Source Code for Module MolKit.pdb2pqr.extensions.chi

 1  """ 
 2      Chi extension 
 3   
 4      Print the backbone chi angle for each residue in the structure. 
 5      Chi angle is determined by the coordinates of the N, CA, CB (if 
 6      available), and CG/OG/SG atoms (if available). 
 7   
 8      Author:  Todd Dolinsky 
 9  """ 
10   
11  __date__ = "17 February 2006" 
12  __author__ = "Todd Dolinsky" 
13   
14  from src.utilities import * 
15  from src.routines import * 
16   
17 -def usage(): 
18      str  = "        --chi         :  Print the per-residue backbone chi\n" 
19      str += "                         angle to {output-path}.chi\n" 
20      return str 
21   
22 -def chi(routines, outroot): 
23      """ 
24          Print the list of psi angles 
25   
26          Parameters 
27              routines:  A link to the routines object 
28              outroot:   The root of the output name 
29      """ 
30   
31      outname = outroot + ".chi" 
32      file = open(outname, "w") 
33   
34      routines.write("\nPrinting chi angles for each residue...\n") 
35      routines.write("Residue     chi\n") 
36      routines.write("----------------\n") 
37       
38      # Initialize some variables 
39   
40      protein = routines.protein 
41   
42      for residue in protein.getResidues(): 
43          if residue.hasAtom("N"): ncoords = residue.getAtom("N").getCoords() 
44          else: continue 
45   
46          if residue.hasAtom("CA"): cacoords = residue.getAtom("CA").getCoords() 
47          else: continue 
48   
49          if residue.hasAtom("CB"): cbcoords = residue.getAtom("CB").getCoords() 
50          else: continue 
51   
52          if residue.hasAtom("CG"): gcoords = residue.getAtom("CG").getCoords() 
53          elif residue.hasAtom("OG"): gcoords = residue.getAtom("OG").getCoords() 
54          elif residue.hasAtom("SG"): gcoords = residue.getAtom("SG").getCoords() 
55          else: continue 
56   
57          chi = getDihedral(ncoords, cacoords, cbcoords, gcoords) 
58          routines.write("%s\t%.4f\n" % (residue, chi)) 
59          file.write("%s\t%.4f\n" % (residue, chi)) 
60           
61      routines.write("\n") 
62      file.close() 
63