mirror of https://github.com/CGAL/cgal
128 lines
4.0 KiB
C++
128 lines
4.0 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 LICENSE.LGPL. 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 <cstdlib>
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#include <iostream>
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#include <fstream>
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#include <CGAL/PDB/Transform.h>
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#include <boost/program_options.hpp>
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int main(int argc, char *argv[]){
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std::string input_file, output_file;
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bool print_help=false;
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bool verbose=false;
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bool dali=false;
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bool matrix=false;
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boost::program_options::options_description o("Allowed options"), po, ao;
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o.add_options()
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("help", boost::program_options::bool_switch(&print_help),
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"produce help message")
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("verbose,v", boost::program_options::bool_switch(&verbose),
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"print out any errors that occur during reading of the pdb file.");
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po.add_options()
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("input-pdb", boost::program_options::value< std::string>(&input_file),
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"input file")
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("output-pdb", boost::program_options::value< std::string>(&output_file),
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"output file");
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ao.add(o).add(po);
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boost::program_options::positional_options_description p;
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p.add("input-pdb", 1);
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p.add("output-pdb", 1);
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boost::program_options::variables_map vm;
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boost::program_options::store(boost::program_options::command_line_parser(argc, argv).
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options(ao).positional(p).run(), vm);
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boost::program_options::notify(vm);
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if (input_file.empty() || output_file.empty() || print_help || (dali && matrix)) {
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std::cout << "This program produces a pdb identical to the input but with no sidechains.\n";
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std::cout << "usage: " << argv[0] << " input-pdb output-pdb\n\n";
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std::cout << o << "\n";
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return EXIT_SUCCESS;
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}
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// std::cout << input_file << " " << output_template << " " << split_domain << " " << split_chains << std::endl;
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//= new char[strlen(argv[2]+1000)];
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std::ifstream in(input_file.c_str());
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if (!in) {
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std::cerr << "Error opening output file " << input_file << std::endl;
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return EXIT_FAILURE;
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}
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CGAL_PDB_NS::PDB pdb(in, verbose);
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if (verbose) std::cout << "Input PDB has " << pdb.number_of_models() << " models." << std::endl;
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CGAL_PDB_NS::PDB outpdb;
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for (unsigned int i=0;i< pdb.number_of_models(); ++i){
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CGAL_PDB_NS::Model &m= pdb.model(i);
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CGAL_PDB_NS::Model om;
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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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CGAL_PDB_NS::Protein op;
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for (CGAL_PDB_NS::Protein::Residues_iterator rit= p.residues_begin(); rit != p.residues_end(); ++rit){
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CGAL_PDB_NS::Residue nr(rit->type());
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nr.set_index(rit->index());
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if (rit->has_atom(CGAL_PDB_NS::Residue::AL_N)) {
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nr.set_atom(CGAL_PDB_NS::Residue::AL_N, rit->atom(CGAL_PDB_NS::Residue::AL_N));
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}
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if (rit->has_atom(CGAL_PDB_NS::Residue::AL_CA)) {
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nr.set_atom(CGAL_PDB_NS::Residue::AL_CA, rit->atom(CGAL_PDB_NS::Residue::AL_CA));
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}
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if (rit->has_atom(CGAL_PDB_NS::Residue::AL_C)) {
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nr.set_atom(CGAL_PDB_NS::Residue::AL_C, rit->atom(CGAL_PDB_NS::Residue::AL_C));
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}
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op.new_residue(nr);
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}
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om.new_chain(op);
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}
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outpdb.new_model(om);
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}
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std::ofstream out(output_file.c_str());
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if (!out) {
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std::cerr << "Error opening output file " << output_file << std::endl;
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return EXIT_FAILURE;
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}
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outpdb.write(out);
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//delete[] buf;
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return EXIT_SUCCESS;
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}
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