/usr/lib/python2.7/dist-packages/chempy/gms.py is in pymol 1.8.4.0+dfsg-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 | #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# THIS MODULE IS OBSOLETE PLEASE DO NOT USE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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