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https://github.com/rdkit/rdkit.git
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2b4202867e
* - added gen_rdkit_stubs Python module to generate rdkit-stubs - added patch_rdkit_docstrings Python module to patch existing C++ sources to fix docstrings missing self parameter and add named parameters taken from C++ signatures where possible - added rdkit-stubs/CMakeLists.txt to build rdkit-stubs as part of the RDKit build - added an option to CMakeLists.txt to enable building rdkit-stubs as part of the RDKit build (defaults to OFF) * fixed CMakeLists.txt, rdkit-stubs/CMakeLists.txt and a doctest * - added missing cmp_func parameter - fixed case with overloads with optional parameters - do not trim params if expected_param_count == -1 - add dummy parameter names if we could not find any - keep into account member functions when making up parameter names - address __init__ and make_constructor __init__ functions - fix incorrectly assigned staticmethods * patched sources * address residual few remarks --------- Co-authored-by: ptosco <paolo.tosco@novartis.com>
115 lines
4.4 KiB
C++
115 lines
4.4 KiB
C++
// $Id$
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//
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// Copyright (C) 2003-2008 Greg Landrum and Rational Discovery LLC
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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/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 <RDBoost/Wrap.h>
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#include <SimDivPickers/DistPicker.h>
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#include <SimDivPickers/HierarchicalClusterPicker.h>
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namespace python = boost::python;
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namespace RDPickers {
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// REVIEW: the poolSize can be pulled from the numeric array
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RDKit::INT_VECT HierarchicalPicks(HierarchicalClusterPicker *picker,
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python::object &distMat, int poolSize,
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int pickSize) {
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if (pickSize >= poolSize) {
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throw ValueErrorException("pickSize must be less than poolSize");
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}
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if (!PyArray_Check(distMat.ptr())) {
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throw ValueErrorException("distance mat argument must be a numpy matrix");
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}
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PyArrayObject *copy;
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// it's painful to have to copy the input matrix, but the
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// picker itself will step on the distance matrix, so use
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// CopyFromObject here instead of ContiguousFromObject
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copy =
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(PyArrayObject *)PyArray_CopyFromObject(distMat.ptr(), NPY_DOUBLE, 1, 1);
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auto *dMat = (double *)PyArray_DATA(copy);
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RDKit::INT_VECT res = picker->pick(dMat, poolSize, pickSize);
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Py_DECREF(copy);
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return res;
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}
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// REVIEW: the poolSize can be pulled from the numeric array
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RDKit::VECT_INT_VECT HierarchicalClusters(HierarchicalClusterPicker *picker,
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python::object &distMat, int poolSize,
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int pickSize) {
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if (!PyArray_Check(distMat.ptr())) {
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throw ValueErrorException("distance mat argument must be a numpy matrix");
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}
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// REVIEW: check pickSize < poolSize, otherwise throw_value_error()
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PyArrayObject *copy;
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// it's painful to have to copy the input matrix, but the
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// picker itself will step on the distance matrix, so use
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// CopyFromObject here instead of ContiguousFromObject
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copy =
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(PyArrayObject *)PyArray_CopyFromObject(distMat.ptr(), NPY_DOUBLE, 1, 1);
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auto *dMat = (double *)PyArray_DATA(copy);
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RDKit::VECT_INT_VECT res = picker->cluster(dMat, poolSize, pickSize);
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Py_DECREF(copy);
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return res;
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}
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struct HierarchCP_wrap {
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static void wrap() {
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std::string docString =
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"A class for diversity picking of items using Hierarchical "
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"Clustering\n";
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python::class_<HierarchicalClusterPicker>(
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"HierarchicalClusterPicker", docString.c_str(),
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python::init<HierarchicalClusterPicker::ClusterMethod>(
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python::args("self", "clusterMethod")))
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.def("Pick", HierarchicalPicks,
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python::args("self", "distMat", "poolSize", "pickSize"),
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"Pick a diverse subset of items from a pool of items using "
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"hierarchical clustering\n"
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"\n"
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"ARGUMENTS: \n"
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" - distMat: 1D distance matrix (only the lower triangle "
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"elements)\n"
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" - poolSize: number of items in the pool\n"
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" - pickSize: number of items to pick from the pool\n")
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.def("Cluster", HierarchicalClusters,
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python::args("self", "distMat", "poolSize", "pickSize"),
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"Return a list of clusters of item from the pool using "
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"hierarchical clustering\n"
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"\n"
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"ARGUMENTS: \n"
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" - distMat: 1D distance matrix (only the lower triangle "
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"elements)\n"
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" - poolSize: number of items in the pool\n"
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" - pickSize: number of items to pick from the pool\n");
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python::enum_<HierarchicalClusterPicker::ClusterMethod>("ClusterMethod")
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.value("WARD", HierarchicalClusterPicker::WARD)
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.value("SLINK", HierarchicalClusterPicker::SLINK)
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.value("CLINK", HierarchicalClusterPicker::CLINK)
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.value("UPGMA", HierarchicalClusterPicker::UPGMA)
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.value("MCQUITTY", HierarchicalClusterPicker::MCQUITTY)
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.value("GOWER", HierarchicalClusterPicker::GOWER)
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.value("CENTROID", HierarchicalClusterPicker::CENTROID)
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.export_values();
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};
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};
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} // namespace RDPickers
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void wrap_HierarchCP() { RDPickers::HierarchCP_wrap::wrap(); }
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