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/**********************************************************************
formalcharge.cpp - Test molecular formal charge perception
This file is part of the Open Babel project.
For more information, see <http://openbabel.sourceforge.net/>
Some portions Copyright (C) 2005-2006 Geoffrey R. Hutchison
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
***********************************************************************/
// used to set import/export for Cygwin DLLs
#ifdef WIN32
#define USING_OBDLL
#endif
#include <openbabel/babelconfig.h>
#include <fstream>
#include <openbabel/mol.h>
#include <openbabel/obconversion.h>
namespace OpenBabel
{
bool SafeOpen(std::ifstream &fs, const char *filename);
bool SafeOpen(std::ofstream &fs, const char *filename);
}
using namespace std;
using namespace OpenBabel;
#ifdef TESTDATADIR
string testdatadir = TESTDATADIR;
string results_file = testdatadir + "formalchargeresults.txt";
string smilestypes_file = testdatadir + "attype.00.smi";
#else
string results_file = "files/formalchargeresults.txt";
string smilestypes_file = "files/attype.00.smi";
#endif
void GenerateFormalChargeReference();
int main(int argc,char *argv[])
{
// turn off slow sync with C-style output (we don't use it anyway).
std::ios::sync_with_stdio(false);
if (argc != 1)
{
if (strncmp(argv[1], "-g", 2))
{
cout << "Usage: formalcharge" << endl;
cout << " Tests Open Babel molecular formal charge perception."
<< endl;
return 0;
}
else
{
GenerateFormalChargeReference();
return 0;
}
}
cout << "# Testing molecular formal charges..." << endl;
std::ifstream mifs;
if (!SafeOpen(mifs, smilestypes_file.c_str()))
{
cout << "Bail out! Cannot read file " << smilestypes_file << endl;
return -1; // test failed
}
std::ifstream rifs;
if (!SafeOpen(rifs, results_file.c_str()))
{
cout << "Bail out! Cannot read file " << results_file << endl;
return -1; // test failed
}
char buffer[BUFF_SIZE];
vector<string> vs;
OBMol mol;
OBConversion conv(&mifs, &cout);
unsigned int currentTest = 1;
if(! conv.SetInAndOutFormats("SMI","SMI"))
{
cout << "Bail out! SMILES format is not loaded" << endl;
return -1;
}
for (;mifs;)
{
mol.Clear();
conv.Read(&mol);
if (mol.Empty())
continue;
if (!rifs.getline(buffer,BUFF_SIZE))
{
cout << "Bail out! error reading reference data" << endl;
return -1; // test failed
}
tokenize(vs,buffer);
// check charges
}
cout << "ok 1\n";
// return number of tests run
cout << "1.." << currentTest << endl;
// Passed tests
return 0;
}
void GenerateFormalChargeReference()
{
std::ifstream ifs;
if (!SafeOpen(ifs, smilestypes_file.c_str()))
return;
std::ofstream ofs;
if (!SafeOpen(ofs, results_file.c_str()))
return;
OBMol mol;
OBConversion conv(&ifs, &cout);
if(! conv.SetInAndOutFormats("SMI","SMI"))
{
cerr << "SMILES format is not loaded" << endl;
return;
}
for (;ifs;)
{
mol.Clear();
conv.Read(&mol);
if (mol.Empty())
continue;
ofs << mol.GetTotalCharge();
FOR_ATOMS_OF_MOL(atom, mol)
{
ofs << " " << atom->GetFormalCharge();
}
ofs << endl;
}
cerr << " Formal charge results written successfully" << endl;
return;
}
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