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# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
fix_deprecated_elements.py - fix deprecated PAM elements in-place in models
@author: Bruce
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
from model.elements import PeriodicTable
from utilities.constants import diDEFAULT
from utilities import debug_flags
from dna.updater.dna_updater_prefs import pref_fix_deprecated_PAM3_atoms
from dna.updater.dna_updater_prefs import pref_fix_deprecated_PAM5_atoms
from dna.updater.dna_updater_prefs import dna_updater_warn_when_transmuting_deprecated_elements
import foundation.env as env
from utilities.Log import orangemsg
from utilities.constants import MODEL_PAM3, MODEL_PAM5
# ==
def fix_deprecated_elements( changed_atoms):
"""
scan for deprecated elements, and fix them
"""
fix_PAM3 = pref_fix_deprecated_PAM3_atoms()
fix_PAM5 = pref_fix_deprecated_PAM5_atoms()
deprecated_atoms = []
for atom in changed_atoms.itervalues():
deprecated_to = atom.element.deprecated_to
# an element symbol, or None, or 'remove'
if deprecated_to:
pam = atom.element.pam
assert pam in (MODEL_PAM3, MODEL_PAM5)
if pam == MODEL_PAM3:
fix = fix_PAM3
elif pam == MODEL_PAM5:
fix = fix_PAM5
else:
fix = False
if fix:
deprecated_atoms.append(atom)
elif debug_flags.DEBUG_DNA_UPDATER:
print "dna updater: debug_pref says don't alter deprecated atom %r" % (atom,)
continue
for atom in deprecated_atoms:
deprecated_to = atom.element.deprecated_to
# an element symbol, or 'remove'
if atom.display != diDEFAULT:
# Atoms of deprecated elements sometimes have funny display modes
# set by the DNA Duplex Generator. Remove these here.
# (This may be needed even after we fix the generator,
# due to old mmp files. REVIEW: can it ever cause harm?)
atom.setDisplayStyle(diDEFAULT)
if deprecated_to == 'remove' or deprecated_to == 'X':
# (Atom.kill might be unideal behavior for 'remove',
# but that's only on Pl3 which never occurs AFAIK, so nevermind)
# Kill the atom (and make sure that new bondpoints get into a good enough position).
# REVIEW: does atom.kill make new bps immediately
# (review whether ok if more than one needs making on one base atom)
# or later
# (review whether it's still going to happen in the current master_updater call)? ####
if debug_flags.DEBUG_DNA_UPDATER_VERBOSE:
print "dna updater: kill deprecated atom %r" % (atom,)
summary_format = \
"Warning: dna updater killed [N] deprecated %s pseudoatom(s)" % \
(atom.element.symbol,)
env.history.deferred_summary_message( orangemsg(summary_format) )
atom.kill()
# TODO: worry about atom being a hotspot, or having a bondpoint which is a hotspot?
else:
# Transmute atom to a new element symbol -- assume its position,
# bonds, and bondpoints are all ok and need no changes.
# (Should be true of as 071119, since this is used only
# to make Ax and Ss PAM atoms from variant atomtypes
# used to mark them as being in special situations.)
#
# Use mvElement to avoid remaking existing bondpoints.
elt = PeriodicTable.getElement(deprecated_to)
if debug_flags.DEBUG_DNA_UPDATER_VERBOSE:
print "dna updater: transmute deprecated atom %r to element %s" % \
(atom, elt.symbol)
if dna_updater_warn_when_transmuting_deprecated_elements():
summary_format = \
"Warning: dna updater transmuted [N] %s to %s pseudoatom(s)" % \
(atom.element.symbol, elt.symbol )
env.history.deferred_summary_message( orangemsg(summary_format) )
# todo: refactor so orangemsg is replaced with a warning option
atom.mvElement(elt)
atom.make_enough_bondpoints()
# REVIEW: do this later, if atom classes should be corrected first
# to help this properly position bondpoints
# (or perhaps, first set correct atom classes, then do this,
# making sure it sets correct bondpoint classes,
# or that we correct them separately afterwards)
continue
return # from fix_deprecated_elements
# end
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