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https://github.com/rdkit/rdkit.git
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a4b63d7df5
* refactor python wrappers * fix FilterHierarchyMatcher converted already registered warning
105 lines
4.1 KiB
C++
105 lines
4.1 KiB
C++
//
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// Copyright (C) 2019 Greg Landrum
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#define NO_IMPORT_ARRAY
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#define PY_ARRAY_UNIQUE_SYMBOL rdpicker_array_API
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#include <RDBoost/python.h>
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#include <RDBoost/Wrap.h>
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#include <RDBoost/boost_numpy.h>
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#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
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#include <numpy/arrayobject.h>
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#include <map>
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#include "PickerHelpers.h"
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#include <DataStructs/BitVects.h>
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#include <DataStructs/BitOps.h>
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#include <SimDivPickers/DistPicker.h>
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#include <SimDivPickers/LeaderPicker.h>
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#include <iostream>
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#include <utility>
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namespace python = boost::python;
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namespace RDPickers {
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namespace {
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template <typename T>
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void LazyLeaderHelper(LeaderPicker *picker, T functor, unsigned int poolSize,
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double &threshold, unsigned int pickSize,
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python::object firstPicks, RDKit::INT_VECT &res,
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int nThreads) {
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RDKit::INT_VECT firstPickVect;
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for (unsigned int i = 0; i < boost::python::len(firstPicks); ++i) {
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firstPickVect.push_back(python::extract<int>(firstPicks[i]));
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}
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res = picker->lazyPick(functor, poolSize, pickSize, firstPickVect, threshold,
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nThreads);
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}
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} // end of anonymous namespace
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RDKit::INT_VECT LazyVectorLeaderPicks(LeaderPicker *picker, python::object objs,
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int poolSize, double threshold,
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int pickSize, python::object firstPicks,
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int numThreads) {
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std::vector<const ExplicitBitVect *> bvs(poolSize);
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for (int i = 0; i < poolSize; ++i) {
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bvs[i] = python::extract<const ExplicitBitVect *>(objs[i]);
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}
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pyBVFunctor<ExplicitBitVect> functor(bvs, TANIMOTO);
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RDKit::INT_VECT res;
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LazyLeaderHelper(picker, functor, poolSize, threshold, pickSize, firstPicks,
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res, numThreads);
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return res;
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}
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RDKit::INT_VECT LazyLeaderPicks(LeaderPicker *picker, python::object distFunc,
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int poolSize, double threshold, int pickSize,
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python::object firstPicks, int numThreads) {
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pyobjFunctor functor(distFunc);
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RDKit::INT_VECT res;
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LazyLeaderHelper(picker, functor, poolSize, threshold, pickSize, firstPicks,
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res, numThreads);
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return res;
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}
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} // end of namespace RDPickers
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struct LeaderPicker_wrap {
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static void wrap() {
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python::class_<RDPickers::LeaderPicker>(
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"LeaderPicker",
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"A class for diversity picking of items using Roger Sayle's Leader "
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"algorithm (analogous to sphere exclusion). The algorithm is "
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"currently unpublished, but a description is available in this "
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"presentation from the 2019 RDKit UGM: "
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"https://github.com/rdkit/UGM_2019/raw/master/Presentations/"
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"Sayle_Clustering.pdf\n")
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.def("LazyBitVectorPick", RDPickers::LazyVectorLeaderPicks,
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(python::arg("self"), python::arg("objects"),
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python::arg("poolSize"), python::arg("threshold"),
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python::arg("pickSize") = 0,
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python::arg("firstPicks") = python::tuple(),
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python::arg("numThreads") = 1),
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"Pick a subset of items from a collection of bit vectors using "
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"Tanimoto distance. The threshold value is a "
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"*distance* (i.e. 1-similarity). Note that the numThreads "
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"argument is currently ignored.")
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.def("LazyPick", RDPickers::LazyLeaderPicks,
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(python::arg("self"), python::arg("distFunc"),
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python::arg("poolSize"), python::arg("threshold"),
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python::arg("pickSize") = 0,
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python::arg("firstPicks") = python::tuple(),
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python::arg("numThreads") = 1),
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"Pick a subset of items from a pool of items using the "
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"user-provided function to determine distances. Note that the "
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"numThreads argument is currently ignored.");
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};
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};
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void wrap_leaderpick() { LeaderPicker_wrap::wrap(); }
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