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//
// Copyright (C) 2018 Susan H. Leung
//
// @@ 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 <RDBoost/Wrap.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/MolStandardize/MolStandardize.h>
#include <vector>
namespace python = boost::python;
namespace {
template <typename FUNCTYPE>
RDKit::ROMol *msHelper(const RDKit::ROMol *mol, python::object params,
FUNCTYPE func) {
if (!mol) {
throw_value_error("Molecule is None");
}
const RDKit::MolStandardize::CleanupParameters *ps =
&RDKit::MolStandardize::defaultCleanupParameters;
if (params) {
ps = python::extract<RDKit::MolStandardize::CleanupParameters *>(params);
}
return static_cast<RDKit::ROMol *>(
func(static_cast<const RDKit::RWMol *>(mol), *ps));
}
RDKit::ROMol *cleanupHelper(const RDKit::ROMol *mol, python::object params) {
return msHelper(
mol, params,
static_cast<
RDKit::RWMol *(*)(const RDKit::RWMol *,
const RDKit::MolStandardize::CleanupParameters &)>(
RDKit::MolStandardize::cleanup));
}
RDKit::ROMol *normalizeHelper(const RDKit::ROMol *mol, python::object params) {
return msHelper(mol, params, RDKit::MolStandardize::normalize);
}
RDKit::ROMol *reionizeHelper(const RDKit::ROMol *mol, python::object params) {
return msHelper(mol, params, RDKit::MolStandardize::reionize);
}
RDKit::ROMol *removeFragsHelper(const RDKit::ROMol *mol,
python::object params) {
return msHelper(mol, params, RDKit::MolStandardize::removeFragments);
}
RDKit::ROMol *canonicalTautomerHelper(const RDKit::ROMol *mol,
python::object params) {
return msHelper(mol, params, RDKit::MolStandardize::canonicalTautomer);
}
template <typename FUNCTYPE>
RDKit::ROMol *parentHelper(const RDKit::ROMol *mol, python::object params,
bool skip_standardize, FUNCTYPE func) {
if (!mol) {
throw_value_error("Molecule is None");
}
const RDKit::MolStandardize::CleanupParameters *ps =
&RDKit::MolStandardize::defaultCleanupParameters;
if (params) {
ps = python::extract<RDKit::MolStandardize::CleanupParameters *>(params);
}
return static_cast<RDKit::ROMol *>(
func(static_cast<const RDKit::RWMol &>(*mol), *ps, skip_standardize));
}
RDKit::ROMol *tautomerParentHelper(const RDKit::ROMol *mol,
python::object params,
bool skip_standardize) {
return parentHelper(mol, params, skip_standardize,
RDKit::MolStandardize::tautomerParent);
}
RDKit::ROMol *fragmentParentHelper(const RDKit::ROMol *mol,
python::object params,
bool skip_standardize) {
return parentHelper(mol, params, skip_standardize,
RDKit::MolStandardize::fragmentParent);
}
RDKit::ROMol *stereoParentHelper(const RDKit::ROMol *mol, python::object params,
bool skip_standardize) {
return parentHelper(mol, params, skip_standardize,
RDKit::MolStandardize::stereoParent);
}
RDKit::ROMol *isotopeParentHelper(const RDKit::ROMol *mol,
python::object params,
bool skip_standardize) {
return parentHelper(mol, params, skip_standardize,
RDKit::MolStandardize::isotopeParent);
}
RDKit::ROMol *chargeParentHelper(const RDKit::ROMol *mol, python::object params,
bool skip_standardize) {
return parentHelper(mol, params, skip_standardize,
RDKit::MolStandardize::chargeParent);
}
RDKit::ROMol *superParentHelper(const RDKit::ROMol *mol, python::object params,
bool skip_standardize) {
return parentHelper(mol, params, skip_standardize,
RDKit::MolStandardize::superParent);
}
} // namespace
void wrap_validate();
void wrap_charge();
void wrap_metal();
void wrap_fragment();
void wrap_normalize();
void wrap_tautomer();
BOOST_PYTHON_MODULE(rdMolStandardize) {
python::scope().attr("__doc__") =
"Module containing functions for molecular standardization";
std::string docString = "";
python::class_<RDKit::MolStandardize::CleanupParameters, boost::noncopyable>(
"CleanupParameters", "Parameters controlling molecular standardization")
.def_readwrite("normalizationsFile",
&RDKit::MolStandardize::CleanupParameters::normalizations,
"file containing the normalization transformations")
.def_readwrite("acidbaseFile",
&RDKit::MolStandardize::CleanupParameters::acidbaseFile,
"file containing the acid and base definitions")
.def_readwrite("fragmentFile",
&RDKit::MolStandardize::CleanupParameters::fragmentFile,
"file containing the acid and base definitions")
.def_readwrite(
"tautomerTransformsFile",
&RDKit::MolStandardize::CleanupParameters::tautomerTransforms,
"file containing the tautomer transformations")
.def_readwrite("maxRestarts",
&RDKit::MolStandardize::CleanupParameters::maxRestarts,
"maximum number of restarts")
.def_readwrite("preferOrganic",
&RDKit::MolStandardize::CleanupParameters::preferOrganic,
"prefer organic fragments to inorganic ones when deciding "
"what to keep")
.def_readwrite("doCanonical",
&RDKit::MolStandardize::CleanupParameters::doCanonical,
"apply atom-order dependent normalizations (like "
"uncharging) in a canonical order")
.def_readwrite("maxTautomers",
&RDKit::MolStandardize::CleanupParameters::maxTautomers,
"maximum number of tautomers to generate (defaults to "
"1000)")
.def_readwrite("maxTransforms",
&RDKit::MolStandardize::CleanupParameters::maxTransforms,
"maximum number of transforms to apply during tautomer "
"enumeration (defaults to 1000)")
.def_readwrite(
"tautomerRemoveSp3Stereo",
&RDKit::MolStandardize::CleanupParameters::tautomerRemoveSp3Stereo,
"remove stereochemistry from sp3 centers involved in "
"tautomerism (defaults to True)")
.def_readwrite(
"tautomerRemoveBondStereo",
&RDKit::MolStandardize::CleanupParameters::tautomerRemoveBondStereo,
"remove stereochemistry from double bonds involved in "
"tautomerism (defaults to True)")
.def_readwrite(
"tautomerRemoveIsotopicHs",
&RDKit::MolStandardize::CleanupParameters::tautomerRemoveIsotopicHs,
"remove isotopic Hs from centers involved in "
"tautomerism (defaults to True)")
.def_readwrite(
"tautomerReassignStereo",
&RDKit::MolStandardize::CleanupParameters::tautomerReassignStereo,
"call AssignStereochemistry on all generated tautomers "
"(defaults to True)")
.def_readwrite("largestFragmentChooserUseAtomCount",
&RDKit::MolStandardize::CleanupParameters::
largestFragmentChooserUseAtomCount,
"Whether LargestFragmentChooser should use atom "
"count as main criterion before MW (defaults to True)")
.def_readwrite("largestFragmentChooserCountHeavyAtomsOnly",
&RDKit::MolStandardize::CleanupParameters::
largestFragmentChooserCountHeavyAtomsOnly,
"whether LargestFragmentChooser should only count "
"heavy atoms (defaults to False)");
python::def("UpdateParamsFromJSON",
&RDKit::MolStandardize::updateCleanupParamsFromJSON,
"updates the cleanup parameters from the provided JSON string");
docString = "Standardizes a molecule";
python::def("Cleanup", cleanupHelper,
(python::arg("mol"), python::arg("params") = python::object()),
docString.c_str(),
python::return_value_policy<python::manage_new_object>());
docString = "Convenience function for standardizing a SMILES";
python::def("StandardizeSmiles", RDKit::MolStandardize::standardizeSmiles,
(python::arg("smiles")), docString.c_str());
docString =
"Returns the tautomer parent of a given molecule. The fragment parent is "
"the standardized canonical tautomer of the molecule";
python::def("TautomerParent", tautomerParentHelper,
(python::arg("mol"), python::arg("params") = python::object(),
python::arg("skipStandardize") = false),
docString.c_str(),
python::return_value_policy<python::manage_new_object>());
docString = "Returns the largest fragment after doing a cleanup";
python::def("FragmentParent", fragmentParentHelper,
(python::arg("mol"), python::arg("params") = python::object(),
python::arg("skipStandardize") = false),
docString.c_str(),
python::return_value_policy<python::manage_new_object>());
docString = "calls removeStereochemistry() on the given molecule";
python::def("StereoParent", stereoParentHelper,
(python::arg("mol"), python::arg("params") = python::object(),
python::arg("skipStandardize") = false),
docString.c_str(),
python::return_value_policy<python::manage_new_object>());
docString = "removes all isotopes specifications from the given molecule";
python::def("IsotopeParent", isotopeParentHelper,
(python::arg("mol"), python::arg("params") = python::object(),
python::arg("skipStandardize") = false),
docString.c_str(),
python::return_value_policy<python::manage_new_object>());
docString = "Returns the uncharged version of the largest fragment";
python::def("ChargeParent", chargeParentHelper,
(python::arg("mol"), python::arg("params") = python::object(),
python::arg("skipStandardize") = false),
docString.c_str(),
python::return_value_policy<python::manage_new_object>());
docString =
"Returns the super parent. The super parent is the fragment, charge, "
"isotope, stereo, and tautomer parent of the molecule.";
python::def("SuperParent", superParentHelper,
(python::arg("mol"), python::arg("params") = python::object(),
python::arg("skipStandardize") = false),
docString.c_str(),
python::return_value_policy<python::manage_new_object>());
docString =
"Applies a series of standard transformations to correct functional "
"groups and recombine charges";
python::def("Normalize", normalizeHelper,
(python::arg("mol"), python::arg("params") = python::object()),
docString.c_str(),
python::return_value_policy<python::manage_new_object>());
docString = "Ensures the strongest acid groups are charged first";
python::def("Reionize", reionizeHelper,
(python::arg("mol"), python::arg("params") = python::object()),
docString.c_str(),
python::return_value_policy<python::manage_new_object>());
docString = "Removes fragments from the molecule";
python::def("RemoveFragments", removeFragsHelper,
(python::arg("mol"), python::arg("params") = python::object()),
docString.c_str(),
python::return_value_policy<python::manage_new_object>());
docString = "Returns the canonical tautomer for the molecule";
python::def("CanonicalTautomer", canonicalTautomerHelper,
(python::arg("mol"), python::arg("params") = python::object()),
docString.c_str(),
python::return_value_policy<python::manage_new_object>());
wrap_validate();
wrap_charge();
wrap_metal();
wrap_fragment();
wrap_normalize();
wrap_tautomer();
}
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