Source Code for Module specific_analyses.model_free.pymol

 1  ############################################################################### 
 2  #                                                                             # 
 3  # Copyright (C) 2003-2013 Edward d'Auvergne                                   # 
 4  #                                                                             # 
 5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
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 7  # This program is free software: you can redistribute it and/or modify        # 
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15  # GNU General Public License for more details.                                # 
16  #                                                                             # 
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18  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
19  #                                                                             # 
20  ############################################################################### 
21   
22  # Module docstring. 
23  """The Pymol macro methods of the specific API for model-free analysis.""" 
24   
25  # relax module imports. 
26  from specific_analyses.model_free.macro_base import Macro 
27   
28   
29 -class Pymol(Macro): 
30      """Class containing the Pymol specific functions for model-free analysis.""" 
31   
32 -    def classic_colour(self, res_num=None, width=None, rgb_array=None): 
33          """Colour the given peptide bond.""" 
34   
35          # Blank line (to make the macro file easier to read for the user). 
36          self.commands.append("") 
37   
38          # Define the colour. 
39          colour_name = 'pept_colour_%i' % res_num 
40          self.commands.append("set_color %s, [%s, %s, %s]" % (colour_name, rgb_array[0], rgb_array[1], rgb_array[2])) 
41   
42          # The peptide bond. 
43          self.commands.append("select pept_bond, (name ca,n and resi %i) or (name ca,c and resi %i)" % (res_num, res_num-1)) 
44          self.commands.append("as sticks, pept_bond") 
45          self.commands.append("set_bond stick_radius, %s, pept_bond" % width) 
46          self.commands.append("set_bond stick_color, %s, pept_bond" % colour_name) 
47   
48          # Delete the selection. 
49          self.commands.append("delete pept_bond") 
50   
51   
52 -    def classic_header(self): 
53          """Create the header for the pymol macro.""" 
54   
55          # Hide all bonds. 
56          self.commands.append("hide") 
57   
58          # Show the backbone bonds as lines. 
59          self.commands.append("select bb, (name ca,n,c)") 
60          self.commands.append("show lines, bb") 
61   
62          # Colour the backbone black. 
63          self.commands.append("color black, bb") 
64   
65          # Delete the selection. 
66          self.commands.append("delete bb") 
67   
68          # Set the background colour to white. 
69          self.commands.append("bg_color white") 
70   
71   
72 -    def pymol_macro(self, data_type, style=None, colour_start=None, colour_end=None, colour_list=None, spin_id=None): 
73          """Wrapper method for the create_macro method. 
74   
75          @param data_type:       The parameter name or data type. 
76          @type data_type:        str 
77          @keyword style:         The Molmol style. 
78          @type style:            None or str 
79          @keyword colour_start:  The starting colour (must be a MOLMOL or X11 name). 
80          @type colour_start:     str 
81          @keyword colour_end:    The ending colour (must be a MOLMOL or X11 name). 
82          @type colour_end:       str 
83          @keyword colour_list:   The colour list used, either 'molmol' or 'x11'. 
84          @type colour_list:      str 
85          @keyword spin_id:       The spin identification string. 
86          @type spin_id:          str 
87          """ 
88   
89          self.create_macro(data_type, style=style, colour_start=colour_start, colour_end=colour_end, colour_list=colour_list, spin_id=spin_id) 
90