mirror of https://github.com/CGAL/cgal
223 lines
7.5 KiB
C++
223 lines
7.5 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 <CGAL/PDB/transforms.h>
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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::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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bool simple=false;
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std::string refine;
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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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("dali,d", boost::program_options::bool_switch(&dali),
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"Use a DALI transformation matrix as pasted from an email from DALI.")
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("matrix,m", boost::program_options::bool_switch(&matrix),
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"Enter a single transformation matrix.")
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("simplified-input,s", boost::program_options::bool_switch(&simple),
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"Enter a translation vector and a quaternion (3 components).")
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("refine,r", boost::program_options::value(&refine),
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"refine the alignment relative to some pdb file.")
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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 transforms a pdb file by reading a transformation"
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<< " matrix. The matrix is either specified by pasting the transform lines"
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<< " from a DALI email, entering a 4x4 transformation matrix (with a"
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<< " coordinate ordering x,y,z,w) or as separate rotational and "
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<< " translational components.\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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CGAL_PDB_NS::Transform t; //(rot, trans);
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if (dali) {
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double rot[3][3];
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double trans[3];
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// const char format[]="%d: %d %s %s %le %le %le %le"
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const char format[]="%le %le %le %le";
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for (unsigned int i=0; i< 3; ++i){
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char buf[1000];
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std::cin.getline(buf, 1000);
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if (sscanf(buf+27, format, &rot[i][0], &rot[i][1], &rot[i][2], &trans[i]) != 4) {
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std::cerr << "Error parsing Dali matrix.\n";
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return EXIT_FAILURE;
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};
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//std::cin >> n >> jc >> js >> js >> x >> y >> z >> t;
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//std::cout << x << " " << y << " " << z << " " << t << std::endl;
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}
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t= CGAL_PDB_NS::Transform(rot, trans);
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} else if (matrix) {
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double rot[3][3];
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double trans[3];
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const char format[]="%le %le %le %le";
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for (unsigned int i=0; i< 4; ++i){
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char buf[1000];
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std::cin.getline(buf, 1000);
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if (sscanf(buf, format, &rot[i][0], &rot[i][1], &rot[i][2], &trans[i]) != 4) {
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std::cerr << "Error parsing matrix, expected 4 floats.\n";
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return EXIT_FAILURE;
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};
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}
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t= CGAL_PDB_NS::Transform(rot, trans);
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} else if (simple) {
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bool done=false;
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double x,y,z, q1, q2, q3;
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do {
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std::cout << "Please enter transformation as \"x y z q1 q2 q3\": " << std::flush;
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char buf[1000];
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std::cin.getline(buf, 1000);
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if (sscanf(buf, "%le %le %le %le %le %le", &x, &y, &z, &q1, &q2, &q3) ==6) {
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done=true;
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}
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} while (!done);
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CGAL_PDB_NS::Quaternion q(q1, q2, q3);
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CGAL_PDB_NS::Vector v(x,y,z);
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t= CGAL_PDB_NS::Transform(v, q);
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} else if (matrix) {
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double rot[3][3];
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double trans[3];
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std::cout << "Rotation:\n";
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std::cout << "> " << std::flush;
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for (unsigned int i=0; i< 3; ++i){
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char buf[1000];
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std::cin.getline(buf, 1000);
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if (sscanf(buf, "%le %le %le", &rot[i][0], &rot[i][1], &rot[i][2]) != 3) {
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std::cerr << "Error parsing rotation matrix, expected 3 floats.\n";
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return EXIT_FAILURE;
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};
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if (i != 2) {
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std::cout << "> " << std::flush;
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}
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}
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std::cout << "Translation:\n";
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std::cout << "> "<< std::flush;
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char buf[1000];
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std::cin.getline(buf, 1000);
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if (sscanf(buf, "%le %le %le", &trans[0], &trans[1], &trans[2]) != 3) {
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std::cerr << "Error parsing translation, expected 3 floats.\n";
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return EXIT_FAILURE;
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};
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t= CGAL_PDB_NS::Transform(rot, trans);
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}
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std::cout << t;
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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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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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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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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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for (CGAL_PDB_NS::Protein::Residues_iterator rit= p.residues_begin(); rit != p.residues_end(); ++rit){
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for (CGAL_PDB_NS::Residue::Atoms_iterator ait= rit->atoms_begin(); ait != rit->atoms_end(); ++ait){
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ait->second.set_cartesian_coords(t(ait->second.cartesian_coords()));
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}
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}
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}
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}
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if (!refine.empty()) {
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std::ifstream rin(refine.c_str());
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if (!rin) {
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std::cerr << "Error opening input file " << refine << std::endl;
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return EXIT_FAILURE;
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}
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std::cout << "Refining against " << refine << std::endl;
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CGAL_PDB_NS::PDB rpdb(rin, verbose);
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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 &rm= rpdb.model((std::min)(rpdb.number_of_models(),
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static_cast<size_t>(i)));
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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 &rp= rm.chain(j);
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CGAL_PDB_NS::refine_alignment_of_second_protein_to_first(rp,p);
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}
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}
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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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pdb.write(out);
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//delete[] buf;
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return EXIT_SUCCESS;
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}
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