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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>
128 lines
4.6 KiB
C++
128 lines
4.6 KiB
C++
//
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//
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// Copyright (C) 2023 Schrödinger, LLC
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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 <memory>
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#include <string>
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#include <maeparser/Writer.hpp>
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#include <GraphMol/FileParsers/MolWriters.h>
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#include <RDBoost/python.h>
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#include <RDBoost/python_streambuf.h>
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#include <RDBoost/Wrap.h>
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#include "ContextManagers.h"
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namespace python = boost::python;
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using boost_adaptbx::python::streambuf;
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namespace RDKit {
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class LocalMaeWriter : public MaeWriter {
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public:
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LocalMaeWriter(python::object &fileobj)
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: dp_streambuf(new streambuf(fileobj, 't')) {
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dp_ostream.reset(new streambuf::ostream(*dp_streambuf));
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}
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LocalMaeWriter(streambuf &output) {
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dp_ostream.reset(new streambuf::ostream(output));
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}
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LocalMaeWriter(const std::string &fname) : RDKit::MaeWriter(fname) {}
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private:
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std::unique_ptr<streambuf> dp_streambuf = nullptr;
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};
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struct wrap_maewriter {
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static void wrap() {
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std::string docStr =
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"An experimental class for writing molecules to Maestro files.\n\
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\n\
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Usage examples:\n\
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\n\
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1) writing to a named file:\n\n\
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>>> writer = MaeWriter('out.mae')\n\
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>>> for mol in list_of_mols:\n\
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... writer.write(mol)\n\
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\n\
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2) writing to a file-like object: \n\n\
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>>> import gzip\n\
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>>> outf=gzip.open('out.mae.gz','wt+')\n\
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>>> writer = MaeWriter(outf)\n\
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>>> for mol in list_of_mols:\n\
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... writer.write(mol)\n\
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>>> writer.close()\n\
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>>> outf.close()\n\
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\n\
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By default all non-private molecule, atom and bond properties are written\n\
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to the Maestro file. This can be changed using the SetProps method:\n\n\
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>>> writer = MaeWriter('out.mae')\n\
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>>> writer.SetProps(['prop1','prop2'])\n\n\
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Properties that are specified, but are not present will be ignored.\n\n\
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Kekulization is mandatory, as the Maestro format does not have\n\
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the concept of an aromatic bond\n\n\
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As this is an experimental writer, many features are not supported yet,\n\
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e.g. chirality and bond stereo labels, stereo groups, substance groups,\n\
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isotopes, or even dummy atoms. Note that these aren't supported by\n\
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MaeMolSupplier either.\n\
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\n ";
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python::class_<LocalMaeWriter, boost::noncopyable>(
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"MaeWriter", docStr.c_str(), python::no_init)
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.def(python::init<python::object &>(
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(python::arg("self"), python::arg("fileobj"))))
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.def(python::init<streambuf &>(
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(python::arg("self"), python::arg("streambuf"))))
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.def(python::init<std::string>(
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(python::arg("self"), python::arg("filename"))))
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.def("__enter__", &MolIOEnter<LocalMaeWriter>,
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python::return_internal_reference<>())
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.def("__exit__", &MolIOExit<LocalMaeWriter>)
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.def(
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"SetProps", &LocalMaeWriter::setProps,
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(python::arg("self"), python::args("props_list")),
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"Sets the atom and mol properties to be written to the output file\n\n"
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" ARGUMENTS:\n\n"
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" - props: a list or tuple of atom and mol property names\n\n")
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.def("write",
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(void(LocalMaeWriter::*)(const ROMol &, int)) &
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LocalMaeWriter::write,
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(python::arg("self"), python::arg("mol"),
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python::arg("confId") = defaultConfId),
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"Writes a molecule to the output file.\n\n"
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" ARGUMENTS:\n\n"
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" - mol: the Mol to be written\n"
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" - confId: (optional) ID of the conformation to write\n\n")
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.def("flush", &LocalMaeWriter::flush, python::args("self"),
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"Flushes the output file (forces the disk file to be "
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"updated).\n\n")
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.def("close", &LocalMaeWriter::close, python::args("self"),
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"Flushes the output file and closes it. The Writer cannot be used "
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"after this.\n\n")
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.def("NumMols", &LocalMaeWriter::numMols, python::args("self"),
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"Returns the number of molecules written so far.\n\n")
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.def("GetText", &LocalMaeWriter::getText,
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(python::arg("mol"), python::arg("confId") = -1,
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python::arg("props_list") = std::vector<std::string>()),
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"returns the Maestro ct block text for a molecule")
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.staticmethod("GetText");
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iterable_converter().from_python<std::vector<std::string>>();
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};
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};
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} // namespace RDKit
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void wrap_maewriter() { RDKit::wrap_maewriter::wrap(); }
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