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// Copyright (c) 2017, Novartis Institutes for BioMedical Research Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above
// copyright notice, this list of conditions and the following
// disclaimer in the documentation and/or other materials provided
// with the distribution.
// * Neither the name of Novartis Institutes for BioMedical Research Inc.
// nor the names of its contributors may be used to endorse or promote
// products derived from this software without specific prior written
// permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
#include <RDBoost/python.h>
#include <RDBoost/Wrap.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/SubstructLibrary/SubstructLibrary.h>
namespace python = boost::python;
namespace RDKit {
const char *MolHolderBaseDoc =
"Base class for holding molecules used in the Substructure Library.\n"
"Instantiations of this class are passed into the SubstructureLibrary.\n"
"The API is quite simple: \n"
" AddMol(mol) -> adds a molecule to the molecule holder, returns index of "
"molecule\n"
" GetMol(idx) -> return the molecule at index idx\n";
const char *MolHolderDoc =
"Holds raw in-memory molecules\n"
" AddMol(mol) -> adds a molecule to the molecule holder, returns index of "
"molecule\n"
" GetMol(idx) -> return the molecule at index idx\n";
const char *CachedMolHolderDoc =
"Holds molecules in their binary representation.\n"
"This allows more molecules to be held in memory at a time\n"
" AddMol(mol) -> adds a molecule to the molecule holder, returns index of "
"molecule\n"
" AddBinary(data) -> adds a picked molecule molecule to the molecule "
"holder, returns index of molecule\n"
" The data is stored as-is, no checking is done for "
"validity.\n"
" GetMol(idx) -> return the molecule at index idx\n";
const char *CachedSmilesMolHolderDoc =
"Holds molecules as smiles string\n"
"This allows more molecules to be held in memory at a time\n"
" AddMol(mol) -> adds a molecule to the molecule holder, returns index of "
"molecule\n"
" AddSmiles(smiles) -> adds a smiles string to the molecule holder, "
"returns index of molecule\n"
" The smiles is stored as-is, no checking is done "
"for validity.\n"
" GetMol(idx) -> return the molecule at index idx\n";
const char *CachedTrustedSmilesMolHolderDoc =
"Holds molecules as trusted smiles string\n"
"This allows more molecules to be held in memory at a time and avoids "
"RDKit sanitization\n"
"overhead\n"
"See: "
"http://rdkit.blogspot.com/2016/09/avoiding-unnecessary-work-and.html\n"
" AddMol(mol) -> adds a molecule to the molecule holder, returns index of "
"molecule\n"
" AddSmiles(smiles) -> adds a smiles string to the molecule holder, "
"returns index of molecule\n"
" The smiles is stored as-is, no checking is done "
"for validity.\n"
" GetMol(idx) -> return the molecule at index idx\n";
const char *PatternHolderDoc =
"Holds fingerprints used for filtering of molecules.";
const char *SubstructLibraryDoc =
"SubstructLibrary: This provides a simple API for substructure searching "
"large datasets\n"
"The SubstructLibrary takes full advantage of available threads during the "
"search operation.\n"
"Basic operation is simple\n"
">>> from __future__ import print_function\n"
">>> import os\n"
">>> from rdkit import Chem, RDConfig\n"
">>> from rdkit.Chem import rdSubstructLibrary\n"
">>> library = rdSubstructLibrary.SubstructLibrary()\n"
">>> for mol in Chem.SDMolSupplier(os.path.join(RDConfig.RDDataDir, \n"
"... 'NCI', 'first_200.props.sdf')):\n"
"... idx = library.AddMol(mol)\n"
">>> core = Chem.MolFromSmarts('CCCCOC')\n"
">>> indices = library.GetMatches(core)\n"
">>> len(indices)\n"
"11\n"
"\n"
"\n"
"Substructure matching options can be sent into GetMatches:\n"
">>> indices = library.GetMatches(core, useChirality=False) \n"
">>> len(indices)\n"
"11\n"
"\n"
"Controlling the number of threads or the maximum number of matches "
"returned:\n"
"is also available (the default is to run on all cores)\n"
">>> indices = library.GetMatches(core, numThreads=2, maxResults=10) \n"
">>> len(indices)\n"
"10\n"
"\n"
"Working on larger datasets:\n"
"\n"
"Molecules are fairly large objects and will limit the number that can be "
"kept in memory.\n"
"To assist this we supply three other molecule holders:\n"
" CachedMolHolder - stores molecules as their pickled representation\n"
" CachedSmilesMolHolder - stores molecules internally as smiles strings\n"
" CachedTrustedSmilesMolHolder = excepts (and stores) molecules as "
"trusted smiles strings\n"
"\n"
"Using Pattern fingerprints as a pre-filter:"
"\n"
"Pattern fingerprints provide an easy way to indicate whether the "
"substructure search should be\n"
"be done at all. This is particulary useful with the Binary and Smiles "
"based molecule holders\n"
"as they have an expensive molecule creation step in addition to the "
"substructure searching step\n "
"\n"
">>> library = "
"rdSubstructLibrary.SubstructLibrary(rdSubstructLibrary."
"CachedSmilesMolHolder(), \n"
"... "
"rdSubstructLibrary.PatternHolder())\n"
">>> for mol in Chem.SDMolSupplier(os.path.join(RDConfig.RDDataDir, \n"
"... 'NCI', 'first_200.props.sdf')):\n"
"... idx = library.AddMol(mol)\n"
">>> indices = library.GetMatches(core)\n"
">>> len(indices)\n"
"11\n"
"\n"
"This (obviously) takes longer to initialize. However, both the molecule "
"and pattern\n"
"holders can be populated with raw data, a simple example is below:\n"
">>> import csv\n"
">>> molholder = rdSubstructLibrary.CachedSmilesMolHolder()\n"
">>> pattern_holder = rdSubstructLibrary.PatternHolder()\n"
">>> for i, row in "
"enumerate(csv.reader(open(os.path.join(RDConfig.RDDataDir, \n"
"... 'NCI', 'first_200.tpsa.csv')))):\n"
"... if i:\n"
"... idx = molholder.AddSmiles(row[0])\n"
"... idx2 = pattern_holder.AddFingerprint(\n"
"... pattern_holder.MakeFingerprint(Chem.MolFromSmiles(row[0])))\n"
"... assert idx==idx2\n"
">>> library = "
"rdSubstructLibrary.SubstructLibrary(molholder,pattern_holder)\n"
">>> indices = library.GetMatches(core)\n"
">>> len(indices)\n"
"11\n"
"";
struct substructlibrary_wrapper {
static void wrap() {
// n.b. there can only be one of these in all wrappings
// python::class_<std::vector<unsigned int> >("UIntVect").def(
// python::vector_indexing_suite<std::vector<unsigned int>, true>());
python::class_<MolHolderBase, boost::noncopyable>("MolHolderBase", "",
python::no_init)
.def("AddMol", &MolHolderBase::addMol,
"Adds molecle to the molecule holder")
.def("GetMol", &MolHolderBase::getMol,
"Returns a particular molecule in the molecule holder\n\n"
" ARGUMENTS:\n"
" - idx: which molecule to return\n\n"
" NOTE: molecule indices start at 0\n")
.def("__len__", &MolHolderBase::size);
python::class_<MolHolder, boost::shared_ptr<MolHolder>,
python::bases<MolHolderBase>>("MolHolder", MolHolderDoc,
python::init<>());
python::class_<CachedMolHolder, boost::shared_ptr<CachedMolHolder>,
python::bases<MolHolderBase>>(
"CachedMolHolder", CachedMolHolderDoc, python::init<>())
.def("AddBinary", &CachedMolHolder::addBinary, (python::args("pickle")),
"Add a binary pickle to the molecule holder, no checking is done "
"on the input data");
python::class_<CachedSmilesMolHolder,
boost::shared_ptr<CachedSmilesMolHolder>,
python::bases<MolHolderBase>>(
"CachedSmilesMolHolder", CachedSmilesMolHolderDoc, python::init<>())
.def("AddSmiles", &CachedSmilesMolHolder::addSmiles,
(python::args("smiles")),
"Add a trusted smiles string to the molecule holder, no checking "
"is done on the input data");
python::class_<CachedTrustedSmilesMolHolder,
boost::shared_ptr<CachedTrustedSmilesMolHolder>,
python::bases<MolHolderBase>>(
"CachedTrustedSmilesMolHolder", CachedTrustedSmilesMolHolderDoc,
python::init<>())
.def("AddSmiles", &CachedTrustedSmilesMolHolder::addSmiles,
(python::args("smiles")),
"Add a trusted smiles string to the molecule holder, no checking "
"is done on the input data");
python::class_<FPHolderBase, boost::shared_ptr<FPHolderBase>,
boost::noncopyable>("FPHolderBase", "", python::no_init)
.def("AddMol", &FPHolderBase::addMol,
"Adds a molecule to the fingerprint database, returns the index "
"of the new pattern")
.def("AddFingerprint", &FPHolderBase::addFingerprint,
"Adds a raw bit vector to the fingerprint database, returns the "
"index of the supplied pattern")
.def("GetFingerprint", &FPHolderBase::getFingerprint,
python::return_value_policy<python::reference_existing_object>(),
"Return the bit vector at the specified index")
.def("PassesFilter", &FPHolderBase::passesFilter,
(python::args("idx"), python::args("query")),
"Returns True if the specified index passes the filter supplied "
"by the query bit vector")
.def("MakeFingerprint", &FPHolderBase::makeFingerprint,
(python::arg("mol")),
python::return_value_policy<python::manage_new_object>(),
"Compute the query bits for the holder");
python::class_<PatternHolder, boost::shared_ptr<PatternHolder>,
python::bases<FPHolderBase>>(
"PatternHolder", PatternHolderDoc, python::init<>());
python::class_<SubstructLibrary, SubstructLibrary *,
const SubstructLibrary *>(
"SubstructLibrary", SubstructLibraryDoc, python::init<>())
.def(python::init<boost::shared_ptr<MolHolderBase>>())
.def(python::init<boost::shared_ptr<MolHolderBase>,
boost::shared_ptr<FPHolderBase>>())
.def("AddMol", &SubstructLibrary::addMol, (python::arg("mol")),
"Adds a molecule to the substruct library")
.def("GetMatches", (std::vector<unsigned int>(SubstructLibrary::*)(
const ROMol &, bool, bool, bool, int, int)) &
SubstructLibrary::getMatches,
(python::arg("query"), python::arg("recursionPossible") = true,
python::arg("useChirality") = true,
python::arg("useQueryQueryMatches") = false,
python::arg("numThreads") = -1, python::arg("maxResults") = 1000),
"Get the matches for the query.\n\n"
" Arguments:\n"
" - query: substructure query\n"
" - numThreads: number of threads to use, -1 means all threads\n"
" - maxResults: maximum number of results to return")
.def("GetMatches", (std::vector<unsigned int>(SubstructLibrary::*)(
const ROMol &, unsigned int, unsigned int, bool,
bool, bool, int, int)) &
SubstructLibrary::getMatches,
(python::arg("query"), python::arg("startIdx"),
python::arg("endIdx"), python::arg("recursionPossible") = true,
python::arg("useChirality") = true,
python::arg("useQueryQueryMatches") = false,
python::arg("numThreads") = -1, python::arg("maxResults") = 1000),
"Get the matches for the query.\n\n"
" Arguments:\n"
" - query: substructure query\n"
" - startIdx: index to search from\n"
" - endIdx: index (non-inclusize) to search to\n"
" - numThreads: number of threads to use, -1 means all threads\n"
" - maxResults: maximum number of results to return")
.def("CountMatches", (unsigned int (SubstructLibrary::*)(
const ROMol &, bool, bool, bool, int)) &
SubstructLibrary::countMatches,
(python::arg("query"), python::arg("recursionPossible") = true,
python::arg("useChirality") = true,
python::arg("useQueryQueryMatches") = false,
python::arg("numThreads") = -1, python::arg("maxResults") = 1000),
"Get the matches for the query.\n\n"
" Arguments:\n"
" - query: substructure query\n"
" - numThreads: number of threads to use, -1 means all threads\n")
.def("CountMatches", (unsigned int (SubstructLibrary::*)(
const ROMol &, unsigned int, unsigned int,
bool, bool, bool, int)) &
SubstructLibrary::countMatches,
(python::arg("query"), python::arg("startIdx"),
python::arg("endIdx"), python::arg("recursionPossible") = true,
python::arg("useChirality") = true,
python::arg("useQueryQueryMatches") = false,
python::arg("numThreads") = -1),
"Get the matches for the query.\n\n"
" Arguments:\n"
" - query: substructure query\n"
" - startIdx: index to search from\n"
" - endIdx: index (non-inclusize) to search to\n"
" - numThreads: number of threads to use, -1 means all threads\n")
.def("HasMatch", (bool (SubstructLibrary::*)(const ROMol &, bool, bool,
bool, int)) &
SubstructLibrary::hasMatch,
(python::arg("query"), python::arg("recursionPossible") = true,
python::arg("useChirality") = true,
python::arg("useQueryQueryMatches") = false,
python::arg("numThreads") = -1),
"Get the matches for the query.\n\n"
" Arguments:\n"
" - query: substructure query\n"
" - numThreads: number of threads to use, -1 means all threads\n")
.def("HasMatch",
(bool (SubstructLibrary::*)(const ROMol &, unsigned int,
unsigned int, bool, bool, bool, int)) &
SubstructLibrary::hasMatch,
(python::arg("query"), python::arg("startIdx"),
python::arg("endIdx"), python::arg("recursionPossible") = true,
python::arg("useChirality") = true,
python::arg("useQueryQueryMatches") = false,
python::arg("numThreads") = -1),
"Get the matches for the query.\n\n"
" Arguments:\n"
" - query: substructure query\n"
" - startIdx: index to search from\n"
" - endIdx: index (non-inclusize) to search to\n"
" - numThreads: number of threads to use, -1 means all threads\n")
.def("GetMol", &SubstructLibrary::getMol,
"Returns a particular molecule in the molecule holder\n\n"
" ARGUMENTS:\n"
" - idx: which molecule to return\n\n"
" NOTE: molecule indices start at 0\n")
.def("__len__", &SubstructLibrary::size)
;
}
};
}
void wrap_substructlibrary() { RDKit::substructlibrary_wrapper::wrap(); }
|
