Source Code for Module specific_fns.model_free.molmol

 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               # 
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20  #                                                                             # 
21  ############################################################################### 
22   
23  # Module docstring. 
24  """The model-free Molmol macro module.""" 
25   
26  # relax module imports. 
27  from specific_fns.model_free.macro_base import Macro 
28   
29   
30 -class Molmol(Macro): 
31      """Class containing the Molmol 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          # Ca to C bond. 
37          self.commands.append("SelectBond 'atom1.name = \"CA\"  & atom2.name = \"C\" & res.num = " + repr(res_num-1) + "'") 
38          self.commands.append("StyleBond neon") 
39          self.commands.append("RadiusBond " + repr(width)) 
40          self.commands.append("ColorBond " + repr(rgb_array[0]) + " " + repr(rgb_array[1]) + " " + repr(rgb_array[2])) 
41   
42          # C to N bond. 
43          self.commands.append("SelectBond 'atom1.name = \"C\"  & atom2.name = \"N\" & res.num = " + repr(res_num-1) + "'") 
44          self.commands.append("StyleBond neon") 
45          self.commands.append("RadiusBond " + repr(width)) 
46          self.commands.append("ColorBond " + repr(rgb_array[0]) + " " + repr(rgb_array[1]) + " " + repr(rgb_array[2])) 
47   
48          # N to Ca bond. 
49          self.commands.append("SelectBond 'atom1.name = \"N\"  & atom2.name = \"CA\" & res.num = " + repr(res_num) + "'") 
50          self.commands.append("StyleBond neon") 
51          self.commands.append("RadiusBond " + repr(width)) 
52          self.commands.append("ColorBond " + repr(rgb_array[0]) + " " + repr(rgb_array[1]) + " " + repr(rgb_array[2])) 
53   
54          # Blank line. 
55          self.commands.append("") 
56   
57   
58 -    def classic_header(self): 
59          """Create the header for the molmol macro.""" 
60   
61          # Hide all bonds. 
62          self.commands.append("SelectBond ''") 
63          self.commands.append("StyleBond invisible") 
64   
65          # Show the backbone bonds as lines. 
66          self.commands.append("SelectBond 'bb'") 
67          self.commands.append("StyleBond line") 
68   
69          # Colour the backbone black. 
70          self.commands.append("ColorBond 0 0 0") 
71   
72   
73 -    def molmol_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