mirror of https://github.com/CGAL/cgal
106 lines
3.3 KiB
C++
106 lines
3.3 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/align.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::vector<std::string> input_files;
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std::string output_file;
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bool print_help=false;
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bool verbose=false;
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bool align=false;
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{
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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), "produce help message")
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("verbose,v", boost::program_options::bool_switch(&verbose),
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"Print error messages from reading the pdb files.")
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("align,a", boost::program_options::bool_switch(&align),
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"Align each protein to the previous.");
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po.add_options()
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("input-pdbs", boost::program_options::value< std::vector<std::string> >(&input_files),
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"The input and output files.");
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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-pdbs", -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_files.size() <2 || print_help) {
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std::cout << "Concatenate a bunch of pdb files into one pdb file with many models.\n";
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std::cout << "usage: " << argv[0] << " input-pdb-0 input-pdb-1 ... output-pdb\n";
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std::cout << o << "\n";
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return EXIT_SUCCESS;
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}
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output_file=input_files.back();
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input_files.pop_back();
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}
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CGAL_PDB_NS::PDB outpdb;
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CGAL_PDB_NS::Model last;
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for (unsigned int i=0; i < input_files.size(); ++i){
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std::ifstream in(input_files[i].c_str());
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if (!in){
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std::cerr << "Error opening input file " << input_files[i] << std::endl;
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return EXIT_FAILURE;
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}
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CGAL_PDB_NS::PDB inpdb(in, verbose);
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for (CGAL_PDB_NS::PDB::Models_iterator mit= inpdb.models_begin(); mit != inpdb.models_end(); ++mit){
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CGAL_PDB_NS::Model m= *mit;
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m.set_index(outpdb.number_of_models());
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if (align && i != 0) {
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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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const CGAL_PDB_NS::Protein &bp= last.chain(j);
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CGAL_PDB_NS::align_second_protein_to_first(bp, p);
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}
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}
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outpdb.new_model(m);
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last= m;
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}
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}
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if (output_file.empty()){
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outpdb.write(std::cout);
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} else {
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std::ofstream out(output_file.c_str());
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outpdb.write(out);
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}
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return EXIT_SUCCESS;
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}
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