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// $Id$
//
// Copyright (c) 2007-2014, 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 <GraphMol/ChemReactions/Reaction.h>
#include <GraphMol/ChemReactions/ReactionParser.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <boost/algorithm/string.hpp>
#include <vector>
#include <string>
#include "ReactionUtils.h"
namespace RDKit {
namespace DaylightParserUtils {
std::vector<std::string> splitSmartsIntoComponents(
const std::string &reactText) {
std::vector<std::string> res;
unsigned int pos = 0;
unsigned int blockStart = 0;
unsigned int level = 0;
unsigned int inBlock = 0;
while (pos < reactText.size()) {
if (reactText[pos] == '(') {
if (pos == blockStart) {
inBlock = 1;
}
++level;
} else if (reactText[pos] == ')') {
if (level == 1 && inBlock) {
// this closes a block
inBlock = 2;
}
--level;
} else if (level == 0 && reactText[pos] == '.') {
if (inBlock == 2) {
std::string element =
reactText.substr(blockStart + 1, pos - blockStart - 2);
res.push_back(element);
} else {
std::string element = reactText.substr(blockStart, pos - blockStart);
res.push_back(element);
}
blockStart = pos + 1;
inBlock = 0;
}
++pos;
}
if (blockStart < pos) {
if (inBlock == 2) {
std::string element =
reactText.substr(blockStart + 1, pos - blockStart - 2);
res.push_back(element);
} else {
std::string element = reactText.substr(blockStart, pos - blockStart);
res.push_back(element);
}
}
return res;
}
ROMol *constructMolFromString(const std::string &txt,
std::map<std::string, std::string> *replacements,
bool useSmiles) {
ROMol *mol;
if (!useSmiles) {
mol = SmartsToMol(txt, 0, false, replacements);
} else {
mol = SmilesToMol(txt, 0, false, replacements);
}
return mol;
}
} // end of namespace DaylightParserUtils
ChemicalReaction *RxnSmartsToChemicalReaction(
const std::string &text, std::map<std::string, std::string> *replacements,
bool useSmiles) {
std::size_t pos1 = text.find(">");
std::size_t pos2 = text.rfind(">");
if (pos1 == std::string::npos) {
throw ChemicalReactionParserException(
"a reaction requires at least one reactant and one product");
}
if (text.find(">", pos1 + 1) != pos2) {
throw ChemicalReactionParserException("multi-step reactions not supported");
}
std::string reactText = text.substr(0, pos1);
std::string agentText = "";
if (pos2 != pos1 + 1) {
agentText = text.substr(pos1 + 1, (pos2 - pos1) - 1);
}
std::string productText = text.substr(pos2 + 1);
// recognize changes within the same molecules, e.g., intra molecular bond
// formation
// therefore we need to correctly interpret parenthesis and dots in the
// reaction smarts
std::vector<std::string> reactSmarts =
DaylightParserUtils::splitSmartsIntoComponents(reactText);
std::vector<std::string> productSmarts =
DaylightParserUtils::splitSmartsIntoComponents(productText);
auto *rxn = new ChemicalReaction();
for (const auto &txt : reactSmarts) {
ROMol *mol;
mol = DaylightParserUtils::constructMolFromString(txt, replacements,
useSmiles);
if (!mol) {
std::string errMsg = "Problems constructing reactant from SMARTS: ";
errMsg += txt;
throw ChemicalReactionParserException(errMsg);
}
rxn->addReactantTemplate(ROMOL_SPTR(mol));
}
for (const auto &txt : productSmarts) {
ROMol *mol;
mol = DaylightParserUtils::constructMolFromString(txt, replacements,
useSmiles);
if (!mol) {
std::string errMsg = "Problems constructing product from SMARTS: ";
errMsg += txt;
throw ChemicalReactionParserException(errMsg);
}
rxn->addProductTemplate(ROMOL_SPTR(mol));
}
updateProductsStereochem(rxn);
ROMol *agentMol;
// allow a reaction template to have no agent specified
if (agentText.size() != 0) {
agentMol = DaylightParserUtils::constructMolFromString(
agentText, replacements, useSmiles);
if (!agentMol) {
std::string errMsg = "Problems constructing agent from SMARTS: ";
errMsg += agentText;
throw ChemicalReactionParserException(errMsg);
}
std::vector<ROMOL_SPTR> agents = MolOps::getMolFrags(*agentMol, false);
delete agentMol;
for (auto &agent : agents) {
rxn->addAgentTemplate(agent);
}
}
// "SMARTS"-based reactions have implicit properties
rxn->setImplicitPropertiesFlag(true);
return rxn;
}
}
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