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"currently unpublished, but a description is available in this "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