Logo Search packages:      
Sourcecode: pymol version File versions

mol.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.models import Indexed
from chempy import Storage,Atom,Bond

import string

class MOL(Storage):

   def fromList(self,molList):

      model = Indexed()

      # read header information
      model.molecule.title = string.strip(molList[0])
      model.molecule.dim_code = string.strip(molList[1][20:22])
      model.molecule.comments = string.strip(molList[2])
      try:
         model.molecule.chiral = int(molList[3][12:15])
      except:
         model.molecule.chiral = 0
      nAtom = int(molList[3][0:3])
      nBond = int(molList[3][3:6])

      # read atoms
      nameDict = {}
      irec = 4
      cnt = 0
      for a in range(nAtom):
         at = Atom()
         at.index = cnt
         at.coord = [float(molList[irec][0:10]), 
            float(molList[irec][10:20]),float(molList[irec][20:30])]
         at.symbol = string.strip(molList[irec][31:33])
         try:
            at.stereo = int(molList[irec][39:42])
         except:
            at.stereo = 0
         chg=int(molList[irec][36:39])
         if chg>0: chg=4-chg
         at.formal_charge = chg
         model.atom.append(at)
         irec = irec + 1
         cnt = cnt + 1

         # read bonds
      for a in range(nBond):
         bnd = Bond()
         bnd.index = [ int(molList[irec][0:3])-1,int(molList[irec][3:6])-1 ]
         bnd.order = int(molList[irec][6:9])
         try:
            bnd.stereo = int(molList[irec][9:12])
         except:
            bnd.stereo = 0
         model.bond.append(bnd)
         irec = irec+1

         # obtain formal charges from M  CHG record
      while molList[irec][0:6]!='M  END':
         if molList[irec][0:6]=='M  CHG':
            cl = string.split(string.strip(molList[irec][6:]))
            cll = int(cl[0])*2
            a=1
            while a<=cll:
               model.atom[int(cl[a])-1].formal_charge=int(cl[a+1])
               a=a+2
         irec =irec+1
         if irec >= len(molList): break

      return model

#------------------------------------------------------------------------------
   def toList(self,model):

      molList = []

      # write header records
      molList.append(model.molecule.title+"\n")
      molList.append("  ChemPy            %2s                             0\n" %
             model.molecule.dim_code)
      molList.append(model.molecule.comments+"\n")
      molList.append("%3d%3d  0  0  %1d  0  0  0  0  0999 V2000\n" %
                     (model.nAtom, model.nBond, model.molecule.chiral))

      # write atom records
      for a in model.atom:
         chg = a.formal_charge
         if chg!=0: chg=4-chg
         molList.append("%10.4f%10.4f%10.4f %-3s 0  %1d  %1d  0  0  0  0  0  0  0  0  0\n" % \
                     (a.coord[0], a.coord[1], a.coord[2], a.symbol, chg, a.stereo))

         # write bond records
      for b in model.bond:
         molList.append("%3d%3d%3d%3d  0  0  0\n" % (b.index[0]+1, 
            b.index[1]+1, b.order,b.stereo))

         # if necessary, write M  CHG records for charged atoms
      charge_atoms = []
      charge_values = []
      for a in model.atom:
         if a.formal_charge != 0:
            charge_atoms.append(a)
      if len(charge_atoms):
         c = 0
         for a in model.atom:
            a.index = c
            c = c + 1
         while len(charge_atoms) != 0:
            chg_set = charge_atoms[0:8]
            charge_atoms = charge_atoms[8:]
            tline = "M  CHG%3d" % (len(chg_set))
            for i in chg_set:
               tline = tline + "%4d%4d" % (i.index+1,i.formal_charge)
            molList.append(tline + "\n")
      molList.append("M  END\n")
      return(molList)



Generated by  Doxygen 1.6.0   Back to index