mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-04 21:54:27 +08:00
ccfb1fa688
* fixleak in CIP labels catch test * fix leak in Murtagh clustering * do not leak writers in streambuf * fix leaks in fingerprintgeneratorwrapper * remove 'minor leak' comments
112 lines
4.6 KiB
C++
112 lines
4.6 KiB
C++
//
|
|
// Copyright (C) 2003-2021 Greg Landrum and Rational Discovery LLC
|
|
//
|
|
// @@ All Rights Reserved @@
|
|
// This file is part of the RDKit.
|
|
// The contents are covered by the terms of the BSD license
|
|
// which is included in the file license.txt, found at the root
|
|
// of the RDKit source tree.
|
|
//
|
|
#define NO_IMPORT_ARRAY
|
|
#include <RDBoost/python.h>
|
|
#include <string>
|
|
|
|
// ours
|
|
#include <GraphMol/FileParsers/MolWriters.h>
|
|
#include <GraphMol/RDKitBase.h>
|
|
#include "rdchem.h"
|
|
#include "ContextManagers.h"
|
|
#include <RDBoost/PySequenceHolder.h>
|
|
#include <RDBoost/python_streambuf.h>
|
|
|
|
namespace python = boost::python;
|
|
|
|
namespace RDKit {
|
|
using boost_adaptbx::python::streambuf;
|
|
SmilesWriter *getSmilesWriter(python::object &fileobj,
|
|
std::string delimiter = " ",
|
|
std::string nameHeader = "Name",
|
|
bool includeHeader = true,
|
|
bool isomericSmiles = true,
|
|
bool kekuleSmiles = false) {
|
|
auto *sb = new streambuf(fileobj, 't');
|
|
auto *ost = new streambuf::ostream(sb);
|
|
return new SmilesWriter(ost, delimiter, nameHeader, includeHeader, true,
|
|
isomericSmiles, kekuleSmiles);
|
|
}
|
|
|
|
void SetSmiWriterProps(SmilesWriter &writer, python::object props) {
|
|
// convert the python list to a STR_VECT
|
|
STR_VECT propNames;
|
|
|
|
PySequenceHolder<std::string> seq(props);
|
|
for (unsigned int i = 0; i < seq.size(); i++) {
|
|
propNames.push_back(seq[i]);
|
|
}
|
|
writer.setProps(propNames);
|
|
}
|
|
std::string swDocStr =
|
|
"Constructor.\n\n"
|
|
" ARGUMENTS:\n\n"
|
|
" - fileName: name of the output file. ('-' to write to stdout)\n"
|
|
" - delimiter: (optional) delimiter to be used to separate entries on "
|
|
"each line.\n"
|
|
" - nameHeader: (optional) text to use for the name column in the "
|
|
"header line.\n"
|
|
" If this is blank, names will not be included in the "
|
|
"output.\n"
|
|
" - includeHeader: (optional) toggles inclusion of a header line in "
|
|
"the output file.\n"
|
|
" - isomericSmiles: (optional) toggles output of isomeric smiles "
|
|
"(includes stereochem information).\n"
|
|
" - kekuleSmiles: (optional) toggles output of kekule smiles (no "
|
|
"aromatic bonds for molecules that have been kekulized).\n\n";
|
|
struct smiwriter_wrap {
|
|
static void wrap() {
|
|
python::class_<SmilesWriter, boost::noncopyable>(
|
|
"SmilesWriter", "A class for writing molecules to text files.",
|
|
python::no_init)
|
|
.def("__init__",
|
|
python::make_constructor(
|
|
&getSmilesWriter, python::default_call_policies(),
|
|
(python::arg("fileObj"), python::arg("delimiter") = " ",
|
|
python::arg("nameHeader") = "Name",
|
|
python::arg("includeHeader") = true,
|
|
python::arg("isomericSmiles") = true,
|
|
python::arg("kekuleSmiles") = false)))
|
|
.def(python::init<std::string, std::string, std::string, bool, bool,
|
|
bool>(
|
|
(python::arg("self"), python::arg("fileName"),
|
|
python::arg("delimiter") = " ", python::arg("nameHeader") = "Name",
|
|
python::arg("includeHeader") = true,
|
|
python::arg("isomericSmiles") = true,
|
|
python::arg("kekuleSmiles") = false),
|
|
swDocStr.c_str()))
|
|
.def("__enter__", &MolIOEnter<SmilesWriter>,
|
|
python::return_internal_reference<>())
|
|
.def("__exit__", &MolIOExit<SmilesWriter>)
|
|
.def("SetProps", SetSmiWriterProps, python::args("self", "props"),
|
|
"Sets the properties to be written to the output file\n\n"
|
|
" ARGUMENTS:\n\n"
|
|
" - props: a list or tuple of property names\n\n")
|
|
.def("write", &SmilesWriter::write,
|
|
(python::arg("self"), python::arg("mol"),
|
|
python::arg("confId") = -1),
|
|
"Writes a molecule to the output file.\n\n"
|
|
" ARGUMENTS:\n\n"
|
|
" - mol: the Mol to be written\n"
|
|
" - confId: (optional) ignored \n\n")
|
|
.def("flush", &SmilesWriter::flush, python::args("self"),
|
|
"Flushes the output file (forces the disk file to be "
|
|
"updated).\n\n")
|
|
.def("close", &SmilesWriter::close, python::args("self"),
|
|
"Flushes the output file and closes it. The Writer cannot be used "
|
|
"after this.\n\n")
|
|
.def("NumMols", &SmilesWriter::numMols, python::args("self"),
|
|
"Returns the number of molecules written so far.\n\n");
|
|
};
|
|
};
|
|
} // namespace RDKit
|
|
|
|
void wrap_smiwriter() { RDKit::smiwriter_wrap::wrap(); }
|