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//
// Copyright (c) 2016, 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.
//
#include "PreprocessRxn.h"
#include "ReactionParser.h"
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <RDGeneral/BoostStartInclude.h>
#include <boost/shared_ptr.hpp>
#include <RDGeneral/BoostEndInclude.h>
#include <GraphMol/FilterCatalog/FunctionalGroupHierarchy.h>
namespace RDKit {
bool preprocessReaction(ChemicalReaction &rxn, const std::string &propName) {
const bool normalized = true;
return preprocessReaction(
rxn, GetFlattenedFunctionalGroupHierarchy(normalized), propName);
}
bool preprocessReaction(
ChemicalReaction &rxn, unsigned int &numWarnings, unsigned int &numErrors,
std::vector<std::vector<std::pair<unsigned int, std::string>>>
&reactantLabels,
const std::string &propName) {
const bool normalized = true;
return preprocessReaction(rxn, numWarnings, numErrors, reactantLabels,
GetFlattenedFunctionalGroupHierarchy(normalized),
propName);
}
bool preprocessReaction(ChemicalReaction &rxn,
const std::map<std::string, ROMOL_SPTR> &queries,
const std::string &propName) {
unsigned int numWarnings, numErrors;
std::vector<std::vector<std::pair<unsigned int, std::string>>> reactantLabels;
return preprocessReaction(rxn, numWarnings, numErrors, reactantLabels,
queries, propName);
}
bool preprocessReaction(
ChemicalReaction &rxn, unsigned int &numWarnings, unsigned int &numErrors,
std::vector<std::vector<std::pair<unsigned int, std::string>>>
&reactantLabels,
const std::map<std::string, ROMOL_SPTR> &queries,
const std::string &propName) {
rxn.setImplicitPropertiesFlag(true);
rxn.initReactantMatchers();
if (rxn.validate(numWarnings, numErrors)) {
addRecursiveQueriesToReaction(rxn, queries, propName, &reactantLabels);
return true;
}
return false;
}
}
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