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#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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