mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-03 21:44:30 +08:00
a4b63d7df5
* refactor python wrappers * fix FilterHierarchyMatcher converted already registered warning
115 lines
4.5 KiB
C++
115 lines
4.5 KiB
C++
//
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// Copyright (C) 2017 Greg Landrum
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//
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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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#include <RDBoost/python.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 <boost/python/list.hpp>
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#include <RDGeneral/Exceptions.h>
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#include <GraphMol/RDKitBase.h>
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#include <CoordGen/CoordGen.h>
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namespace python = boost::python;
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namespace RDKit {
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namespace {
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void SetCoordMap(CoordGen::CoordGenParams *self, python::dict &coordMap) {
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self->coordMap.clear();
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python::list ks = coordMap.keys();
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for (unsigned int i = 0; i < boost::python::len(ks); ++i) {
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unsigned int id = python::extract<unsigned int>(ks[i]);
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self->coordMap[id] = python::extract<RDGeom::Point2D>(coordMap[id]);
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}
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}
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void addCoordsHelper(ROMol &mol, python::object ¶ms) {
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CoordGen::CoordGenParams *ps = nullptr;
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if (params != python::object()) {
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ps = python::extract<CoordGen::CoordGenParams *>(params);
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}
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CoordGen::addCoords(mol, ps);
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}
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void SetTemplateMol(CoordGen::CoordGenParams *self, const ROMol *templ) {
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self->templateMol = templ;
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}
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void SetDefaultTemplateFileDir(const std::string &dir) {
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CoordGen::defaultParams.templateFileDir = dir;
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}
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} // end of anonymous namespace
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struct coordgen_wrapper {
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static void wrap() {
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std::string docString = "";
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python::class_<CoordGen::CoordGenParams>(
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"CoordGenParams", "Parameters controlling coordinate generation")
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.def(
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"SetCoordMap", SetCoordMap, python::args("self", "coordMap"),
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"expects a dictionary of Point2D objects with template coordinates")
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.def("SetTemplateMol", SetTemplateMol,
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python::with_custodian_and_ward<1, 2>(),
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python::args("self", "templ"),
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"sets a molecule to be used as the template")
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.def_readwrite("coordgenScaling",
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&CoordGen::CoordGenParams::coordgenScaling,
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"scaling factor for a single bond")
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.def_readwrite("dbg_useConstrained",
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&CoordGen::CoordGenParams::dbg_useConstrained,
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"for debugging use")
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.def_readwrite("dbg_useFixed", &CoordGen::CoordGenParams::dbg_useFixed,
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"for debugging use")
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.def_readwrite("templateFileDir",
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&CoordGen::CoordGenParams::templateFileDir,
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"directory containing the templates.mae file")
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.def_readonly("sketcherBestPrecision",
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&CoordGen::CoordGenParams::sketcherBestPrecision,
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"highest quality (and slowest) precision setting")
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.def_readonly("sketcherStandardPrecision",
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&CoordGen::CoordGenParams::sketcherStandardPrecision,
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"standard quality precision setting, the default for the "
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"coordgen project")
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.def_readonly("sketcherQuickPrecision",
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&CoordGen::CoordGenParams::sketcherQuickPrecision,
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"faster precision setting")
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.def_readonly(
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"sketcherCoarsePrecision",
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&CoordGen::CoordGenParams::sketcherCoarsePrecision,
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"\"coarse\" (fastest) precision setting, produces good-quality "
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"coordinates"
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" most of the time, this is the default setting for the RDKit")
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.def_readwrite("minimizerPrecision",
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&CoordGen::CoordGenParams::minimizerPrecision,
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"controls sketcher precision")
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.def_readwrite(
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"treatNonterminalBondsToMetalAsZOBs",
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&CoordGen::CoordGenParams::treatNonterminalBondsToMetalAsZeroOrder);
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python::def("SetDefaultTemplateFileDir", SetDefaultTemplateFileDir,
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python::args("dir"));
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docString =
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"Add 2D coordinates.\n"
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"ARGUMENTS:\n"
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" - mol: molecule to modify\n"
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" - params: (optional) parameters controlling the coordinate "
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"generation\n"
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"\n";
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python::def("AddCoords", addCoordsHelper,
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(python::arg("mol"), python::arg("params") = python::object()),
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docString.c_str());
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}
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};
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} // end of namespace RDKit
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BOOST_PYTHON_MODULE(rdCoordGen) {
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python::scope().attr("__doc__") =
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"Module containing interface to the CoordGen library.";
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RDKit::coordgen_wrapper::wrap();
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}
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