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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>>())
.def("FromStringArray", &FromStringArray, (
(
python::arg("vec")
),
"Creates a MHFP vector from a list of arbitrary strings."
))
.def("FromArray", &FromArray, (
(
python::arg("vec")
),
"Creates a MHFP vector from a list of unsigned integers."
))
.def("CreateShinglingFromSmiles", CreateShinglingFromSmiles, CreateShinglingFromSmilesOverloads(
(
python::arg("smiles"),
python::arg("radius") = 3,
python::arg("rings") = true,
python::arg("isomeric") = false,
python::arg("kekulize") = true,
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("mol"),
python::arg("radius") = 3,
python::arg("rings") = true,
python::arg("isomeric") = false,
python::arg("kekulize") = true,
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("smiles"),
python::arg("radius") = 3,
python::arg("rings") = true,
python::arg("isomeric") = false,
python::arg("kekulize") = true,
python::arg("min_radius") = 1
),
"Creates a MHFP vector from a SMILES string."
))
.def("EncodeMol", EncodeMol, EncodeMolOverloads(
(
python::arg("mol"),
python::arg("radius") = 3,
python::arg("rings") = true,
python::arg("isomeric") = false,
python::arg("kekulize") = true,
python::arg("min_radius") = 1
),
"Creates a MHFP vector from an RDKit Mol instance."
))
.def("EncodeSmilesBulk", EncodeSmilesBulk, EncodeSmilesBulkOverloads(
(
python::arg("smiles"),
python::arg("radius") = 3,
python::arg("rings") = true,
python::arg("isomeric") = false,
python::arg("kekulize") = true,
python::arg("min_radius") = 1
),
"Creates a MHFP vector from a list of SMILES strings."
))
.def("EncodeMolsBulk", EncodeMolsBulk, EncodeMolsBulkOverloads(
(
python::arg("mols"),
python::arg("radius") = 3,
python::arg("rings") = true,
python::arg("isomeric") = false,
python::arg("kekulize") = true,
python::arg("min_radius") = 1
),
"Creates a MHFP vector from a list of RDKit Mol instances."
))
.def("EncodeSECFPSmiles", EncodeSECFPSmiles, EncodeSECFPSmilesOverloads(
(
python::arg("smiles"),
python::arg("radius") = 3,
python::arg("rings") = true,
python::arg("isomeric") = false,
python::arg("kekulize") = true,
python::arg("min_radius") = 1,
python::arg("length") = 2048
),
"Creates a SECFP binary vector from a SMILES string."
))
.def("EncodeSECFPMol", EncodeSECFPMol, EncodeSECFPMolOverloads(
(
python::arg("smiles"),
python::arg("radius") = 3,
python::arg("rings") = true,
python::arg("isomeric") = false,
python::arg("kekulize") = true,
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("smiles"),
python::arg("radius") = 3,
python::arg("rings") = true,
python::arg("isomeric") = false,
python::arg("kekulize") = true,
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("smiles"),
python::arg("radius") = 3,
python::arg("rings") = true,
python::arg("isomeric") = false,
python::arg("kekulize") = true,
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)
.staticmethod("Distance");
}
} // namespace MHFPWrapper
} // namespace RDKit
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