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xyz.py

#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific. 
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove this copyright notice.
#F* -------------------------------------------------------------------
#G* Please see the accompanying LICENSE file for further information. 
#H* -------------------------------------------------------------------
#I* Additional authors of this source file include:
#-* 
#-* 
#-*
#Z* -------------------------------------------------------------------

from chempy import Storage,Atom,feedback
from chempy.models import Indexed,Connected
import string
import copy

generics =  {
   'CT' : 1,
   'C'  : 2,
   'CA' : 3,
   'CM' : 4,
   'CC' : 5,
   'CV' : 6,
   'CW' : 7,
   'CR' : 8,
   'CB' : 9,
   'C*' : 10,
   'CN' : 11,
   'CK' : 12,
   'CQ' : 13,
   'N'  : 14,
   'NA' : 15,
   'NB' : 16,
   'NC' : 17,
   'N*' : 18,
   'N2' : 19,
   'N3' : 20,
   'OW' : 21,
   'OH' : 22,
   'OS' : 23,
   'O'  : 24,
   'O2' : 25,
   'S'  : 26,
   'SH' : 27,
   'P'  : 28,
   'H'  : 29,
   'HW' : 30,
   'HO' : 31,
   'HS' : 32,
   'HA' : 33,
   'HC' : 34,
   'H1' : 35,
   'H2' : 36,
   'H3' : 37,
   'HP' : 38,
   'H4' : 39,
   'H5' : 40,
}

class XYZ(Storage):
   
#------------------------------------------------------------------------------
   def toList(self,model,mapping=None):

      conn = copy.deepcopy(model)
      conn = conn.convert_to_connected()
      
      list = []

      if len(model.atom):
         if not model.atom[0].has('numeric_type'):
            if not mapping:
               mapping = generics
               if feedback['warnings']:
                  print ' '+str(self.__class__)+': no numeric atom types found, using defaults.'
         list.append("%6d\n" % conn.nAtom)
         c = 0
         for a in conn.atom:
            if mapping:
               n_type = mapping[a.text_type]
            else:
               n_type = a.numeric_type
            if n_type<0:
               print str(self.__class__)+\
                     '-WARNING: negative numeric type (%d) for atom %d'% (n_type,c)
            st = "%6d  %-3s%12.6f%12.6f%12.6f%6d" % (
               c+1,a.text_type,a.coord[0],a.coord[1],a.coord[2],int(n_type))
            for b in conn.bond[c]:
               idx = b.index[0]
               if idx == c:
                  idx = b.index[1]
               st = st + "%6d" % (idx+1)
            st = st + "\n"
            list.append(st)
            c = c + 1
      return(list)

#----------------------------------------------------------------------------
   def updateFromList(self,model,list):

      c = 0
      for a in list[1:]:
         model.atom[c].coord = [ float(a[11:23]),float(a[23:35]),float(a[35:47])]
         c = c + 1


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