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