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//
// Copyright (C) 2022 Greg Landrum
//
// @@ 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 <string>
#include <RDBoost/python.h>
#include <GraphMol/GraphMol.h>
#include <RDBoost/Wrap.h>
#include <RDGeneral/ControlCHandler.h>
#include <GraphMol/DetermineBonds/DetermineBonds.h>
namespace python = boost::python;
using namespace RDKit;
namespace {
void determineConnectivityHelper(ROMol &mol, bool useHueckel, int charge,
double covFactor, bool useVdw) {
auto &wmol = static_cast<RWMol &>(mol);
determineConnectivity(wmol, useHueckel, charge, covFactor, useVdw);
}
void determineBondOrdersHelper(ROMol &mol, int charge,
bool allowChargedFragments, bool embedChiral,
bool useAtomMap, size_t maxIterations) {
auto &wmol = static_cast<RWMol &>(mol);
determineBondOrders(wmol, charge, allowChargedFragments, embedChiral,
useAtomMap, maxIterations);
if (ControlCHandler::getGotSignal()) {
PyErr_SetString(PyExc_KeyboardInterrupt, "Determine Bond Orders cancelled");
boost::python::throw_error_already_set();
}
}
void determineBondsHelper(ROMol &mol, bool useHueckel, int charge,
double covFactor, bool allowChargedFragments,
bool embedChiral, bool useAtomMap, bool useVdw,
size_t maxIterations) {
auto &wmol = static_cast<RWMol &>(mol);
determineBonds(wmol, useHueckel, charge, covFactor, allowChargedFragments,
embedChiral, useAtomMap, useVdw, maxIterations);
if (ControlCHandler::getGotSignal()) {
PyErr_SetString(PyExc_KeyboardInterrupt, "Determine Bond Orders cancelled");
boost::python::throw_error_already_set();
}
}
bool hueckelSupportEnabled() {
#ifdef RDK_BUILD_YAEHMOP_SUPPORT
return true;
#else
return false;
#endif
}
} // namespace
void rdMaxFindBondOrdersItersExceededTranslator(
const RDKit::MaxFindBondOrdersItersExceeded &x) {
PyErr_SetString(PyExc_RuntimeError, x.what());
}
BOOST_PYTHON_MODULE(rdDetermineBonds) {
python::scope().attr("__doc__") =
"Module containing a C++ implementation of the xyz2mol algorithm. This is based on xyz2mol: https://github.com/jensengroup/xyz2mol";
python::register_exception_translator<RDKit::MaxFindBondOrdersItersExceeded>(
&rdMaxFindBondOrdersItersExceededTranslator);
std::string docs;
docs =
R"DOC(Assigns atomic connectivity to a molecule using atomic coordinates,
disregarding pre-existing bonds
Args:
mol : the molecule of interest; it must have a 3D conformer
useHueckel : (optional) if this is \c true, extended Hueckel theory
will be used to determine connectivity rather than the van der Waals
or connect-the-dots methods
charge : (optional) the charge of the molecule; it must be provided if
the Hueckel method is used and charge is non-zero
covFactor : (optional) the factor with which to multiply each covalent
radius if the van der Waals method is used
useVdw: (optional) if this is false, the connect-the-dots method
will be used instead of the van der Waals method
)DOC";
python::def("DetermineConnectivity", &determineConnectivityHelper,
(python::arg("mol"), python::arg("useHueckel") = false,
python::arg("charge") = 0, python::arg("covFactor") = 1.3,
python::arg("useVdw") = false),
docs.c_str());
docs =
R"DOC(Assigns atomic connectivity to a molecule using atomic coordinates,
disregarding pre-existing bonds
Args:
mol : the molecule of interest; it must have a 3D conformer
charge : (optional) the charge of the molecule; it must be provided if
the Hueckel method is used and charge is non-zero
allowChargedFragments : (optional) if this is true, formal charges
will be placed on atoms according to their valency; otherwise, radical
electrons will be placed on the atoms
embedChiral : (optional) if this is true,
chirality information will be embedded into the molecule; the function calls
sanitizeMol() when this is true
useAtomMap : (optional) if this is true, an atom map will be created for the
molecule
maxIterations: (optional) maximum number of iterations to run in the bond order
determination algorithm, after which a MaxFindBondOrdersItersExceeded
exception will be thrown. Defaults to 0 (no limit)
)DOC";
python::def(
"DetermineBondOrders", &determineBondOrdersHelper,
(python::arg("mol"), python::arg("charge") = 0,
python::arg("allowChargedFragments") = true,
python::arg("embedChiral") = true, python::arg("useAtomMap") = false,
python::arg("maxIterations") = 0),
docs.c_str());
docs =
R"DOC(Assigns atomic connectivity to a molecule using atomic coordinates,
disregarding pre-existing bonds
Args:
mol : the molecule of interest; it must have a 3D conformer
useHueckel : (optional) if this is true, extended Hueckel theory
will be used to determine connectivity rather than the van der Waals
or connect-the-dots methods
charge : (optional) the charge of the molecule; it must be provided if
the Hueckel method is used and charge is non-zero
covFactor : (optional) the factor with which to multiply each covalent
radius if the van der Waals method is used
allowChargedFragments : (optional) if this is true, formal charges
will be placed on atoms according to their valency; otherwise, radical
electrons will be placed on the atoms
embedChiral : (optional) if this is true,
chirality information will be embedded into the molecule; the function calls
sanitizeMol() when this is true
useAtomMap : (optional) if this is true, an atom map will be created for the
molecule
useVdw: (optional) if this is false, the connect-the-dots method
will be used instead of the van der Waals method
maxIterations: (optional) maximum number of iterations to run in the bond order
determination algorithm, after which a MaxFindBondOrdersItersExceeded
exception will be thrown. Defaults to 0 (no limit)
)DOC";
python::def(
"DetermineBonds", &determineBondsHelper,
(python::arg("mol"), python::arg("useHueckel") = false,
python::arg("charge") = 0, python::arg("covFactor") = 1.3,
python ::arg("allowChargedFragments") = true,
python::arg("embedChiral") = true, python::arg("useAtomMap") = false,
python::arg("useVdw") = false, python::arg("maxIterations") = 0),
docs.c_str());
python::def("hueckelEnabled", &hueckelSupportEnabled,
"whether or not the RDKit was compiled with YAeHMOP support");
}
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