/usr/lib/python2.7/dist-packages/chempy/mol.py is in pymol 1.7.2.1-1.
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 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 | #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
try:
from pymol import CmdException
except ImportError:
CmdException = Exception
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):
if len(model.atom) > 999:
raise CmdException("Cannot write file, too many atoms for MOL format: %d > 999." % len(model.atom))
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)
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