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//
// 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, Sept. 2006
//
#include <GraphMol/RDKitBase.h>
#include <GraphMol/RDKitQueries.h>
#include <GraphMol/SLNParse/SLNParse.h>
#include <GraphMol/SLNParse/SLNAttribs.h>
#include <RDGeneral/RDLog.h>
#include <RDGeneral/Invariant.h>
#include <boost/algorithm/string.hpp>
#include <regex>
int yysln_parse(const char *, std::vector<RDKit::RWMol *> *, bool, void *);
int yysln_lex_init(void **);
void yysln_set_extra(void *, void *);
int yysln_lex_destroy(void *);
void setup_sln_string(const std::string &text, void *);
extern int yysln_debug;
int sln_parse(const std::string &inp, bool doQueries,
std::vector<RDKit::RWMol *> &molVect) {
void *scanner;
TEST_ASSERT(!yysln_lex_init(&scanner));
setup_sln_string(inp, scanner);
yysln_set_extra((void *)doQueries, scanner);
int res = yysln_parse(inp.c_str(), &molVect, doQueries, scanner);
yysln_lex_destroy(scanner);
return res;
}
namespace RDKit {
namespace SLNParse {
std::vector<RDKit::RWMol *> molList_g;
void finalizeQueryMol(ROMol *mol, bool mergeHs) {
PRECONDITION(mol, "bad query molecule");
// do we need to remove the Hs from the molecule?
if (mergeHs) {
for (ROMol::AtomIterator atomIt = mol->beginAtoms();
atomIt != mol->endAtoms(); ++atomIt) {
// set a query for the H count:
if ((*atomIt)->getNumExplicitHs()) {
(*atomIt)->expandQuery(
makeAtomHCountQuery((*atomIt)->getNumExplicitHs()));
}
}
}
// we don't want to sanitize, but we do need to get
// some ring info:
VECT_INT_VECT sssr;
MolOps::symmetrizeSSSR(*mol, sssr);
int rootIdx = -1;
for (ROMol::AtomIterator atomIt = mol->beginAtoms();
atomIt != mol->endAtoms(); ++atomIt) {
SLNParse::parseFinalAtomAttribs(*atomIt, true);
if ((*atomIt)->hasProp(common_properties::_starred)) {
if (rootIdx > -1) {
BOOST_LOG(rdErrorLog) << "SLN Error: mulitple starred atoms in a "
"recursive query. Extra stars ignored"
<< std::endl;
} else {
rootIdx = (*atomIt)->getIdx();
}
}
}
if (rootIdx > -1) {
mol->setProp(common_properties::_queryRootAtom, rootIdx);
}
}
std::string replaceSLNMacroAtoms(std::string inp, int debugParse) {
RDUNUSED_PARAM(debugParse);
const std::regex defn("\\{(.+?):(.+?)\\}");
const char *empty = "";
std::string res;
// remove any macro definitions:
res = std::regex_replace(
inp, defn, empty,
std::regex_constants::match_default | std::regex_constants::format_sed);
if (res != inp) {
// there are macro definitions, we're going to replace
// the macro atoms in the input:
std::string::const_iterator start, end;
start = inp.begin();
end = inp.end();
std::match_results<std::string::const_iterator> what;
std::regex_constants::match_flag_type flags =
std::regex_constants::match_default;
while (std::regex_search(start, end, what, defn, flags)) {
std::string macroNm(what[1].first, what[1].second);
std::string macroVal(what[2].first, what[2].second);
res = std::regex_replace(res, std::regex(macroNm), macroVal.c_str(),
std::regex_constants::match_default |
std::regex_constants::format_sed);
// update search position:
start = what[0].second;
// update flags:
flags |= std::regex_constants::match_prev_avail;
}
}
return res;
}
RWMol *toMol(std::string inp, bool doQueries, int debugParse) {
RWMol *res;
boost::trim_if(inp, boost::is_any_of(" \t\r\n"));
inp = replaceSLNMacroAtoms(inp, debugParse);
if (debugParse) {
std::cerr << "****** PARSING SLN: ->" << inp << "<-" << std::endl;
}
std::vector<RDKit::RWMol *> molVect;
try {
sln_parse(inp, doQueries, molVect);
if (molVect.size() <= 0) {
res = nullptr;
} else {
res = molVect[0];
molVect[0] = nullptr;
for (ROMol::BOND_BOOKMARK_MAP::const_iterator bmIt =
res->getBondBookmarks()->begin();
bmIt != res->getBondBookmarks()->end(); ++bmIt) {
if (bmIt->first > 0 &&
bmIt->first < static_cast<int>(res->getNumAtoms())) {
std::stringstream err;
err << "SLN Parser error: Ring closure " << bmIt->first
<< " does not have a corresponding opener.";
throw SLNParseException(err.str());
}
}
}
} catch (SLNParseException &e) {
BOOST_LOG(rdErrorLog) << e.message() << std::endl;
res = nullptr;
}
if (res) {
// cleanup:
res->clearAllAtomBookmarks();
res->clearAllBondBookmarks();
// set up the chirality flags as soon as the molecule is finished
// since we'll be removing Hs later and that will break things:
adjustAtomChiralities(res);
}
for (auto &iter : molVect) {
if (iter) delete iter;
}
return res;
};
} // end of SLNParse namespace
RWMol *SLNToMol(const std::string &sln, bool sanitize, int debugParse) {
// FIX: figure out how to reset lexer state
yysln_debug = debugParse;
// strip any leading/trailing whitespace:
// boost::trim_if(sln,boost::is_any_of(" \t\r\n"));
RWMol *res = SLNParse::toMol(sln, false, debugParse);
if (res) {
for (ROMol::AtomIterator atomIt = res->beginAtoms();
atomIt != res->endAtoms(); ++atomIt) {
SLNParse::parseFinalAtomAttribs(*atomIt, false);
}
if (sanitize) {
// we're going to remove explicit Hs from the graph,
// this triggers a sanitization, so we do not need to
// worry about doing one here:
try {
MolOps::removeHs(*res, false, false);
} catch (...) {
delete res;
throw;
}
}
}
return res;
};
RWMol *SLNQueryToMol(const std::string &sln, bool mergeHs, int debugParse) {
yysln_debug = debugParse;
// strip any leading/trailing whitespace:
// boost::trim_if(sln,boost::is_any_of(" \t\r\n"));
RWMol *res = SLNParse::toMol(sln, true, debugParse);
if (res) {
SLNParse::finalizeQueryMol(res, mergeHs);
}
return res;
};
}
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