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# Copyright 2004-2009 Nanorex, Inc. See LICENSE file for details.
"""
move_atoms_and_normalize_bondpoints.py -- post-simulation helper function
@author: Josh, Bruce
@version: $Id$
@copyright: 2004-2009 Nanorex, Inc. See LICENSE file for details.
History:
090112 renamed from move_alist_and_snuggle, moved into new file from chem.py
"""
from geometry.VQT import A
def move_atoms_and_normalize_bondpoints(alist, newPositions):
"""
Move the atoms in alist to the new positions in the given array or sequence
(which must have the same length);
then for any singlets in alist, correct their positions using Atom.snuggle.
@warning: it would be wrong to call this on several alists in a row if they
might overlap or were connected by bonded atoms, for the same
reason that the snuggle has to be done in a separate loop
(see snuggle docstring for details, re bug 1239).
@warning: I'm not sure this does all required invals; doesn't do gl_update.
"""
#bruce 051221 split this out of class Movie so its bug1239 fix can be used
# in jig_Gamess. [later: Those callers have duplicated code which should be
# cleaned up.]
#bruce 090112 renamed from move_alist_and_snuggle
#todo: refile into a new file in operations package
assert len(alist) == len(newPositions)
singlets = []
for a, newPos in zip(alist, newPositions):
#bruce 050406 this needs a special case for singlets, in case they are H
# in the xyz file (and therefore have the wrong distance from their base
# atom). Rather than needing to know whether or not they were H during
# the sim, we can just regularize the singlet-baseatom distance for all
# singlets. For now I'll just use setposn to set the direction and
# snuggle to fix the distance.
# REVIEW: should it also regularize the distance for H itself? Maybe
# only if sim value is wildly wrong, and it should also complain.
# I won't do this for now.
a.setposn(A(newPos))
if a.is_singlet(): # same code as in movend()
#bruce 051221 to fix bug 1239: do all snuggles after all moves;
# see snuggle docstring warning
singlets.append(a)
continue
for a in singlets:
a.snuggle() # includes a.setposn
return
# end
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