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/**********************************************************************
obseq.cpp - Output residue sequence information for biomolecules
Copyright (C) 2005-2006 Geoffrey R. Hutchison
This file is part of the Open Babel project.
For more information, see <http://openbabel.org/>
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 <openbabel/mol.h>
#include <openbabel/obconversion.h>
#if !HAVE_STRNCASECMP
extern "C" int strncasecmp(const char *s1, const char *s2, size_t n);
#endif
#include <stdio.h>
#include <iostream>
#include <fstream>
using namespace std;
using namespace OpenBabel;
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 != 2)
{
cout << "Usage: aromatest <file>" << endl;
cout << " Tests aromaticity perception -- all non-hydrogen atoms"
<< " are expected to be aromatic." << endl;
return(-1);
}
cout << endl << "# Testing aromaticity perception... " << endl;
ifstream ifs(argv[1]);
if (!ifs)
{
cout << "Bail out! Cannot read input file!" << endl;
return(-1);
}
OBConversion conv(&ifs, &cout);
OBFormat* pFormat;
pFormat = conv.FormatFromExt(argv[1]);
if ( pFormat == NULL )
{
cout << "Bail out! Cannot read file format!" << endl;
return(-1);
}
// Finally, we can do some work!
OBMol mol;
unsigned int testCount = 1;
if (! conv.SetInAndOutFormats(pFormat, pFormat))
{
cout << "Bail out! File format isn't loaded" << endl;
return (-1);
}
int molCount = 0;
while(ifs.peek() != EOF && ifs.good())
{
mol.Clear();
conv.Read(&mol);
molCount++;
vector<string> chains;
unsigned int currentChain = 0;
string residueList;
FOR_RESIDUES_OF_MOL(r, mol)
{
if (r->GetChainNum() != currentChain)
{
if (residueList.size() != 0)
{
residueList.erase(residueList.size() - 1);
chains.push_back(residueList);
cout << residueList << endl;
}
currentChain = r->GetChainNum();
residueList.clear();
}
residueList += r->GetName();
residueList += "-";
}
residueList.erase(residueList.size() - 1);
cout << residueList << endl;
} // while reading molecules
// output the number of tests run
cout << "1.." << testCount-1 << endl;
return(0);
}
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