1 /* Copyright 2004
2 Stanford University
3
4 This file is part of the DSR PDB Library.
5
6 The DSR PDB Library is free software; you can redistribute it and/or modify
7 it under the terms of the GNU Lesser General Public License as published by
8 the Free Software Foundation; either version 2.1 of the License, or (at your
9 option) any later version.
10
11 The DSR PDB Library is distributed in the hope that it will be useful, but
12 WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
13 or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
14 License for more details.
15
16 You should have received a copy of the GNU Lesser General Public License
17 along with the DSR PDB Library; see the file COPYING.LIB. If not, write to
18 the Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston,
19 MA 02111-1307, USA. */
20
21 #include "dsrpdb/PDB.h"
22 #include <cstdlib>
23 #include <iostream>
24 #include <fstream>
25
26 #include <dsrpdb/Transform.h>
27
28 #ifdef PDB_USE_BOOST_PROGRAM_OPTIONS
29 #include <boost/program_options.hpp>
30 #endif
31
32
main(int argc,char * argv[])33 int main(int argc, char *argv[]){
34 std::string input_file, output_file;
35 bool print_help=false;
36 bool verbose=false;
37 bool dali=false;
38 bool matrix=false;
39
40 #ifdef PDB_USE_BOOST_PROGRAM_OPTIONS
41 boost::program_options::options_description o("Allowed options"), po, ao;
42 o.add_options()
43 ("help", boost::program_options::bool_switch(&print_help),
44 "produce help message")
45 ("dali,d", boost::program_options::bool_switch(&dali),
46 "Use a DALI transformation matrix as pasted from an email from DALI.")
47 ("matrix,m", boost::program_options::bool_switch(&matrix),
48 "Enter a single transformation matrix.")
49 ("verbose,v", boost::program_options::bool_switch(&verbose),
50 "print out any errors that occur during reading of the pdb file.");
51
52 po.add_options()
53 ("input-pdb", boost::program_options::value< std::string>(&input_file),
54 "input file")
55 ("output-pdb", boost::program_options::value< std::string>(&output_file),
56 "output file");
57 ao.add(o).add(po);
58
59 boost::program_options::positional_options_description p;
60 p.add("input-pdb", 1);
61 p.add("output-pdb", 1);
62
63 boost::program_options::variables_map vm;
64 boost::program_options::store(boost::program_options::command_line_parser(argc, argv).
65 options(ao).positional(p).run(), vm);
66 boost::program_options::notify(vm);
67
68 if (input_file.empty() || output_file.empty() || print_help || (dali && matrix)) {
69 std::cout << "This program transforms a pdb file by reading a transformation"
70 << " matrix. The matrix is either specified by pasting the transform lines"
71 << " from a DALI email, entering a 4x4 transformation matrix (with a"
72 << " coordinate ordering x,y,z,w) or as separate rotational and "
73 << " translational components.\n";
74 std::cout << "usage: " << argv[0] << " input-pdb output-pdb\n\n";
75 std::cout << o << "\n";
76 return EXIT_FAILURE;
77 }
78
79 #else
80 if (argc != 3){
81 std::cerr << "The program is built without boost/program_options.hpp.\n";
82 std::cerr << "useage: " << argv[0] << " [-c] file.pdb output.pdb" << std::endl;
83 return EXIT_FAILURE;
84 }
85 input_file = argv[1];
86 output_file = argv[2];
87 #endif
88
89
90 // std::cout << input_file << " " << output_template << " " << split_domain << " " << split_chains << std::endl;
91
92
93
94 //= new char[strlen(argv[2]+1000)];
95
96 double rot[3][3];
97 double trans[3];
98 if (dali) {
99 // const char format[]="%d: %d %s %s %le %le %le %le"
100 const char format[]="%le %le %le %le";
101 for (unsigned int i=0; i< 3; ++i){
102 char buf[1000];
103 std::cin.getline(buf, 1000);
104 if (sscanf(buf+27, format, &rot[i][0], &rot[i][1], &rot[i][2], &trans[i]) != 4) {
105 std::cerr << "Error parsing Dali matrix.\n";
106 return EXIT_FAILURE;
107 };
108 //std::cin >> n >> jc >> js >> js >> x >> y >> z >> t;
109 //std::cout << x << " " << y << " " << z << " " << t << std::endl;
110 }
111 } else if (matrix) {
112 const char format[]="%le %le %le %le";
113 for (unsigned int i=0; i< 4; ++i){
114 char buf[1000];
115 std::cin.getline(buf, 1000);
116 if (sscanf(buf, format, &rot[i][0], &rot[i][1], &rot[i][2], &trans[i]) != 4) {
117 std::cerr << "Error parsing matrix, expected 4 floats.\n";
118 return EXIT_FAILURE;
119 };
120 }
121 } else {
122 std::cout << "Rotation:\n";
123 std::cout << "> " << std::flush;
124 for (unsigned int i=0; i< 3; ++i){
125 char buf[1000];
126 std::cin.getline(buf, 1000);
127 if (sscanf(buf, "%le %le %le", &rot[i][0], &rot[i][1], &rot[i][2]) != 3) {
128 std::cerr << "Error parsing rotation matrix, expected 3 floats.\n";
129 return EXIT_FAILURE;
130 };
131 if (i != 2) {
132 std::cout << "> " << std::flush;
133 }
134 }
135 std::cout << "Translation:\n";
136 std::cout << "> "<< std::flush;
137 char buf[1000];
138 std::cin.getline(buf, 1000);
139 if (sscanf(buf, "%le %le %le", &trans[0], &trans[1], &trans[2]) != 3) {
140 std::cerr << "Error parsing translation, expected 3 floats.\n";
141 return EXIT_FAILURE;
142 };
143 }
144
145 dsrpdb::Transform t(rot, trans);
146 std::cout << t;
147 std::ifstream in(input_file.c_str());
148 if (!in) {
149 std::cerr << "Error opening input file " << input_file << std::endl;
150 return EXIT_FAILURE;
151 }
152
153 dsrpdb::PDB pdb(in, verbose);
154
155 if (verbose) std::cout << "Input PDB has " << pdb.number_of_models() << " models." << std::endl;
156
157 for (unsigned int i=0;i< pdb.number_of_models(); ++i){
158 dsrpdb::Model &m= pdb.model(i);
159 std::cout << "Model " << i << " has " << m.number_of_chains() << " chains."<< std::endl;
160 for (unsigned int j=0; j< m.number_of_chains(); ++j){
161 dsrpdb::Protein &p= m.chain(j);
162 for (dsrpdb::Protein::Residues_iterator rit= p.residues_begin(); rit != p.residues_end(); ++rit){
163 for (dsrpdb::Residue::Atoms_iterator ait= rit->atoms_begin(); ait != rit->atoms_end(); ++ait){
164 ait->second.set_cartesian_coords(t(ait->second.cartesian_coords()));
165 }
166 }
167 }
168 }
169
170 std::ofstream out(output_file.c_str());
171 if (!out) {
172 std::cerr << "Error opening output file " << output_file << std::endl;
173 return EXIT_FAILURE;
174 }
175
176 pdb.write(out);
177
178 //delete[] buf;
179 return EXIT_SUCCESS;
180 }
181