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gms.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

#
# THIS MODULE IS OBSOLETE PLEASE DO NOT USE
#

import string

atNum = {
   'H'  : 1,
   'C'  : 6,
   'N'  : 7,
   'O'  : 8,
   'F'  : 9,
   'P'  : 15,
   'S'  : 16,
   'Cl' : 17,
   'Br' : 35,
   'I'  : 53,
   }

class GMS(Storage):

   def toList(self,model,runtyp='OPTIMIZE',exetyp='RUN',
              gbasis='N31',ngauss=6,ndfunc=1,dirscf=1):

         
      gmsList = []

      # write header records

      nzvar = (model.nAtom*3)-6
      chg = 0
      for a in model.atom:
         chg = chg + a.formal_charge
      chg = int(chg)
      if chg==0:
         icharg=''
         diffsp=''
      else:
         icharg='ICHARG=%d' % chg
         if chg<0:
            diffsp='DIFFSP=.TRUE.'
         else:
            diffsp=''
      gmsList.append(
         " $CONTRL RUNTYP=%s COORD=UNIQUE EXETYP=%s NZVAR=%d %s $END\n" % 
         (runtyp,exetyp,nzvar,icharg))
      if ndfunc>0:
         gmsList.append(" $BASIS GBASIS=%s NGAUSS=%d NDFUNC=%d %s $END\n" %
                        (gbasis,ngauss,ndfunc,diffsp))
      else:
         gmsList.append(" $BASIS GBASIS=%s NGAUSS=%d %s $END\n",
                        (gbasis,ngauss,diffsp))
      if dirscf:
         gmsList.append(" $SCF DIRSCF=.TRUE. $END\n")
      gmsList.append(" $DATA\n")
      gmsList.append(model.molecule.title+" 6-31G* optimization\n")
      gmsList.append("C1\n")

      # write atom records in an ordering compatible with internal
      # coordinate generation
      c = 1
      for z in model.get_internal_tuples():
         a = model.atom[z[0]]
         if not len(a.name):
            name = a.symbol + "%02d"%c
         else:
            name = a.name
         gmsList.append("%4s %5.2f %12.6f %12.6f %12.6f\n" %
                        (name,atNum[a.symbol],a.coord[0],
                         a.coord[1],a.coord[2]))
         c = c + 1
      gmsList.append(" $END\n")
      gmsList.append(" $ZMAT DLC=.TRUE. AUTO=.TRUE. $END\n")
      if runtyp=='OPTIMIZE':
         gmsList.append(" $STATPT NPRT=-2 NPUN=-2 NSTEP=50 $END\n")
      gmsList.append(" $ELPOT IEPOT=1 WHERE=PDC $END\n")
      gmsList.append(" $PDC PTSEL=GEODESIC CONSTR=CHARGE $END\n")
                     
      return(gmsList)








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