mirror of https://github.com/CGAL/cgal
206 lines
7.1 KiB
C++
206 lines
7.1 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 <cstdlib>
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#include <iostream>
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#include <fstream>
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#include <cctype>
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#include <boost/program_options.hpp>
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/*!
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\example pdb_split.cc
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This example shows how to split a pdb file various ways. A pdb can
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be split into different models, chains or event cut a particular
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chain.
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*/
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int main(int argc, char *argv[]){
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bool split_chains=false;
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std::string input_file, output_template;
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int split_domain=-1;
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bool print_help=false;
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bool verbose=false;
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char split_chain='\0';
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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 verbose messages about reading and writing pdb files")
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("split-chains,c", boost::program_options::bool_switch(&split_chains),
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"Split all chains into separate files.")
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("select-chain,C", boost::program_options::value<char>(&split_chain),
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"Select this chain only.")
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("domain-split,s", boost::program_options::value<int>(&split_domain),
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"Split a chain into domains at this residue.");
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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-template", boost::program_options::value< std::string>(&output_template),
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"A sprintf style string that will be used to generate the names for the 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-pdb", 1);
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p.add("output-pdb-template", 2);
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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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//boost::program_options::store(boost::program_options::parse_command_line(argc, argv, desc), vm);
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//boost::program_options::notify(vm);
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if (input_file.empty()
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|| output_template.empty()
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|| (split_chains && split_chain != '\0')
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|| (split_chains && split_domain != -1)
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|| (split_chain != '\0' && split_domain != -1)
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|| print_help) {
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std::cout << "This program splits a pdb file with multiple models or multiple domains into multiple files each with one model .\n";
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std::cout << "useage: " << argv[0]
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<< " [-c] input-pdb template%d[%c].pdb\n" << std::endl;
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std::cout << "The second argument is an sprintf style string that will be used to generate the names for the output files.\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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if (split_chain != '\0'){
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std::cout << "Splitting on chain " << split_chain << std::endl;
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} else if (split_domain != -1) {
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std::cout << "Splitting on residue " << split_domain << std::endl;
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} else {
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std::cout << "Splitting into chains " << std::endl;
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}
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// std::cout << input_file << " " << output_template << " " << split_domain << " " << split_chains << std::endl;
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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 input file " << input_file << std::endl;
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return EXIT_FAILURE;
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}
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//= new char[strlen(argv[2]+1000)];
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CGAL_PDB_NS::PDB pdb(in, verbose);
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std::cout << "Input PDB has " << pdb.number_of_models() << " models." << std::endl;
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if (split_domain != -1 && pdb.number_of_models()!= 1){
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std::cerr << "Splitting a domain can only work if there is only one model and chain.\n";
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return EXIT_FAILURE;
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}
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for (unsigned int i=0; i< pdb.number_of_models(); ++i){
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const CGAL_PDB_NS::Model &m= pdb.model(i);
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if (split_chain != '\0' || split_chains || split_domain!= -1) {
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std::cout << "Model " << i << " has " << m.number_of_chains() << " chains."<< std::endl;
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if (split_domain != -1 && m.number_of_chains()!= 1){
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std::cerr << "Splitting a domain can only work if there is only one model and chain.\n";
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return EXIT_FAILURE;
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}
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for (unsigned int j=0; j< m.number_of_chains(); ++j){
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const CGAL_PDB_NS::Protein &p= m.chain(j);
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if (split_chain != '\0') {
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if (p.chain() == split_chain || p.chain() == std::toupper(split_chain) ) {
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std::cout << "Writing chain " << p.chain() << std::endl;
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assert(split_domain ==-1);
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std::ofstream out(output_template.c_str());
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CGAL_PDB_NS::PDB npdb;
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CGAL_PDB_NS::Model nm;
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nm.new_chain(p);
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npdb.new_model(nm);
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npdb.set_header(pdb.header_begin(), pdb.header_end());
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npdb.write(out);
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} else {
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std::cout << "Skipping chain " << p.chain() << std::endl;
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}
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} else if (split_chains) {
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std::cout << "Writing chain " << p.chain() << std::endl;
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assert(split_domain ==-1);
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char buf[100000];
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if (pdb.number_of_models()==1) {
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sprintf(buf, output_template.c_str(),p.chain());
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} else {
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sprintf(buf, output_template.c_str(), m.index(), p.chain());
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}
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std::ofstream out(buf);
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CGAL_PDB_NS::PDB npdb;
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CGAL_PDB_NS::Model nm;
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nm.new_chain(p);
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npdb.new_model(nm);
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npdb.set_header(pdb.header_begin(), pdb.header_end());
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npdb.write(out);
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} else {
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CGAL_PDB_NS::Protein ps[2]={CGAL_PDB_NS::Protein(), CGAL_PDB_NS::Protein()};
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for (CGAL_PDB_NS::Protein::Const_residues_iterator rit = p.residues_begin();
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rit != p.residues_end(); ++rit){
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//rit->write('c', std::cout);
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if (rit->index().to_index()
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< static_cast<unsigned int>(split_domain)){
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ps[0].new_residue(*rit);
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} else {
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ps[1].new_residue(*rit);
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}
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}
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assert(ps[0].number_of_residues() + ps[1].number_of_residues()
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== p.number_of_residues());
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for (unsigned int j=0; j< 2; ++j){
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std::cout << "Writing pdb with " << ps[j].number_of_residues() << " residues.\n";
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char buf[100000];
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sprintf(buf, output_template.c_str(), j);
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std::ofstream out(buf);
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CGAL_PDB_NS::PDB npdb;
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CGAL_PDB_NS::Model nm(0);
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nm.new_chain(ps[j]);
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npdb.new_model(nm);
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npdb.set_header(pdb.header_begin(), pdb.header_end());
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npdb.write(out);
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}
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}
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}
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} else {
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char buf[100000];
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sprintf(buf, argv[2], m.index());
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std::ofstream out(buf);
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CGAL_PDB_NS::PDB npdb;
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npdb.new_model(m);
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npdb.set_header(pdb.header_begin(), pdb.header_end());
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npdb.write(out);
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}
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}
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//delete[] buf;
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return EXIT_SUCCESS;
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}
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