Source Code for Module gui.analyses.results_analysis

 1  ############################################################################### 
 2  #                                                                             # 
 3  # Copyright (C) 2009 Michael Bieri                                            # 
 4  # Copyright (C) 2010-2012 Edward d'Auvergne                                   # 
 5  #                                                                             # 
 6  # This file is part of the program relax.                                     # 
 7  #                                                                             # 
 8  # relax is free software; you can redistribute it and/or modify               # 
 9  # it under the terms of the GNU General Public License as published by        # 
10  # the Free Software Foundation; either version 2 of the License, or           # 
11  # (at your option) any later version.                                         # 
12  #                                                                             # 
13  # relax is distributed in the hope that it will be useful,                    # 
14  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
15  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               # 
16  # GNU General Public License for more details.                                # 
17  #                                                                             # 
18  # You should have received a copy of the GNU General Public License           # 
19  # along with relax; if not, write to the Free Software                        # 
20  # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA   # 
21  #                                                                             # 
22  ############################################################################### 
23   
24  # Python module imports. 
25  from os import sep 
26   
27  # relax module imports. 
28  from generic_fns.mol_res_spin import spin_loop 
29  from status import Status; status = Status() 
30   
31   
32 -def color_code_noe(target_dir, pdb_file): 
33      """Create PyMol Macro for NOE colouring.""" 
34   
35      # Open the macro file. 
36      file = open(target_dir + sep + 'noe.pml', 'w') 
37   
38      # PDB loading. 
39      if pdb_file: 
40          file.write("load " + pdb_file + '\n') 
41   
42      # PyMOL set up commands. 
43      file.write("bg_color white\n") 
44      file.write("color gray90\n") 
45      file.write("hide all\n") 
46      file.write("show ribbon\n") 
47   
48      # Loop over the spins. 
49      for spin, mol_name, res_num, res_name in spin_loop(full_info=True): 
50          # Skip deselected spins. 
51          if not spin.select: 
52              continue 
53   
54          # Skip spins with no data. 
55          if not hasattr(spin, 'noe') or spin.noe == None: 
56              continue 
57   
58          # Ribbon colour. 
59          width = ((1.0 - spin.noe) * 2.0) 
60          colour = 1.0 - ((spin.noe)**3) 
61          colour = colour ** 3 
62          colour = 1.0 - colour 
63   
64          # Write out the PyMOL commands. 
65          file.write("set_color resicolor%s, [0, %s, 1]\n" % (res_num, colour)) 
66          file.write("color resicolor%s, resi %s\n" % (res_num, res_num)) 
67          file.write("set_bond stick_radius, %s, resi %s\n" % (width, res_num)) 
68   
69      # Final PyMOL commands. 
70      file.write("hide all\n") 
71      file.write("show sticks, name C+N+CA\n") 
72      file.write("set stick_quality, 10\n") 
73      file.write("ray\n") 
74   
75      # Close the macro. 
76      file.close() 
77