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ae51ed9dde
iterators to OBAtom and OBBond respectively. Follows on 2006-11-20 change contributed by Gerd Menche. Switch many iterators to preincrement for minor optimization. * tools/*.cpp: Ditto.
118 lines
3.1 KiB
C++
118 lines
3.1 KiB
C++
/**********************************************************************
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obseq.cpp - Output residue sequence information for biomolecules
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Copyright (C) 2005-2006 Geoffrey R. Hutchison
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This file is part of the Open Babel project.
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For more information, see <http://openbabel.sourceforge.net/>
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This program is free software; you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation version 2 of the License.
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This program is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License for more details.
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***********************************************************************/
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// used to set import/export for Cygwin DLLs
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#ifdef WIN32
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#define USING_OBDLL
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#endif
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#include "babelconfig.h"
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#include "mol.h"
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#include "obconversion.h"
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#if !HAVE_STRNCASECMP
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extern "C" int strncasecmp(const char *s1, const char *s2, size_t n);
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#endif
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#include <stdio.h>
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#include <iostream>
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#include <fstream>
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using namespace std;
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using namespace OpenBabel;
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int main(int argc,char *argv[])
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{
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// turn off slow sync with C-style output (we don't use it anyway).
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std::ios::sync_with_stdio(false);
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if (argc != 2)
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{
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cout << "Usage: aromatest <file>" << endl;
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cout << " Tests aromaticity perception -- all non-hydrogen atoms"
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<< " are expected to be aromatic." << endl;
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return(-1);
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}
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cout << endl << "# Testing aromaticity perception... " << endl;
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ifstream ifs(argv[1]);
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if (!ifs)
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{
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cout << "Bail out! Cannot read input file!" << endl;
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return(-1);
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}
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OBConversion conv(&ifs, &cout);
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OBFormat* pFormat;
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pFormat = conv.FormatFromExt(argv[1]);
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if ( pFormat == NULL )
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{
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cout << "Bail out! Cannot read file format!" << endl;
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return(-1);
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}
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// Finally, we can do some work!
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OBMol mol;
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unsigned int testCount = 1;
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if (! conv.SetInAndOutFormats(pFormat, pFormat))
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{
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cout << "Bail out! File format isn't loaded" << endl;
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return (-1);
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}
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int molCount = 0;
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while(ifs.peek() != EOF && ifs.good())
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{
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mol.Clear();
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conv.Read(&mol);
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molCount++;
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vector<string> chains;
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unsigned int currentChain = 0;
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string residueList;
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FOR_RESIDUES_OF_MOL(r, mol)
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{
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if (r->GetChainNum() != currentChain)
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{
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if (residueList.size() != 0)
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{
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residueList.erase(residueList.size() - 1);
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chains.push_back(residueList);
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cout << residueList << endl;
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}
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currentChain = r->GetChainNum();
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residueList.clear();
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}
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residueList += r->GetName();
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residueList += "-";
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}
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residueList.erase(residueList.size() - 1);
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cout << residueList << endl;
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} // while reading molecules
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// output the number of tests run
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cout << "1.." << testCount-1 << endl;
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return(0);
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}
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