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// $Id$
//
// Copyright (c) 2008, Novartis Institutes for BioMedical Research Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above
// copyright notice, this list of conditions and the following
// disclaimer in the documentation and/or other materials provided
// with the distribution.
// * Neither the name of Novartis Institutes for BioMedical Research Inc.
// nor the names of its contributors may be used to endorse or promote
// products derived from this software without specific prior
// written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// Created by Greg Landrum, September 2006
//
#include <RDBoost/python.h>
#include <GraphMol/SLNParse/SLNParse.h>
#include <RDBoost/Wrap.h>
#include <RDGeneral/Exceptions.h>
#include <GraphMol/SanitException.h>
#include <RDGeneral/FileParseException.h>
namespace python = boost::python;
void rdSLNParseExceptionTranslator(RDKit::SLNParseException const &x) {
std::ostringstream ss;
ss << "SLNParseException: " << x.message();
PyErr_SetString(PyExc_ValueError, ss.str().c_str());
}
namespace RDKit {
ROMol *MolFromSLN(std::string sln, bool sanitize = 1,
bool debugParser = false) {
RWMol *newM = SLNToMol(sln, sanitize, debugParser);
return static_cast<ROMol *>(newM);
}
ROMol *MolFromQuerySLN(std::string sln, bool mergeHs = 1,
bool debugParser = false) {
RWMol *newM = SLNQueryToMol(sln, mergeHs, debugParser);
return static_cast<ROMol *>(newM);
}
}
BOOST_PYTHON_MODULE(rdSLNParse) {
python::scope().attr("__doc__") =
"Module containing classes and functions for working with Sybyl line "
"notation (SLN).";
python::register_exception_translator<RDKit::SLNParseException>(
&rdSLNParseExceptionTranslator);
std::string docString;
docString =
"Construct a molecule from an SLN string.\n\n\
ARGUMENTS:\n\
\n\
- SLN: the SLN string\n\
\n\
- sanitize: (optional) toggles sanitization of the molecule.\n\
Defaults to True.\n\
\n\
RETURNS:\n\
\n\
a Mol object, None on failure.\n\
\n\
NOTE: the SLN should not contain query information or properties. To build a\n\
query from SLN, use MolFromQuerySLN.\n\
\n";
python::def("MolFromSLN", RDKit::MolFromSLN,
(python::arg("SLN"), python::arg("sanitize") = true,
python::arg("debugParser") = false),
docString.c_str(),
python::return_value_policy<python::manage_new_object>());
docString =
"Construct a query molecule from an SLN string.\n\n\
ARGUMENTS:\n\
\n\
- SLN: the SLN string\n\
\n\
- mergeHs: (optional) toggles the merging of explicit Hs in the query into the attached\n\
heavy atoms. Defaults to False.\n\
\n\
RETURNS:\n\
\n\
a Mol object suitable for using in substructure queries, None on failure.\n\
\n";
python::def("MolFromQuerySLN", RDKit::MolFromQuerySLN,
(python::arg("SLN"), python::arg("mergeHs") = true,
python::arg("debugParser") = false),
docString.c_str(),
python::return_value_policy<python::manage_new_object>());
}
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