mirror of
https://github.com/rdkit/rdkit.git
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d15efc1ac9
* auto generate coords in mol block writer if includeChirality = True * default to include chirality when writing mol blocks/files * make isomeric smiles the default; note that not all tests are passing at the moment * update a reaction test * update expected cartridge search results at this point all python, c++, and cartridge tests pass * docs * update incompatibility docs * update doctests * these now build * minor example update * update expected c++ * typo * make allowCXSMILES=true the default * add auto perception of chirality when reading 3D structures from mol blocks * explain changes in release notes * further doc update
110 lines
4.3 KiB
C++
110 lines
4.3 KiB
C++
// $Id$
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//
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// Copyright (C) 2003-2011 Greg Landrum and Rational Discovery 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 <RDBoost/python.h>
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#include <string>
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// ours
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#include <GraphMol/FileParsers/MolWriters.h>
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#include <GraphMol/RDKitBase.h>
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#include "rdchem.h"
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#include <RDBoost/PySequenceHolder.h>
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#include <RDBoost/python_streambuf.h>
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namespace python = boost::python;
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namespace RDKit {
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using boost_adaptbx::python::streambuf;
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SmilesWriter *getSmilesWriter(python::object &fileobj,
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std::string delimiter = " ",
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std::string nameHeader = "Name",
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bool includeHeader = true,
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bool isomericSmiles = true,
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bool kekuleSmiles = false) {
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// FIX: minor leak here
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auto *sb = new streambuf(fileobj);
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auto *ost = new streambuf::ostream(*sb);
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return new SmilesWriter(ost, delimiter, nameHeader, includeHeader, true,
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isomericSmiles, kekuleSmiles);
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}
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void SetSmiWriterProps(SmilesWriter &writer, python::object props) {
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// convert the python list to a STR_VECT
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STR_VECT propNames;
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PySequenceHolder<std::string> seq(props);
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for (unsigned int i = 0; i < seq.size(); i++) {
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propNames.push_back(seq[i]);
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}
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writer.setProps(propNames);
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}
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std::string swDocStr =
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"Constructor.\n\n"
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" ARGUMENTS:\n\n"
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" - fileName: name of the output file. ('-' to write to stdout)\n"
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" - delimiter: (optional) delimiter to be used to separate entries on "
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"each line.\n"
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" - nameHeader: (optional) text to use for the name column in the "
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"header line.\n"
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" If this is blank, names will not be included in the "
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"output.\n"
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" - includeHeader: (optional) toggles inclusion of a header line in "
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"the output file.\n"
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" - isomericSmiles: (optional) toggles output of isomeric smiles "
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"(includes stereochem information).\n"
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" - kekuleSmiles: (optional) toggles output of kekule smiles (no "
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"aromatic bonds for molecules that have been kekulized).\n\n";
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struct smiwriter_wrap {
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static void wrap() {
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python::class_<SmilesWriter>("SmilesWriter",
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"A class for writing molecules to text files.",
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python::no_init)
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.def("__init__",
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python::make_constructor(
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&getSmilesWriter, python::default_call_policies(),
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(python::arg("fileObj"), python::arg("delimiter") = " ",
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python::arg("nameHeader") = "Name",
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python::arg("includeHeader") = true,
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python::arg("isomericSmiles") = true,
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python::arg("kekuleSmiles") = false)))
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.def(python::init<std::string, std::string, std::string, bool, bool,
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bool>(
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(python::arg("fileName"), python::arg("delimiter") = " ",
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python::arg("nameHeader") = "Name",
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python::arg("includeHeader") = true,
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python::arg("isomericSmiles") = true,
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python::arg("kekuleSmiles") = false),
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swDocStr.c_str()))
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.def("SetProps", SetSmiWriterProps,
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"Sets the 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 property names\n\n")
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.def("write", &SmilesWriter::write,
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(python::arg("self"), python::arg("mol"),
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python::arg("confId") = -1),
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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) ignored \n\n")
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.def("flush", &SmilesWriter::flush,
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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", &SmilesWriter::close,
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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", &SmilesWriter::numMols,
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"Returns the number of molecules written so far.\n\n");
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};
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};
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}
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void wrap_smiwriter() { RDKit::smiwriter_wrap::wrap(); }
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