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https://github.com/rdkit/rdkit.git
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81 lines
3.1 KiB
C++
Executable File
81 lines
3.1 KiB
C++
Executable File
// $Id$
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//
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// Copyright (C) 2003-2010 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 <boost/python.hpp>
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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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namespace python = boost::python;
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namespace RDKit {
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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="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 each line.\n"
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" - nameHeader: (optional) text to use for the name column in the header line.\n"
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" If this is blank, names will not be dumped.\n"
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" - includeHeader: (optional) toggles inclusion of a header line in the output file.\n"
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" - isomericSmiles: (optional) toggles output of isomeric smiles (includes stereochem information).\n"
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" - includeHeader: (optional) toggles output of kekule smiles (no 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::init<std::string,std::string,std::string,bool,bool,bool>((python::arg("fileName"),
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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")=false,
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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"), 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 updated).\n\n"
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)
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.def("close", &SmilesWriter::close,
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"Flushes the output file and closes it. The Writer cannot be used after this.\n\n"
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)
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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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};
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}
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void wrap_smiwriter() {
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RDKit::smiwriter_wrap::wrap();
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}
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