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# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
delete_bare_atoms.py - delete atoms lacking required neighbors
@author: Bruce
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
from dna.updater.dna_updater_prefs import pref_fix_bare_PAM3_atoms
from dna.updater.dna_updater_prefs import pref_fix_bare_PAM5_atoms
from dna.model.PAM_atom_rules import PAM_atoms_allowed_in_same_ladder
from model.elements import Pl5
from utilities.constants import MODEL_PAM3, MODEL_PAM5
import foundation.env as env
from utilities.Log import orangemsg
# ==
def delete_bare_atoms( changed_atoms): # rename; also make not delete, just error (### need to review error propogation system)
"""
Delete excessively-bare atoms (defined as axis atoms without strand atoms,
or any other PAM atoms that are not allowed to exist with as few neighbors
as they have -- note that the rules for strand atoms are in flux as of
080117 since the representation of single-stranded DNA is as well).
[must tolerate killed atoms; can kill more atoms and break bonds;
can record more changes to neighbors of deleted atoms]
"""
# Q. Which changes recorded by our side effects are needed in subsequent
# dna updater steps?
# A. The changed neighbor atoms are needed, in case they're the only
# indicator of a change to the chain they're on (especially if the killed
# atom was in a different dna ladder). But their classes needn't be changed,
# and their deletion can't cause any more atoms to become bare (due to
# the current meaning of bare), so no earlier updater steps need to be
# repeated.
# Note: if these debug prefs are not both True, errors might occur in the
# dna updater. The goal is for these errors to be harmless (just debug
# prints). As of 071205 the defaults are True, False, respectively.
# TODO: revise following code to debug-print when these prefs make it
# refrain from killing a bare atom (giving a count, per PAM model).
fix_PAM3 = pref_fix_bare_PAM3_atoms()
fix_PAM5 = pref_fix_bare_PAM5_atoms()
delete_these_atoms = [] # change to mark them as errors
fix_these_bonds = {} # id(bond) -> bond
for atom in changed_atoms.itervalues():
pam = atom.element.pam
if pam: # optimization
if (pam == MODEL_PAM3 and fix_PAM3) or \
(pam == MODEL_PAM5 and fix_PAM5):
if not atom.killed():
if atom_is_bare(atom):
delete_these_atoms.append(atom)
else:
# Do something about rung bonds between mismatched PAM atoms
# (in pam model or pam3+5 properties)
# [bruce 080405 new feature, for PAM3+5 safety]
# Note: if this kills bonds, we'd need to do that first,
# then recheck atom_is_bare (or always check it later).
# But it doesn't.
#
#update 080407: maybe this is not necessary:
# - we could permit these mismatches until DnaLadders
# are formed, then fix them much more easily;
# - or we could even permit them then
# (each rail would be uniform within itself),
# with a little extra complexity in PAM conversion,
# but it might even be useful to display "one strand
# in PAM5", for example.
# So for now, I won't finish this code here, though I'll
# leave it in for long enough to see if it prints
# anything; then it should be removed, in case it's
# slow. ##### @@@@@
for bond in atom.bonds:
if bond.is_rung_bond():
if not PAM_atoms_allowed_in_same_ladder(bond.atom1, bond.atom2):
fix_these_bonds[id(bond)] = bond
for bond in fix_these_bonds.values():
# REVIEW: can one of its atoms be in delete_these_atoms?
# (probably doesn't matter even if it is)
print "*** need to fix this bad rung bond (nim, so bugs will ensue): %r" % bond #####
# pam model mismatch: mark them as errors, so not in any chains or ladders
# pam option mismatch: reset options to default on all chunks connected by rung bonds (or could mark as errors)
# other (if possible) (eg display styles, if that matters) --
# those differences would be ok here, only matters along axis
# (we'll make the func distinguish this if it ever looks at those)
#
# no need to be fast, this only happens for rare errors
a1, a2 = bond.atom1, bond.atom2
if a1.element.pam != a2.element.pam:
# since it's a rung bond, we know the pams are both set
print " nim: mark as errors", a1, a2 ## NIM here, look up how other code does it before propogation
elif a1.molecule.display_as_pam != a2.molecule.display_as_pam or \
a1.molecule.save_as_pam != a2.molecule.save_as_pam:
# transclose to find chunks connected by rung bonds, put in a dict, reset pam props below
print " nim: reset pam props starting at", a1, a2
continue
for atom in delete_these_atoms:
#bruce 080515: always emit a deferred_summary_message,
# since it can seem like a bug otherwise
# (review this, if it happens routinely)
summary_format = \
"Warning: dna updater deleted [N] \"bare\" %s pseudoatom(s)" % \
( atom.element.symbol, )
env.history.deferred_summary_message( orangemsg(summary_format) )
atom.kill()
return
def atom_is_bare(atom): # fyi: only used in this file as of 080312; ### REVIEW [080320]: better to mark as errors, not delete?
"""
Is atom an axis atom with no axis-strand bonds,
or (IF this is not allowed -- as of 080117 it *is* allowed)
a strand base atom with no strand-axis bonds,
or any other PAM atom with illegally-few neighbor atoms
of the types it needs?
(Note that a strand non-base atom, like Pl, can never be
considered bare by this code.)
"""
if atom.element.role == 'axis':
strand_neighbors = filter(lambda other: other.element.role == 'strand', atom.neighbors())
return not strand_neighbors
elif atom.element.role == 'strand' and not atom.element is Pl5:
return False # bruce 080117 revision, might be temporary --
# but more likely, we'll replace it with some "bigger fix"
# like adding Ub (or we might just do that manually later
# and allow this with no change in old files)
## axis_neighbors = filter(lambda other: other.element.role == 'axis', atom.neighbors())
## return not axis_neighbors
elif atom.element.role == 'unpaired-base':
# guess, bruce 080117
strand_neighbors = filter(lambda other: other.element.role == 'strand', atom.neighbors())
return not strand_neighbors
else:
return False
pass
# end
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