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// $Id$
//
// Copyright (C) 2003-2008 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
#include <RDBoost/python.h>
#define PY_ARRAY_UNIQUE_SYMBOL rdinfotheory_array_API
#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
#include <numpy/arrayobject.h>
#include <RDBoost/Wrap.h>
#include <RDBoost/PySequenceHolder.h>
#include <ML/InfoTheory/CorrMatGenerator.h>
#include <RDGeneral/types.h>
namespace python = boost::python;
namespace RDInfoTheory {
PyObject *getCorrMatrix(BitCorrMatGenerator *cmGen) {
double *dres = cmGen->getCorrMat();
unsigned int nb = cmGen->getCorrBitList().size();
npy_intp dim = nb * (nb - 1) / 2;
PyArrayObject *res = (PyArrayObject *)PyArray_SimpleNew(1, &dim, NPY_DOUBLE);
memcpy(static_cast<void *>(PyArray_DATA(res)), static_cast<void *>(dres),
dim * sizeof(double));
return PyArray_Return(res);
}
void setBitList(BitCorrMatGenerator *cmGen, python::object bitList) {
PySequenceHolder<int> blist(bitList);
unsigned int nb = blist.size();
RDKit::INT_VECT res;
res.reserve(nb);
for (unsigned int i = 0; i < nb; i++) {
res.push_back(blist[i]);
}
cmGen->setBitIdList(res);
}
void CollectVotes(BitCorrMatGenerator *cmGen, python::object bitVect) {
python::extract<ExplicitBitVect> ebvWorks(bitVect);
python::extract<SparseBitVect> sbvWorks(bitVect);
if (ebvWorks.check()) {
ExplicitBitVect ev = python::extract<ExplicitBitVect>(bitVect);
cmGen->collectVotes(ev);
} else if (sbvWorks.check()) {
SparseBitVect sv = python::extract<SparseBitVect>(bitVect);
cmGen->collectVotes(sv);
} else {
throw_value_error(
"CollectVote can only take ExplicitBitVects or SparseBitVects");
}
}
struct corrmat_wrap {
static void wrap() {
std::string docString =
"A class to generate a pariwise correlation matrix between a list of "
"bits\n"
"The mode of operation for this class is something like this\n"
" >>> cmg = BitCorrMatGenerator() \n"
" >>> cmg.SetBitList(blist) \n"
" >>> for fp in fpList: \n"
" >>> cmg.CollectVotes(fp) \n"
" >>> corrMat = cmg.GetCorrMatrix() \n"
" \n"
" The resulting correlation matrix is a one dimensional nummeric "
"array containing the \n"
" lower triangle elements\n";
python::class_<BitCorrMatGenerator>("BitCorrMatGenerator",
docString.c_str())
.def("SetBitList", setBitList,
"Set the list of bits that need to be correllated\n\n"
" This may for example be ther top ranking ensemble bits\n\n"
"ARGUMENTS:\n\n"
" - bitList : an integer list of bit IDs\n")
.def("CollectVotes", CollectVotes,
"For each pair of on bits (bi, bj) in fp increase the correlation "
"count for the pair by 1\n\n"
"ARGUMENTS:\n\n"
" - fp : a bit vector to collect the fingerprints from\n")
.def("GetCorrMatrix", getCorrMatrix,
"Get the correlation matrix following the collection of votes "
"from a bunch of fingerprints\n");
};
};
}
void wrap_corrmatgen() { RDInfoTheory::corrmat_wrap::wrap(); }
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