/usr/lib/python2.7/dist-packages/chempy/tinker/keyword.py is in pymol 1.8.4.0+dfsg-1build1.
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 | #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:
#-* Scott Dixon, Metaphorics, LLC
#-*
#-*
#Z* -------------------------------------------------------------------
from __future__ import print_function
import chempy
def get_partial_charge(model):
if chempy.feedback['verbose']:
print(' '+str(__name__)+': generating partial charge keywords...')
list = []
c = -1
for a in model.atom:
list.append("CHARGE %d %6.4f\n" %(c,a.partial_charge))
c = c - 1
return list
def get_restrain_positions(model,flag,w_width,f_cnst):
list = []
n = 0
c = 1
mask = 1<<flag
for a in model.atom:
if (a.flags&mask):
list.append("RESTRAIN-POSITION %5d %12.6f %12.6f %12.6f %6.3f %6.1f\n" %
(c,a.coord[0],a.coord[1],a.coord[2],w_width,f_cnst))
n = n + 1
c = c + 1
if chempy.feedback['actions']:
print(' '+str(__name__)+': %d atoms restrained using flag %d ...' % (n,flag))
return list
def get_inactive(model,flag):
list = []
n = 0
c = 1
mask = 1<<flag
for a in model.atom:
if (a.flags&mask):
list.append("INACTIVE %d\n" % (c))
n = n + 1
c = c + 1
if chempy.feedback['actions']:
print(' '+str(__name__)+': %d atoms fixed using flag %d ...' % (n,flag))
return list
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