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# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
fix_atom_classes.py - fix classes of PAM atoms
@author: Bruce
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
from dna.updater.dna_updater_utils import replace_atom_class
from model.chem import Atom
StrandAtom = Atom # stub
AxisAtom = Atom # stub
UnpairedBaseAtom = Atom # stub
##issues: bondpoint classes. need a separate func to fix them later?
##which ones do we fix, all new bps and all bps on changed atoms? (yes)
##for all these, fix all bps on on base at once, so store base in a dict
##after all transmutes and breaks.
##
##other issues:
## Atom vs ChemAtom
## code on Atom or on Element?
## or Atomtype?
##
##guess: as we fix atoms colect bps and their base atoms into sep dict
##when it's full, incl of busted bonds,
##then fix all the bps of those base atoms.
##using a separate func, to fix bp classes and reposition them too.
##
##so this present code can ignore bps for now.
# ==
# obs cmt?
# Give bondpoints and real atoms the desired Atom subclasses.
# (Note: this can affect bondpoints and real atoms created by earlier steps
# of the same call of this function.)
## atom._f_actual_class_code != atom._f_desired_class_code:
def real_atom_desired_class(atom): #e refile into an Atom method? return classname only?
"""
Which class do we wish a real atom was in, based on its element,
and if it's a bondpoint, on its neighbor atom?
"""
assert not atom.killed()
## if atom.is_singlet():
## # WRONG. true desire is for special atoms to have the right pattern of special bps...
## base = atom.singlet_neighbor()
## assert not base.killed()
## else:
## base = atom
## element = base.element
assert not atom.is_singlet()
element = atom.element
pam = element.pam # MODEL_PAM3 or MODEL_PAM5 or None ### use this?
role = element.role # 'strand' or 'axis' or 'unpaired-base' or None
if role == 'strand':
return StrandAtom # PAM3_StrandAtom? subclass of StrandAtom? What about Pl?
elif role == 'axis':
return AxisAtom
elif role == 'unpaired-base':
return UnpairedBaseAtom
else:
return Atom # ChemAtom?
def fix_atom_classes( changed_atoms): #e rename, real_atom; call differently, see comment above ### @@@
"""
Fix classes of PAM atoms in changed_atoms, ignoring bondpoints
and/or killed atoms.
(Also patch changed_atoms with replaced atoms if necessary.)
"""
for atom in changed_atoms.itervalues():
if not atom.killed() and not atom.is_singlet():
old_class = atom.__class__
## new_class = atom._f_desired_class ### IMPLEM, maybe revise details
new_class = real_atom_desired_class( atom)
if old_class is not new_class:
replace_atom_class( atom, new_class, changed_atoms)
# note: present implem is atom.__class__ = new_class;
# and any implem only changes changed_atoms
# at atom.key (which is unchanged),
# so is legal during itervalues.
continue
return
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