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//
// Copyright (C) 2003-2017 Greg Landrum and Rational Discovery LLC
// @@ 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 <DataStructs/BitVects.h>
#include <DataStructs/BitOps.h>
#include <SimDivPickers/DistPicker.h>
#include <SimDivPickers/MaxMinPicker.h>
#include <SimDivPickers/HierarchicalClusterPicker.h>
#include <iostream>
#include <utility>
namespace python = boost::python;
namespace RDPickers {
// REVIEW: the poolSize can be pulled from the numeric array
RDKit::INT_VECT MaxMinPicks(MaxMinPicker *picker, python::object distMat,
int poolSize, int pickSize,
python::object firstPicks, int seed) {
if (pickSize >= poolSize) {
throw ValueErrorException("pickSize must be less than poolSize");
}
if (!PyArray_Check(distMat.ptr())) {
throw ValueErrorException("distance mat argument must be a numpy matrix");
}
PyArrayObject *copy;
copy = (PyArrayObject *)PyArray_ContiguousFromObject(distMat.ptr(),
NPY_DOUBLE, 1, 1);
double *dMat = (double *)PyArray_DATA(copy);
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]));
}
RDKit::INT_VECT res =
picker->pick(dMat, poolSize, pickSize, firstPickVect, seed);
Py_DECREF(copy);
return res;
}
class pyobjFunctor {
public:
pyobjFunctor(python::object obj) : dp_obj(std::move(obj)) {}
~pyobjFunctor() {}
double operator()(unsigned int i, unsigned int j) {
return python::extract<double>(dp_obj(i, j));
}
private:
python::object dp_obj;
};
namespace {
template <typename T>
void LazyMaxMinHelper(MaxMinPicker *picker, T functor, unsigned int poolSize,
unsigned int pickSize, python::object firstPicks,
int seed, RDKit::INT_VECT &res, double &threshold) {
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, seed,
threshold);
}
} // end of anonymous namespace
RDKit::INT_VECT LazyMaxMinPicks(MaxMinPicker *picker, python::object distFunc,
int poolSize, int pickSize,
python::object firstPicks, int seed,
python::object useCache) {
if (useCache != python::object()) {
BOOST_LOG(rdWarningLog) << "the useCache argument is deprecated and ignored"
<< std::endl;
}
pyobjFunctor functor(distFunc);
RDKit::INT_VECT res;
double threshold = -1.;
LazyMaxMinHelper(picker, functor, poolSize, pickSize, firstPicks, seed, res,
threshold);
return res;
}
python::tuple LazyMaxMinPicksWithThreshold(
MaxMinPicker *picker, python::object distFunc, int poolSize, int pickSize,
double threshold, python::object firstPicks, int seed) {
pyobjFunctor functor(distFunc);
RDKit::INT_VECT res;
LazyMaxMinHelper(picker, functor, poolSize, pickSize, firstPicks, seed, res,
threshold);
return python::make_tuple(res, threshold);
}
// NOTE: TANIMOTO and DICE provably return the same results for the diversity
// picking this is still here just in case we ever later want to support other
// methods.
typedef enum { TANIMOTO = 1, DICE } DistanceMethod;
template <typename BV>
class pyBVFunctor {
public:
pyBVFunctor(const std::vector<const BV *> &obj, DistanceMethod method)
: d_obj(obj), d_method(method) {}
~pyBVFunctor() {}
double operator()(unsigned int i, unsigned int j) {
double res = 0.0;
switch (d_method) {
case TANIMOTO:
res = 1. - TanimotoSimilarity(*d_obj[i], *d_obj[j]);
break;
case DICE:
res = 1. - DiceSimilarity(*d_obj[i], *d_obj[j]);
break;
default:
throw_value_error("unsupported similarity value");
}
return res;
}
private:
const std::vector<const BV *> &d_obj;
DistanceMethod d_method;
};
RDKit::INT_VECT LazyVectorMaxMinPicks(MaxMinPicker *picker, python::object objs,
int poolSize, int pickSize,
python::object firstPicks, int seed,
python::object useCache) {
if (useCache != python::object()) {
BOOST_LOG(rdWarningLog) << "the useCache argument is deprecated and ignored"
<< std::endl;
}
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;
double threshold = -1.;
LazyMaxMinHelper(picker, functor, poolSize, pickSize, firstPicks, seed, res,
threshold);
return res;
}
python::tuple LazyVectorMaxMinPicksWithThreshold(
MaxMinPicker *picker, python::object objs, int poolSize, int pickSize,
double threshold, python::object firstPicks, int seed) {
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;
LazyMaxMinHelper(picker, functor, poolSize, pickSize, firstPicks, seed, res,
threshold);
return python::make_tuple(res, threshold);
}
} // end of namespace RDPickers
struct MaxMin_wrap {
static void wrap() {
python::class_<RDPickers::MaxMinPicker>(
"MaxMinPicker",
"A class for diversity picking of items using the MaxMin Algorithm\n")
.def("Pick", RDPickers::MaxMinPicks,
(python::arg("self"), python::arg("distMat"),
python::arg("poolSize"), python::arg("pickSize"),
python::arg("firstPicks") = python::tuple(),
python::arg("seed") = -1),
"Pick a subset of items from a pool of items using the MaxMin "
"Algorithm\n"
"Ashton, M. et. al., Quant. Struct.-Act. Relat., 21 (2002), "
"598-604 \n\n"
"ARGUMENTS:\n"
" - distMat: 1D distance matrix (only the lower triangle "
"elements)\n"
" - poolSize: number of items in the pool\n"
" - pickSize: number of items to pick from the pool\n"
" - firstPicks: (optional) the first items to be picked (seeds "
"the list)\n"
" - seed: (optional) seed for the random number generator\n")
.def("LazyPick", RDPickers::LazyMaxMinPicks,
(python::arg("self"), python::arg("distFunc"),
python::arg("poolSize"), python::arg("pickSize"),
python::arg("firstPicks") = python::tuple(),
python::arg("seed") = -1,
python::arg("useCache") = python::object()),
"Pick a subset of items from a pool of items using the MaxMin "
"Algorithm\n"
"Ashton, M. et. al., Quant. Struct.-Act. Relat., 21 (2002), "
"598-604 \n"
"ARGUMENTS:\n\n"
" - distFunc: a function that should take two indices and return "
"the\n"
" distance between those two points.\n"
" NOTE: the implementation caches distance values, "
"so the\n"
" client code does not need to do so; indeed, it "
"should not.\n"
" - poolSize: number of items in the pool\n"
" - pickSize: number of items to pick from the pool\n"
" - firstPicks: (optional) the first items to be picked (seeds "
"the list)\n"
" - seed: (optional) seed for the random number generator\n"
" - useCache: IGNORED\n")
.def("LazyBitVectorPick", RDPickers::LazyVectorMaxMinPicks,
(python::arg("self"), python::arg("objects"),
python::arg("poolSize"), python::arg("pickSize"),
python::arg("firstPicks") = python::tuple(),
python::arg("seed") = -1,
python::arg("useCache") = python::object()),
"Pick a subset of items from a pool of bit vectors using the "
"MaxMin Algorithm\n"
"Ashton, M. et. al., Quant. Struct.-Act. Relat., 21 (2002), "
"598-604 \n"
"ARGUMENTS:\n\n"
" - vectors: a sequence of the bit vectors that should be picked "
"from.\n"
" - poolSize: number of items in the pool\n"
" - pickSize: number of items to pick from the pool\n"
" - firstPicks: (optional) the first items to be picked (seeds "
"the list)\n"
" - seed: (optional) seed for the random number generator\n"
" - useCache: IGNORED.\n")
.def("LazyPickWithThreshold", RDPickers::LazyMaxMinPicksWithThreshold,
(python::arg("self"), python::arg("distFunc"),
python::arg("poolSize"), python::arg("pickSize"),
python::arg("threshold"),
python::arg("firstPicks") = python::tuple(),
python::arg("seed") = -1),
"Pick a subset of items from a pool of items using the MaxMin "
"Algorithm\n"
"Ashton, M. et. al., Quant. Struct.-Act. Relat., 21 (2002), "
"598-604 \n"
"ARGUMENTS:\n\n"
" - distFunc: a function that should take two indices and return "
"the\n"
" distance between those two points.\n"
" NOTE: the implementation caches distance values, "
"so the\n"
" client code does not need to do so; indeed, it "
"should not.\n"
" - poolSize: number of items in the pool\n"
" - pickSize: number of items to pick from the pool\n"
" - threshold: stop picking when the distance goes below this "
"value\n"
" - firstPicks: (optional) the first items to be picked (seeds "
"the list)\n"
" - seed: (optional) seed for the random number generator\n")
.def("LazyBitVectorPickWithThreshold",
RDPickers::LazyVectorMaxMinPicksWithThreshold,
(python::arg("self"), python::arg("objects"),
python::arg("poolSize"), python::arg("pickSize"),
python::arg("threshold"),
python::arg("firstPicks") = python::tuple(),
python::arg("seed") = -1),
"Pick a subset of items from a pool of bit vectors using the "
"MaxMin Algorithm\n"
"Ashton, M. et. al., Quant. Struct.-Act. Relat., 21 (2002), "
"598-604 \n"
"ARGUMENTS:\n\n"
" - vectors: a sequence of the bit vectors that should be picked "
"from.\n"
" - poolSize: number of items in the pool\n"
" - pickSize: number of items to pick from the pool\n"
" - threshold: stop picking when the distance goes below this "
"value\n"
" - firstPicks: (optional) the first items to be picked (seeds "
"the list)\n"
" - seed: (optional) seed for the random number generator\n");
};
};
void wrap_maxminpick() { MaxMin_wrap::wrap(); }
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