Source Code for Module specific_fns.model_free.pymol

 1  ############################################################################### 
 2  #                                                                             # 
 3  # Copyright (C) 2003-2011 Edward d'Auvergne                                   # 
 4  #                                                                             # 
 5  # This file is part of the program relax.                                     # 
 6  #                                                                             # 
 7  # relax is free software; you can redistribute it and/or modify               # 
 8  # it under the terms of the GNU General Public License as published by        # 
 9  # the Free Software Foundation; either version 2 of the License, or           # 
10  # (at your option) any later version.                                         # 
11  #                                                                             # 
12  # relax is distributed in the hope that it will be useful,                    # 
13  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
14  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               # 
15  # GNU General Public License for more details.                                # 
16  #                                                                             # 
17  # You should have received a copy of the GNU General Public License           # 
18  # along with relax; if not, write to the Free Software                        # 
19  # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA   # 
20  #                                                                             # 
21  ############################################################################### 
22   
23  # Module docstring. 
24  """The model-free PyMOL macro module.""" 
25   
26  # relax module imports. 
27  from specific_fns.model_free.macro_base import Macro 
28   
29   
30 -class Pymol(Macro): 
31      """Class containing the Pymol specific functions for model-free analysis.""" 
32   
33 -    def classic_colour(self, res_num=None, width=None, rgb_array=None): 
34          """Colour the given peptide bond.""" 
35   
36          # Blank line (to make the macro file easier to read for the user). 
37          self.commands.append("") 
38   
39          # Define the colour. 
40          colour_name = 'pept_colour_%i' % res_num 
41          self.commands.append("set_color %s, [%s, %s, %s]" % (colour_name, rgb_array[0], rgb_array[1], rgb_array[2])) 
42   
43          # The peptide bond. 
44          self.commands.append("select pept_bond, (name ca,n and resi %i) or (name ca,c and resi %i)" % (res_num, res_num-1)) 
45          self.commands.append("as sticks, pept_bond") 
46          self.commands.append("set_bond stick_radius, %s, pept_bond" % width) 
47          self.commands.append("set_bond stick_color, %s, pept_bond" % colour_name) 
48   
49          # Delete the selection. 
50          self.commands.append("delete pept_bond") 
51   
52   
53 -    def classic_header(self): 
54          """Create the header for the pymol macro.""" 
55   
56          # Hide all bonds. 
57          self.commands.append("hide") 
58   
59          # Show the backbone bonds as lines. 
60          self.commands.append("select bb, (name ca,n,c)") 
61          self.commands.append("show lines, bb") 
62   
63          # Colour the backbone black. 
64          self.commands.append("color black, bb") 
65   
66          # Delete the selection. 
67          self.commands.append("delete bb") 
68   
69          # Set the background colour to white. 
70          self.commands.append("bg_color white") 
71   
72   
73 -    def pymol_macro(self, data_type, style=None, colour_start=None, colour_end=None, colour_list=None, spin_id=None): 
74          """Wrapper method for the create_macro method. 
75   
76          @param data_type:       The parameter name or data type. 
77          @type data_type:        str 
78          @keyword style:         The Molmol style. 
79          @type style:            None or str 
80          @keyword colour_start:  The starting colour (must be a MOLMOL or X11 name). 
81          @type colour_start:     str 
82          @keyword colour_end:    The ending colour (must be a MOLMOL or X11 name). 
83          @type colour_end:       str 
84          @keyword colour_list:   The colour list used, either 'molmol' or 'x11'. 
85          @type colour_list:      str 
86          @keyword spin_id:       The spin identification string. 
87          @type spin_id:          str 
88          """ 
89   
90          self.create_macro(data_type, style=style, colour_start=colour_start, colour_end=colour_end, colour_list=colour_list, spin_id=spin_id) 
91