mirror of https://github.com/CGAL/cgal
213 lines
6.8 KiB
C++
213 lines
6.8 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/distance.h>
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#include <boost/program_options.hpp>
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#ifdef PDB_USE_MAGICK
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#include <Magick++.h>
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/*!
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\example pdb_write_distmat.cc
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This example shows how to write a distance matrix to a file.
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*/
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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 interactive=false;
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bool backbone=false;
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bool all_atoms=false;
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double contact_map_threshold=std::numeric_limits<double>::infinity();
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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), "print verbose error messages")
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("all-atoms,a", boost::program_options::bool_switch(&all_atoms),
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"Output the distances between all atoms, not just the C_alphas.")
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("backbone-atoms,b", boost::program_options::bool_switch(&backbone),
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"Output the distances between all backbone atoms, not just the C_alphas.")
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("image,i",boost::program_options::value<std::string>(&output_file), "Output image file.")
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("contact-threshold,c",boost::program_options::value<double>(&contact_map_threshold), "Output a contact map with the given threshold. (assuming the image argument is passed).")
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("query,q", boost::program_options::bool_switch(&interactive), "Enter a mode to do interactive queries about edge lengths.");
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po.add_options()
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("input-pdb", boost::program_options::value< std::string>(&input_file), "input 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-image", 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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//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() || print_help || (all_atoms && backbone)) {
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std::cout << "This program writes the distance matrix to an image file.\n";
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std::cout << "Only one of -b or -a may be used.\n";
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std::cout << "usage: " << argv[0] << " input-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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}
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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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if (pdb.number_of_models() != 1){
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std::cout << "Attempting to write multiple image files: assuming the output argument has a %d in it.\n";
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}
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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::Matrix arr;
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if (all_atoms) {
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arr= distance_matrix(m);
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} else if (backbone) {
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arr= backbone_distance_matrix(m);
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} else {
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arr= ca_distance_matrix(m);
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}
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//std::cout << arr.dim1() << " " << arr.dim2() << std::endl;
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if (interactive) {
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std::cout << "Entering interactive mode for model " << i << std::endl;
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std::cout << "There are " << arr.dim1() << " atoms." << std::endl;
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while (true) {
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std::cout << "> " << std::flush;
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char buf[100];
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std::cin.getline(buf, 100);
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if (strcmp(buf, "quit") ==0 || strcmp(buf,"exit") ==0){
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break;
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} else {
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int a,b;
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if (sscanf(buf, "%d %d", &a, &b)==2){
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if (a > arr.dim1() || b > arr.dim1() || a<0 || b <0){
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std::cerr << "Index " << a << " or " << b << " out of range." << std::endl;
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} else {
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std::cout << arr[a][b] << std::endl;
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}
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} else if (sscanf(buf, "r %d %d", &a, &b) ==2) {
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if (a > 0 && b > 0) {
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CGAL_PDB_NS::Residue::Index ia(a), ib(b);
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if (m.chain(0).has_residue(ia) && m.chain(0).has_residue(ib)) {
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CGAL_PDB_NS::Point pa= m.chain(0).residue(ia).atom(CGAL_PDB_NS::Residue::AL_CA).cartesian_coords();
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CGAL_PDB_NS::Point pb= m.chain(0).residue(ib).atom(CGAL_PDB_NS::Residue::AL_CA).cartesian_coords();
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CGAL_PDB_NS::Squared_distance sd;
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double d= std::sqrt(sd(pa,pb));
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std::cout << "The Ca distance is " << d << std::endl;
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} else {
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std::cerr << "Invalid residues picked.\n";
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}
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} else {
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std::cerr << "Invalid residues indices picked (must be greater than 0).\n";
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}
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} else {
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std::cerr << "Error parsing input. Please enter a pair of indices or 'exit'." << std::endl;
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}
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}
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}
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}
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if (!output_file.empty()) {
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char buf[100000];
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if (pdb.number_of_models() != 1){
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sprintf(buf, output_file.c_str(), i);
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} else {
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sprintf(buf, output_file.c_str());
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}
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Magick::Geometry geom(arr.dim1(),arr.dim2());
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Magick::Image im(geom, "red");
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if (contact_map_threshold != std::numeric_limits<double>::infinity()){
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for (int j=0; j< arr.dim1(); ++j){
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for (int k=0; k< arr.dim2(); ++k){
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if (arr[j][k] < contact_map_threshold){
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im.pixelColor(j, k, Magick::ColorGray(1));
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} else {
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im.pixelColor(j,k, Magick::ColorGray(0));
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}
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}
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}
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} else {
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double lmax=0;
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for (int i=0; i< arr.dim1(); ++i){
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for (int j=0; j< arr.dim2(); ++j){
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lmax=std::max BOOST_PREVENT_MACRO_SUBSTITUTION(max, arr[i][j]);
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//min=std::min(min, arr[i][j]);
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}
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}
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//std::cout << "Maximum distance is " << max << std::endl;
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for (int i=0; i< arr.dim1(); ++i){
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for (int j=0; j< arr.dim2(); ++j){
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im.pixelColor(i,j, Magick::ColorGray(arr[i][j]/lmax));
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}
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}
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}
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im.write(buf);
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}
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}
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return EXIT_SUCCESS;
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}
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#else
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int main(int, char*[]){
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//bool this_program_requires_image_magick;
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std::cerr << "This program requires Image Magick++\n";
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// so that the test suite is not red
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return EXIT_SUCCESS;
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}
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#endif
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