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//
// 2019, Daniel Probst, Reymond Group @ University of Bern
//
// @@ 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 <boost/python.hpp>
#include <RDBoost/Wrap.h>
#include <GraphMol/Fingerprints/MHFP.h>
#include <vector>
namespace python = boost::python;
using RDKit::MHFPFingerprints::MHFPEncoder;
namespace RDKit {
namespace MHFPWrapper {
typedef std::vector<std::vector<uint32_t>> VectMinHashVect;
typedef std::vector<ExplicitBitVect> VectExplicitBitVect;
template <typename T>
std::vector<T> ListToVector(const python::object &obj) {
return std::vector<T>(python::stl_input_iterator<T>(obj),
python::stl_input_iterator<T>());
}
UINT_VECT
FromStringArray(MHFPEncoder *mhfpEnc, python::list &vec) {
std::vector<std::string> vec_tmp = ListToVector<std::string>(vec);
return mhfpEnc->FromStringArray(vec_tmp);
}
UINT_VECT
FromArray(MHFPEncoder *mhfpEnc, python::list &vec) {
std::vector<uint32_t> vec_tmp = ListToVector<uint32_t>(vec);
return mhfpEnc->FromArray(vec_tmp);
}
STR_VECT
CreateShinglingFromSmiles(MHFPEncoder *mhfpEnc, std::string smiles,
unsigned char radius = 3, bool rings = true,
bool isomeric = false, bool kekulize = true,
unsigned char min_radius = 1) {
return mhfpEnc->CreateShingling(smiles, radius, rings, isomeric, kekulize,
min_radius);
}
STR_VECT
CreateShinglingFromMol(MHFPEncoder *mhfpEnc, ROMol mol,
unsigned char radius = 3, bool rings = true,
bool isomeric = false, bool kekulize = true,
unsigned char min_radius = 1) {
return mhfpEnc->CreateShingling(mol, radius, rings, isomeric, kekulize,
min_radius);
}
UINT_VECT
EncodeSmiles(MHFPEncoder *mhfpEnc, std::string smiles, unsigned char radius = 3,
bool rings = true, bool isomeric = false, bool kekulize = true,
unsigned char min_radius = 1) {
return mhfpEnc->Encode(smiles, radius, rings, isomeric, kekulize, min_radius);
}
UINT_VECT
EncodeMol(MHFPEncoder *mhfpEnc, ROMol mol, unsigned char radius = 3,
bool rings = true, bool isomeric = false, bool kekulize = true,
unsigned char min_radius = 1) {
return mhfpEnc->Encode(mol, radius, rings, isomeric, kekulize, min_radius);
}
VectMinHashVect EncodeSmilesBulk(MHFPEncoder *mhfpEnc, python::list &smiles,
unsigned char radius = 3, bool rings = true,
bool isomeric = false, bool kekulize = true,
unsigned char min_radius = 1) {
std::vector<std::string> vec = ListToVector<std::string>(smiles);
return mhfpEnc->Encode(vec, radius, rings, isomeric, kekulize, min_radius);
}
// There are access problems for vector_indexing_suite and std::vector<ROMol>.
// So let's fallback to a unefficient Python list.
VectMinHashVect EncodeMolsBulk(MHFPEncoder *mhfpEnc, python::list &mols,
unsigned char radius = 3, bool rings = true,
bool isomeric = false, bool kekulize = true,
unsigned char min_radius = 1) {
std::vector<ROMol> vec = ListToVector<ROMol>(mols);
return mhfpEnc->Encode(vec, radius, rings, isomeric, kekulize, min_radius);
}
// SECFP
ExplicitBitVect EncodeSECFPSmiles(MHFPEncoder *mhfpEnc, std::string smiles,
unsigned char radius = 3, bool rings = true,
bool isomeric = false, bool kekulize = true,
unsigned char min_radius = 1,
size_t length = 2048) {
return mhfpEnc->EncodeSECFP(smiles, radius, rings, isomeric, kekulize,
min_radius, length);
}
ExplicitBitVect EncodeSECFPMol(MHFPEncoder *mhfpEnc, ROMol mol,
unsigned char radius = 3, bool rings = true,
bool isomeric = false, bool kekulize = true,
unsigned char min_radius = 1,
size_t length = 2048) {
return mhfpEnc->EncodeSECFP(mol, radius, rings, isomeric, kekulize,
min_radius, length);
}
VectExplicitBitVect EncodeSECFPSmilesBulk(
MHFPEncoder *mhfpEnc, python::list &smiles, unsigned char radius = 3,
bool rings = true, bool isomeric = false, bool kekulize = true,
unsigned char min_radius = 1, size_t length = 2048) {
std::vector<std::string> vec = ListToVector<std::string>(smiles);
return mhfpEnc->EncodeSECFP(vec, radius, rings, isomeric, kekulize,
min_radius, length);
}
VectExplicitBitVect EncodeSECFPMolsBulk(
MHFPEncoder *mhfpEnc, python::list &mols, unsigned char radius = 3,
bool rings = true, bool isomeric = false, bool kekulize = true,
unsigned char min_radius = 1, size_t length = 2048) {
std::vector<ROMol> vec = ListToVector<ROMol>(mols);
return mhfpEnc->EncodeSECFP(vec, radius, rings, isomeric, kekulize,
min_radius, length);
}
BOOST_PYTHON_FUNCTION_OVERLOADS(CreateShinglingFromSmilesOverloads,
CreateShinglingFromSmiles, 2, 7)
BOOST_PYTHON_FUNCTION_OVERLOADS(CreateShinglingFromMolOverloads,
CreateShinglingFromMol, 2, 7)
BOOST_PYTHON_FUNCTION_OVERLOADS(EncodeSmilesOverloads, EncodeSmiles, 2, 7)
BOOST_PYTHON_FUNCTION_OVERLOADS(EncodeMolOverloads, EncodeMol, 2, 7)
BOOST_PYTHON_FUNCTION_OVERLOADS(EncodeSmilesBulkOverloads, EncodeSmilesBulk, 2,
7)
BOOST_PYTHON_FUNCTION_OVERLOADS(EncodeMolsBulkOverloads, EncodeMolsBulk, 2, 7)
BOOST_PYTHON_FUNCTION_OVERLOADS(EncodeSECFPSmilesOverloads, EncodeSECFPSmiles,
2, 8)
BOOST_PYTHON_FUNCTION_OVERLOADS(EncodeSECFPMolOverloads, EncodeSECFPMol, 2, 8)
BOOST_PYTHON_FUNCTION_OVERLOADS(EncodeSECFPSmilesBulkOverloads,
EncodeSECFPSmilesBulk, 2, 8)
BOOST_PYTHON_FUNCTION_OVERLOADS(EncodeSECFPMolsBulkOverloads,
EncodeSECFPMolsBulk, 2, 8)
BOOST_PYTHON_MODULE(rdMHFPFingerprint) {
python::class_<MHFPEncoder>(
"MHFPEncoder", python::init<python::optional<unsigned int, unsigned int>>(
python::args("self", "n_permutations", "seed")))
.def("FromStringArray", FromStringArray, python::args("self", "vec"),
"Creates a MHFP vector from a list of arbitrary strings.")
.def("FromArray", FromArray, python::args("self", "vec"),
"Creates a MHFP vector from a list of unsigned integers.")
.def("CreateShinglingFromSmiles", CreateShinglingFromSmiles,
CreateShinglingFromSmilesOverloads(
(python::arg("self"), python::arg("smiles"),
python::arg("radius") = 3, python::arg("rings") = true,
python::arg("isomeric") = false,
python::arg("kekulize") = false, python::arg("min_radius") = 1),
"Creates a shingling (a list of circular n-grams / "
"substructures) from a SMILES string."))
.def("CreateShinglingFromMol", CreateShinglingFromMol,
CreateShinglingFromMolOverloads(
(python::arg("self"), python::arg("mol"),
python::arg("radius") = 3, python::arg("rings") = true,
python::arg("isomeric") = false,
python::arg("kekulize") = false, python::arg("min_radius") = 1),
"Creates a shingling (a list of circular n-grams / "
"substructures) from a RDKit Mol instance."))
.def("EncodeSmiles", EncodeSmiles,
EncodeSmilesOverloads(
(python::arg("self"), python::arg("smiles"),
python::arg("radius") = 3, python::arg("rings") = true,
python::arg("isomeric") = false,
python::arg("kekulize") = false, python::arg("min_radius") = 1),
"Creates a MHFP vector from a SMILES string."))
.def("EncodeMol", EncodeMol,
EncodeMolOverloads(
(python::arg("self"), python::arg("mol"),
python::arg("radius") = 3, python::arg("rings") = true,
python::arg("isomeric") = false,
python::arg("kekulize") = false, python::arg("min_radius") = 1),
"Creates a MHFP vector from an RDKit Mol instance."))
.def("EncodeSmilesBulk", EncodeSmilesBulk,
EncodeSmilesBulkOverloads(
(python::arg("self"), python::arg("smiles"),
python::arg("radius") = 3, python::arg("rings") = true,
python::arg("isomeric") = false,
python::arg("kekulize") = false, python::arg("min_radius") = 1),
"Creates a MHFP vector from a list of SMILES strings."))
.def("EncodeMolsBulk", EncodeMolsBulk,
EncodeMolsBulkOverloads(
(python::arg("self"), python::arg("mols"),
python::arg("radius") = 3, python::arg("rings") = true,
python::arg("isomeric") = false,
python::arg("kekulize") = false, python::arg("min_radius") = 1),
"Creates a MHFP vector from a list of RDKit Mol instances."))
.def(
"EncodeSECFPSmiles", EncodeSECFPSmiles,
EncodeSECFPSmilesOverloads(
(python::arg("self"), python::arg("smiles"),
python::arg("radius") = 3, python::arg("rings") = true,
python::arg("isomeric") = false, python::arg("kekulize") = false,
python::arg("min_radius") = 1, python::arg("length") = 2048),
"Creates a SECFP binary vector from a SMILES string."))
.def(
"EncodeSECFPMol", EncodeSECFPMol,
EncodeSECFPMolOverloads(
(python::arg("self"), python::arg("smiles"),
python::arg("radius") = 3, python::arg("rings") = true,
python::arg("isomeric") = false, python::arg("kekulize") = false,
python::arg("min_radius") = 1, python::arg("length") = 2048),
"Creates a SECFP binary vector from an RDKit Mol instance."))
.def(
"EncodeSECFPSmilesBulk", EncodeSECFPSmilesBulk,
EncodeSECFPSmilesBulkOverloads(
(python::arg("self"), python::arg("smiles"),
python::arg("radius") = 3, python::arg("rings") = true,
python::arg("isomeric") = false, python::arg("kekulize") = false,
python::arg("min_radius") = 1, python::arg("length") = 2048),
"Creates a SECFP binary vector from a list of SMILES strings."))
.def(
"EncodeSECFPMolsBulk", EncodeSECFPMolsBulk,
EncodeSECFPMolsBulkOverloads(
(python::arg("self"), python::arg("smiles"),
python::arg("radius") = 3, python::arg("rings") = true,
python::arg("isomeric") = false, python::arg("kekulize") = false,
python::arg("min_radius") = 1, python::arg("length") = 2048),
"Creates a SECFP binary vector from a list of RDKit Mol "
"instances."))
.def("Distance", &MHFPEncoder::Distance, python::args("a", "b"))
.staticmethod("Distance");
}
} // namespace MHFPWrapper
} // namespace RDKit
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