mirror of https://github.com/CGAL/cgal
83 lines
3.0 KiB
C++
83 lines
3.0 KiB
C++
/* Copyright 2004
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Stanford University
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This file is part of the DSR PDB Library.
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The DSR PDB Library is free software; you can redistribute it and/or modify
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it under the terms of the GNU Lesser General Public License as published by
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the Free Software Foundation; either version 2.1 of the License, or (at your
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option) any later version.
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The DSR PDB Library is distributed in the hope that it will be useful, but
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WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
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or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
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License for more details.
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You should have received a copy of the GNU Lesser General Public License
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along with the DSR PDB Library; see the file COPYING.LIB. If not, write to
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the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
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MA 02110-1301, USA. */
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#include <CGAL/PDB/PDB.h>
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#include <fstream>
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#include <cassert>
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#include <CGAL/PDB/align.h>
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#include <CGAL/PDB/align.h>
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#include <CGAL/PDB/distance.h>
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#include <CGAL/PDB/Transform.h>
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int main(int , char *[]){
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using namespace CGAL_PDB_NS;
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//dsr::Residue res= dsr::Residue(dsr::Residue::VAL);
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//res.write(std::cout);
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//assert(argc==2);
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std::ifstream in("data/check_protein.pdb");
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CGAL_PDB_NS::PDB p(in);
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std::cout << "There are " << p.number_of_models() << " models." << std::endl;
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for (unsigned int i=0; i< p.number_of_models(); ++i){
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const CGAL_PDB_NS::Model &m= p.model(i);
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std::cout << "Model " << i << " has " << m.number_of_chains() << " chains" << std::endl;
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for (unsigned int j=0; j< m.number_of_chains(); ++j){
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CGAL_PDB_NS::Protein p = m.chain(j);
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double rot[3][3]={{0.309976, 0.851651, -0.422618},
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{-0.741526, 0.494764, 0.453154},
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{0.595025, 0.172916, 0.78488}},
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trans[3]={4,5,6};
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CGAL_PDB_NS::Transform tr(rot, trans);
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std::cout << "tr is " << tr<< std::endl;
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for (CGAL_PDB_NS::Protein::Residues_iterator rit= p.residues_begin();
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rit != p.residues_end(); ++rit){
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for (CGAL_PDB_NS::Residue::Atoms_iterator ait= rit->atoms_begin();
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ait != rit->atoms_end(); ++ait){
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ait->second.set_cartesian_coords(tr(ait->second.cartesian_coords()));
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}
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}
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std::cout << "iterated" << std::endl;
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std::vector<CGAL_PDB_NS::Point> pa, pp;
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CGAL_PDB_NS::backbone_coordinates(m.chain(j).atoms_begin(), m.chain(j).atoms_end(),
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std::back_inserter(pa));
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CGAL_PDB_NS::backbone_coordinates(p.atoms_begin(), p.atoms_end(),
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std::back_inserter(pp));
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std::cout << "m has " << pa.size() << " p has " << pp.size() << std::endl;
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CGAL_PDB_NS::Transform trp= CGAL_PDB_NS::transform_taking_first_to_second( pa, pp);
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std::cout << "trp is " << trp<< std::endl;
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double mdiff=tr.error(trp);
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assert(mdiff<.1);
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CGAL_PDB_NS::align_second_protein_to_first( m.chain(j), p);
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double err= no_align_cRMS(m.chain(j), p);
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double ca_err= cRMS(m.chain(j), p);
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assert(err < 1e-5);
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std::cout << err << " " << ca_err << std::endl;
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}
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}
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return EXIT_SUCCESS;
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}
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