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// $Id$
//
// Copyright (C) 2002-2006 Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <RDGeneral/test.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/RDKitQueries.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <stdlib.h>
#include <iostream>
#include <fstream>
#include <RDGeneral/types.h>
#include <RDGeneral/Invariant.h>
#include <RDGeneral/RDLog.h>
#include <GraphMol/MolOps.h>
#include <GraphMol/SanitException.h>
using namespace RDKit;
int testArom(RWMol m) {
// BOOST_LOG(rdErrorLog) << "********************************************\n";
// BOOST_LOG(rdErrorLog) << "Testing aromaticity :\n";
int res = MolOps::setAromaticity(m);
// BOOST_LOG(rdErrorLog) << "\nDone testing aromaticity \n";
// BOOST_LOG(rdErrorLog) << "********************************************\n";
return res;
}
void testKekule(RWMol &m) { MolOps::Kekulize(m); }
void getSmiles(std::string line, std::string &smi) {
int x = line.find("\t");
if (x == -1) {
x = line.find(" ");
}
smi = line.substr(0, x);
std::string rem = line.substr(x + 1, line.length() - x);
x = rem.find(" ");
std::string name;
name = rem.substr(0, x);
BOOST_LOG(rdInfoLog) << smi << " " << name << " ";
}
int main(int argc, char *argv[]) {
RDLog::InitLogs();
std::string fname;
if (argc > 1) {
fname = argv[1];
} else {
BOOST_LOG(rdErrorLog) << "Pass in the list of smiles\n";
}
std::ifstream inStream(fname.c_str());
const int MAX_LINE_LEN = 256;
char inLine[MAX_LINE_LEN];
std::string tmpstr;
std::string smi;
inStream.getline(inLine, MAX_LINE_LEN, '\n');
tmpstr = inLine;
// MolOps molop;
while (tmpstr.size() > 0) {
getSmiles(tmpstr, smi);
RWMol *m = SmilesToMol(smi, 0, 0);
try {
// testKekule(*m);
MolOps::sanitizeMol(*m);
int nar;
m->getProp(common_properties::numArom, nar);
BOOST_LOG(rdInfoLog) << nar << "\n";
// MolOps::setHybridization(*m);
delete m;
} catch (MolSanitizeException) {
BOOST_LOG(rdErrorLog) << smi << "\n";
delete m;
}
inStream.getline(inLine, MAX_LINE_LEN, '\n');
tmpstr = inLine;
}
return 1;
}
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