Package Pmv :: Module pmvPalettes
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Source Code for Module Pmv.pmvPalettes

 1  # 
 2  # $Header: /opt/cvs/python/packages/share1.5/Pmv/pmvPalettes.py,v 1.3 2006/06/13 22:06:16 vareille Exp $ 
 3  # 
 4  # $Id: pmvPalettes.py,v 1.3 2006/06/13 22:06:16 vareille Exp $ 
 5  # 
 6   
 7  RasmolAmino = { 'ALA':(.781, 0.781, 0.781), 'ARG':(0.078, 0.352, 0.999), 
 8                  'ASN':(0.,.898, 0.898), 'ASP':(0.898, 0.039, 0.039), 
 9                  'CYS':(0.898, 0.898, 0.0), 'GLN':(0.,0.898, 0.898),  
10                  'GLU':(0.898, 0.039, 0.039), 
11                  'GLY':(0.918, 0.918, 0.918), 
12                  'HIS':(0.508, 0.508, 0.820), 
13                  'ILE':(0.059, 0.508, 0.059), 
14                  'LEU':(0.059, 0.508, 0.059), 
15                  'LYS':(0.078, 0.352, 0.999), 
16                  'MET':(0.898, 0.898, 0.0), 'PHE':(0.195, 0.195, 0.664), 
17                  'PRO':(0.859, 0.586, 0.508), 'SER':(0.977,0.586,0.), 
18                  'THR':(0.977,0.586,0.0), 'TRP':(0.703,0.352,0.703), 
19                  'TYR':(0.195,0.195,0.664), 'VAL':(0.059,0.508,0.059) } 
20   
21  RasmolAminoSortedKeys = [ 'ALA', 'GLY', 'PRO', 'LEU', 'ILE', 'VAL', 
22                            'MET', 'CYS', 'THR', 'SER', 'GLU', 'ASP', 'TRP',  
23                           'HIS','GLN', 'ASN', 'ARG', 'LYS', 'TYR', 'PHE' ] 
24   
25  AtomElements = { 'N':(0.,0.,1.), 'C':(.7,.7,.7), 'O':(1.,0.,0.), 
26                   'H':(0.,1.,1.), 'S':(1.,1.,0.), 'CA':(1.,0.,1.), 
27                   'P':(1.,0.,1.), 'A':(0.,1.,0.) } 
28   
29  DavidGoodsell = { 'N':(0.7,0.7,1.), 'C':(1.,1.,1.), 'O':(1.0,.7,.7), 
30                    'H':(1.,1.,1.), 'HN':(0.7,0.7,1.0),  
31                    'S':(0.9,0.85,0.1), 'ASPOD1':(1.,0.2,0.2), 
32                    'ASPOD2':(1.,0.2,0.2), 'GLUOE1':(1.,0.2,0.2), 
33                    'GLUOE2':(1.,0.2,0.2), 'SERHG':(1.0,.7,.7), 
34                    'THRHG1':(1.0,.7,.7), 'TYROH':(1.0,.7,.7), 
35                    'TYRHH':(1.0,.7,.7), 'LYSNZ':(0.2,0.3,1.0),  
36                    'LYSHZ1':(0.2,0.3,1.0), 'LYSHZ2':(0.2,0.3,1.0),  
37                    'LYSHZ3':(0.2,0.3,1.0), 'ARGNE':(0.2,0.3,1.0), 
38                    'ARGNH1':(0.2,0.3,1.0), 'ARGNH2':(0.2,0.3,1.0), 
39                    'ARGHH11':(0.2,0.3,1.0), 'ARGHH12':(0.2,0.3,1.0),  
40                    'ARGHH21':(0.2,0.3,1.0), 'ARGHH22':(0.2,0.3,1.0),  
41                    'ARGHE':(0.2,0.3,1.0),  
42                    'GLNHE21':(0.7,0.7,1.0), 'GLNHE22':(0.7,0.7,1.0), 
43                    'ASNHD21':(0.7,0.7,1.0), 'ASNHD22':(0.7,0.7,1.0), 
44                    'HISHD1':(0.7,0.7,1.0), 'HISHE2':(0.7,0.7,1.0), 
45                    'GLNHE2':(0.7,0.7,1.0),'ASNHD2':(0.7,0.7,1.0), 
46                    'CYSHG':(0.9,0.85,0.1), 'HH':(1.,1.,1.) } 
47  DavidGoodsellSortedKeys = [ 
48      'C', 'HN', 'HH', 'H', 'O', 'SERHG', 'TYROH', 'TYRHH', 'THRHG1', 
49      'N', 'ASNHD21', 'ASNHD22', 'GLNHE21', 'GLNHE22', 'GLNHE2', 'ASNHD2', 
50      'HISHE2', 'HISHD1', 'S', 'CYSHG', 'GLUOE1', 'GLUOE2', 'ASPOD1', 
51      'ASPOD2', 'LYSNZ', 'LYSHZ1', 'LYSHZ2','LYSHZ3','ARGNE', 'ARGNH1', 'ARGNH2', 
52      'ARGHH11','ARGHH12','ARGHH21','ARGHH22','ARGHE', ] 
53   
54  SecondaryStructureSides = { 'up': (1., 0., 0.), 'down': (0., 1., 0.), 
55                              'left': (0., 0., 1.), 
56                              'right': (0., 0., 1.) } 
57   
58  SecondaryStructureType = {'Helix': (0.937, 0.0, 0.5), 
59                            'Strand': (1.0, 1.0, 0.0), 
60                            'Turn': (0.375, .5, 1.0), 
61                            'Coil': (1.0, 1.0, 1.0) } 
62   
63  Shapely = { 'ALA':(0.117, 0.703, 0.117), 'ARG':(0.222, 0.222, 0.406), 
64              'ASN':(0.734, 0.558, 0.558), 'ASP':(0.996, 0.117, 0.117), 
65              'CYS':(0.996, 0.996, 0.000), 'GLN':(0.996, 0.558, 0.558),  
66              'GLU':(0.703, 0.078, 0.039), 'GLY':(0.937, 0.937, 0.937), 
67              'HIS':(0.390, 0.757, 0.996), 'ILE':(0.183, 0.308, 0.183), 
68              'LEU':(0.417, 0.554, 0.136), 'LYS':(0.195, 0.195, 0.996), 
69              'MET':(0.578, 0.578, 0.066), 'PHE':(0.722, 0.281, 0.242), 
70              'PRO':(0.750, 0.750, 0.750), 'SER':(0.996, 0.484, 0.054), 
71              'THR':(0.996, 0.328, 0.054), 'TRP':(0.429, 0.105, 0.097), 
72              'TYR':(0.855, 0.574, 0.437), 'VAL':(0.000, 0.996, 0.000) } 
73   
74  #Rainbow= {0: (0.,0.,1.),  1: (0.,1.,0.), 2: (1.,0.,0.), 
75  #          3: (0.,1.,1.),  4: (1.,1.,0.), 5: (1.,0.,1.), 
76  #          6: (0.,.75,1.), 7: (0.,1.,.5), 8: (.6,1.,0.), 
77  #          9: (1.,.5,0.), 10: (1.,0.,.5), 11:(.5,0.,1.), 
78  #          12:(.5,0.,.2), 13: (0.,.5,.2), 14:(0.75,0,1), 
79  #          15:(1.,0.75,0),16:(1.,0.,0.75,),17:(0., 1., .75), 
80  #          18:(1.,0.,0.25,), 19: (0.,.5,1.)} 
81  #                     
82  #RainbowSortedKey = [0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19] 
83   
84  Rainbow= {'0': (0.,0.,1.),  '1': (0.,1.,0.), '2': (1.,0.,0.), 
85            '3': (0.,1.,1.),  '4': (1.,1.,0.), '5': (1.,0.,1.), 
86            '6': (0.,.75,1.), '7': (0.,1.,.5), '8': (.6,1.,0.), 
87            '9': (1.,.5,0.), '10': (1.,0.,.5), '11':(.5,0.,1.), 
88            '12':(.5,0.,.2), '13': (0.,.5,.2), '14':(0.75,0,1), 
89            '15':(1.,0.75,0),'16':(1.,0.,0.75,),'17':(0., 1., .75), 
90            '18':(1.,0.,0.25,), '19': (0.,.5,1.)} 
91                       
92  RainbowSortedKey = ['0','1','2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19'] 
93