std::string &mmffVariant) {
PRECONDITION((mmffVariant == "MMFF94") || (mmffVariant == "MMFF94s"),
"bad MMFF variant");
this->d_mmffs = mmffVariant == "MMFF94s";
}
const std::string getMMFFVariant() {
const std::string getMMFFVariant() const {
return (this->d_mmffs ? "MMFF94s" : "MMFF94");
}
void setMMFFDielectricConstant(const double dielConst) {
@@ -136,42 +136,42 @@ class RDKIT_FORCEFIELDHELPERS_EXPORT MMFFMolProperties {
this->d_dielConst = dielConst;
}
double getMMFFDielectricConstant() { return this->d_dielConst; }
double getMMFFDielectricConstant() const { return this->d_dielConst; }
void setMMFFDielectricModel(std::uint8_t dielModel) {
this->d_dielModel = dielModel;
}
std::uint8_t getMMFFDielectricModel() { return this->d_dielModel; }
std::uint8_t getMMFFDielectricModel() const { return this->d_dielModel; }
void setMMFFVerbosity(std::uint8_t verbosity) {
this->d_verbosity = verbosity;
}
std::uint8_t getMMFFVerbosity() { return this->d_verbosity; }
std::uint8_t getMMFFVerbosity() const { 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 isValid() const { return d_valid; }
bool getMMFFBondStretchParams(const ROMol &mol, const unsigned int idx1,
const unsigned int idx2, unsigned int &bondType,
MMFFBond &mmffBondStretchParams);
MMFFBond &mmffBondStretchParams) const;
bool getMMFFAngleBendParams(const ROMol &mol, const unsigned int idx1,
const unsigned int idx2, const unsigned int idx3,
unsigned int &angleType,
MMFFAngle &mmffAngleBendParams);
MMFFAngle &mmffAngleBendParams) const;
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);
MMFFAngle &mmffAngleBendParams) const;
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);
MMFFTor &mmffTorsionParams) const;
bool getMMFFOopBendParams(const ROMol &mol, const unsigned int idx1,
const unsigned int idx2, const unsigned int idx3,
const unsigned int idx4,
MMFFOop &mmffOopBendParams);
MMFFOop &mmffOopBendParams) const;
bool getMMFFVdWParams(const unsigned int idx1, const unsigned int idx2,
MMFFVdWRijstarEps &mmffVdWParams);
MMFFVdWRijstarEps &mmffVdWParams) const;
private:
void setMMFFHeavyAtomType(const RingMembershipSize &rmSize, const Atom *atom);

33
Code/GraphMol/ForceFieldHelpers/Wrap/testHelpers.py
View File

@@ -416,6 +416,39 @@ M END"""
self.assertIsNotNone(ff)
self.assertTrue(hasattr(ff, "CalcEnergy"))
def testMMFFMolPropertiesScalarGetters(self):
mol = Chem.AddHs(Chem.MolFromSmiles("CCO"))
mp = ChemicalForceFields.MMFFGetMoleculeProperties(mol)
self.assertIsNotNone(mp)
mp.SetMMFFVariant("MMFF94s")
self.assertEqual(mp.GetMMFFVariant(), "MMFF94s")
mp.SetMMFFVariant("MMFF94")
self.assertEqual(mp.GetMMFFVariant(), "MMFF94")
mp.SetMMFFDielectricConstant(2.5)
self.assertAlmostEqual(mp.GetMMFFDielectricConstant(), 2.5)
mp.SetMMFFDielectricModel(2)
self.assertEqual(mp.GetMMFFDielectricModel(), 2)
mp.SetMMFFDielectricModel(1)
self.assertEqual(mp.GetMMFFDielectricModel(), 1)
term_pairs = [
(mp.SetMMFFBondTerm, mp.GetMMFFBondTerm),
(mp.SetMMFFAngleTerm, mp.GetMMFFAngleTerm),
(mp.SetMMFFStretchBendTerm, mp.GetMMFFStretchBendTerm),
(mp.SetMMFFOopTerm, mp.GetMMFFOopTerm),
(mp.SetMMFFTorsionTerm, mp.GetMMFFTorsionTerm),
(mp.SetMMFFVdWTerm, mp.GetMMFFVdWTerm),
(mp.SetMMFFEleTerm, mp.GetMMFFEleTerm),
]
for setter, getter in term_pairs:
setter(False)
self.assertFalse(getter())
setter(True)
self.assertTrue(getter())
if __name__ == "__main__":
unittest.main()