def pref_fix_after_readmmp_after_updaters():
# temporary kluge (since probably not enough to protect this
# from making updater exceptions much worse in effect):
# disable when dna updater is off, to work around bug in that case
# (described in checkin mail today)
# (only needed in "after" version) [bruce 080319]
if not dna_updater_is_enabled():
print "bug: the permanent version of this fix is not working, noticed in pref_fix_after_readmmp_after_updaters"
res = debug_pref("DNA: do fix_after_readmmp_after_updaters? ",
Choice_boolean_True, # same comment as for before_updaters version
## non_debug = True,
prefs_key = True )
return res and dna_updater_is_enabled() # only ok to do this if dna updater is on
def pref_fix_after_readmmp_after_updaters():
# temporary kluge (since probably not enough to protect this
# from making updater exceptions much worse in effect):
# disable when dna updater is off, to work around bug in that case
# (described in checkin mail today)
# (only needed in "after" version) [bruce 080319]
if not dna_updater_is_enabled():
print "bug: the permanent version of this fix is not working, noticed in pref_fix_after_readmmp_after_updaters"
res = debug_pref(
"DNA: do fix_after_readmmp_after_updaters? ",
Choice_boolean_True, # same comment as for before_updaters version
## non_debug = True,
prefs_key=True)
return res and dna_updater_is_enabled(
) # only ok to do this if dna updater is on
def __init__(self, mapping, chunk):
# immediately memoize some settings which need to be constant
# during use, as a bug precaution. Also do whatever precomputes
# are convenient.
writemmp_mapping_memo.__init__(self, mapping)
self.chunk = chunk
self.ladder = chunk.ladder
if not dna_updater_is_enabled():
msg = "Warning: can't convert PAM model when dna updater is disabled; affects [N] chunk(s)"
env.history.deferred_summary_message( orangemsg( msg))
elif not self.ladder:
# (might happen if dna updater is turned off at runtime -- not sure;
# note, doing that might have worse effects, like self.ladder existing
# but being out of date, causing traceback errors. #### FIX those sometime (elsewhere).)
print "error: ladder not set during writemmp, can't convert pam model, in %r" % chunk
msg = "Error: [N] chunk(s) don't have ladders set"
env.history.deferred_summary_message( redmsg( msg))
else:
self.convert_pam_enabled = True
if self.convert_pam_enabled:
# Note: this only means conversion is possible -- we don't yet know
# if it's requested by options on this mapping and chunk.
# The ladder memo will decide that.
self._ladder_memo = mapping.get_memo_for(self.ladder)
self._save_as_pam = self._ladder_memo._f_save_as_what_PAM_model()
return
def __init__(self, mapping, chunk):
# immediately memoize some settings which need to be constant
# during use, as a bug precaution. Also do whatever precomputes
# are convenient.
writemmp_mapping_memo.__init__(self, mapping)
self.chunk = chunk
self.ladder = chunk.ladder
if not dna_updater_is_enabled():
msg = "Warning: can't convert PAM model when dna updater is disabled; affects [N] chunk(s)"
env.history.deferred_summary_message(orangemsg(msg))
elif not self.ladder:
# (might happen if dna updater is turned off at runtime -- not sure;
# note, doing that might have worse effects, like self.ladder existing
# but being out of date, causing traceback errors. #### FIX those sometime (elsewhere).)
print "error: ladder not set during writemmp, can't convert pam model, in %r" % chunk
msg = "Error: [N] chunk(s) don't have ladders set"
env.history.deferred_summary_message(redmsg(msg))
else:
self.convert_pam_enabled = True
if self.convert_pam_enabled:
# Note: this only means conversion is possible -- we don't yet know
# if it's requested by options on this mapping and chunk.
# The ladder memo will decide that.
self._ladder_memo = mapping.get_memo_for(self.ladder)
self._save_as_pam = self._ladder_memo._f_save_as_what_PAM_model()
return
def __init__(self, mapping, ladder):
# assume never created except by chunks, so we know dna updater is enabled
writemmp_mapping_memo.__init__(self, mapping)
assert dna_updater_is_enabled()
self.ladder = ladder
self.save_as_pam = self._compute_save_as_pam()
self.wrote_axis_chunks = [] # public attrs
self.wrote_strand_chunks = []
return
def __init__(self, mapping, ladder):
# assume never created except by chunks, so we know dna updater is enabled
writemmp_mapping_memo.__init__(self, mapping)
assert dna_updater_is_enabled()
self.ladder = ladder
self.save_as_pam = self._compute_save_as_pam()
self.wrote_axis_chunks = [] # public attrs
self.wrote_strand_chunks = []
return
def initialize():
"""
Register one or more related post_event_model_updaters
(in the order in which they should run). These will be
run by env.do_post_event_updates().
"""
if dna_updater_is_enabled():
## from dna_updater import dna_updater_init
## dna_updater_init.initialize()
_ensure_ok_to_call_dna_updater() # TODO: replace with the commented out 2 lines above
env.register_post_event_model_updater( _master_model_updater)
return
def initialize():
"""
Register one or more related post_event_model_updaters
(in the order in which they should run). These will be
run by env.do_post_event_updates().
"""
if dna_updater_is_enabled():
## from dna_updater import dna_updater_init
## dna_updater_init.initialize()
_ensure_ok_to_call_dna_updater(
) # TODO: replace with the commented out 2 lines above
env.register_post_event_model_updater(_master_model_updater)
return
def _run_dna_updater(): #bruce 080210 split this out
# TODO: check some dicts first, to optimize this call when not needed?
# TODO: zap the temporary function calls here
#bruce 080319 added sets of status_of_last_dna_updater_run
if dna_updater_is_enabled():
# never implemented sufficiently: if ...: _reload_dna_updater()
_ensure_ok_to_call_dna_updater() # soon will not be needed here
from dna.updater.dna_updater_main import full_dna_update
# soon will be toplevel import
global_model_changedicts.status_of_last_dna_updater_run = LAST_RUN_IS_ONGOING
try:
full_dna_update()
except:
global_model_changedicts.status_of_last_dna_updater_run = LAST_RUN_FAILED
msg = "\n*** exception in dna updater; will attempt to continue"
print_compact_traceback(msg + ": ")
msg2 = "Error: exception in dna updater (see console for details); will attempt to continue"
env.history.message(redmsg(msg2))
else:
global_model_changedicts.status_of_last_dna_updater_run = LAST_RUN_SUCCEEDED
pass
else:
global_model_changedicts.status_of_last_dna_updater_run = LAST_RUN_DIDNT_HAPPEN
return
def _run_dna_updater(): #bruce 080210 split this out
# TODO: check some dicts first, to optimize this call when not needed?
# TODO: zap the temporary function calls here
#bruce 080319 added sets of status_of_last_dna_updater_run
if dna_updater_is_enabled():
# never implemented sufficiently: if ...: _reload_dna_updater()
_ensure_ok_to_call_dna_updater() # soon will not be needed here
from dna.updater.dna_updater_main import full_dna_update
# soon will be toplevel import
global_model_changedicts.status_of_last_dna_updater_run = LAST_RUN_IS_ONGOING
try:
full_dna_update()
except:
global_model_changedicts.status_of_last_dna_updater_run = LAST_RUN_FAILED
msg = "\n*** exception in dna updater; will attempt to continue"
print_compact_traceback(msg + ": ")
msg2 = "Error: exception in dna updater (see console for details); will attempt to continue"
env.history.message(redmsg(msg2))
else:
global_model_changedicts.status_of_last_dna_updater_run = LAST_RUN_SUCCEEDED
pass
else:
global_model_changedicts.status_of_last_dna_updater_run = LAST_RUN_DIDNT_HAPPEN
return
def make_or_remove_crossover(twoPls, make=True, cmdname=None):
"""
Make or Remove (according to make option) a crossover, given Pl5_recognizers for its two Pl atoms.
"""
# What we are doing is recognizing one local structure and replacing it with another
# made from the same atoms. It'd sure be easier if I could do the manipulation in an mmp file,
# save that somewhere, and read those to generate the operation! I'd have two sets of atoms, before and after,
# and see how bonds and atomtypes got changed.
# In this case it's not too hard to hand-code... I guess only the Pl atoms and their bonds are affected.
# We probably do have to look at strand directions -- hmm, probably we should require them to exist before saying it's ok!
# Or maybe better to give history error message when the command is chosen, saying you need to set them (or repair them) first...
# Then we have to move the new/moved Pl atoms into a good position...
# Note: Pl.ordered_bases are ordered by bond direction, to make this easier...
# but if we want to patch up the directions in the end, do we need to care exactly which ones were defined?
# or only "per-Pl"? hmm... it's per-Pl for now
assert cmdname
for pl in twoPls:
if pl.ordered_bases is None: # should no longer be possible -- now checked before menu commands are offered [bruce 070604]
###BUG: this could have various causes, not only the one reported below! Somehow we need access to the
# message supplied to the RecognizerError, for use here.
###REVIEW: Does that mean it should pass through compute methods (probably in a controlled way)
# rather than making computed values None?
# Or, should the value not be None, but a "frozen" examinable and reraisable version of the error exception??
msg = "%s: Error: bond direction is locally undefined or inconsistent around %s" % (
cmdname, pl.atom) ###UNTESTED
print "should no longer be possible:", msg #bruce 070604
env.history.message(redmsg(quote_html(msg)))
return
Pl1, Pl2 = twoPls
a, b = Pl1.ordered_bases
d, c = Pl2.ordered_bases # note: we use d,c rather than c,d so that the atom arrangement is as shown in the diagram below.
# Note: for either the Make or Remove operation, the geometric arrangement is initially:
#
# c <-- Pl2 <-- d
#
# a --> Pl1 --> b
#
# and it ends up being (where dots indicate arrowheads, to show bond direction):
#
# c d
# . /
# \ .
# Pl1 Pl2
# . \
# / .
# a b
#
# Note: Pl1 stays attached to a, and Pl2 to d. Which two opposite bonds to preserve like that
# is an arbitrary choice -- as long as Make and Remove make the same choice about that,
# they'll reverse each other's effects precisely (assuming the sugars were initially correct as Ss or Sj).
# break the bonds we no longer want
for obj1, obj2 in [(Pl1, b), (Pl2, c)]:
bond = find_bond(obj1.atom, obj2.atom)
bond.bust(make_bondpoints=False)
# make the bonds we want and didn't already have
for obj1, obj2 in [(Pl1, c), (Pl2, b)]:
assert not atoms_are_bonded(obj1.atom, obj2.atom)
###e we should make bond_atoms do this assert itself, or maybe tolerate it (or does it already??)
bond_atoms_faster(obj1.atom, obj2.atom, V_SINGLE)
# set directions of all 4 bonds (even the preserved ones -- it's possible they were not set before,
# if some but not all bonds had directions set in the part of a strand whose directions we look at.)
for obj1, obj2 in [(a, Pl1), (Pl1, c), (d, Pl2), (Pl2, b)]:
bond = find_bond(obj1.atom, obj2.atom)
bond.set_bond_direction_from(obj1.atom, 1)
# WARNING: after that bond rearrangement, don't use our Pl5_recognizers in ways that depend on Pl bonding,
# since it's not well defined whether they think about the old or new bonding to give their answers.
Pl_atoms = Pl1.atom, Pl2.atom
del Pl1, Pl2, twoPls
# transmute base sugars to Sj or Ss as appropriate
if dna_updater_is_enabled():
want = Element_Ss5 #bruce 080320 bugfix
else:
want = make and Element_Sj5 or Element_Ss5
for obj in (a, b, c, d):
obj.atom.Transmute(want)
# Note: we do this after the bond making/breaking so it doesn't add singlets which mess us up.
# move Pl atoms into better positions
# (someday, consider using local minimize; for now, just place them directly between their new neighbor atoms,
# hopefully we leave them selected so user can easily do their own local minimize.)
for pl in Pl_atoms:
pl.setposn(
average_value(map(lambda neighbor: neighbor.posn(),
pl.neighbors())))
env.history.message(
greenmsg(cmdname + ": ") + quote_html("(%s - %s)" % tuple(Pl_atoms)))
#e need assy.changed()? evidently not.
return # from make_or_remove_crossover
def make_or_remove_crossover(twoPls, make = True, cmdname = None):
"""
Make or Remove (according to make option) a crossover, given Pl5_recognizers for its two Pl atoms.
"""
# What we are doing is recognizing one local structure and replacing it with another
# made from the same atoms. It'd sure be easier if I could do the manipulation in an mmp file,
# save that somewhere, and read those to generate the operation! I'd have two sets of atoms, before and after,
# and see how bonds and atomtypes got changed.
# In this case it's not too hard to hand-code... I guess only the Pl atoms and their bonds are affected.
# We probably do have to look at strand directions -- hmm, probably we should require them to exist before saying it's ok!
# Or maybe better to give history error message when the command is chosen, saying you need to set them (or repair them) first...
# Then we have to move the new/moved Pl atoms into a good position...
# Note: Pl.ordered_bases are ordered by bond direction, to make this easier...
# but if we want to patch up the directions in the end, do we need to care exactly which ones were defined?
# or only "per-Pl"? hmm... it's per-Pl for now
assert cmdname
for pl in twoPls:
if pl.ordered_bases is None: # should no longer be possible -- now checked before menu commands are offered [bruce 070604]
###BUG: this could have various causes, not only the one reported below! Somehow we need access to the
# message supplied to the RecognizerError, for use here.
###REVIEW: Does that mean it should pass through compute methods (probably in a controlled way)
# rather than making computed values None?
# Or, should the value not be None, but a "frozen" examinable and reraisable version of the error exception??
msg = "%s: Error: bond direction is locally undefined or inconsistent around %s" % (cmdname, pl.atom) ###UNTESTED
print "should no longer be possible:", msg #bruce 070604
env.history.message( redmsg( quote_html( msg)))
return
Pl1, Pl2 = twoPls
a,b = Pl1.ordered_bases
d,c = Pl2.ordered_bases # note: we use d,c rather than c,d so that the atom arrangement is as shown in the diagram below.
# Note: for either the Make or Remove operation, the geometric arrangement is initially:
#
# c <-- Pl2 <-- d
#
# a --> Pl1 --> b
#
# and it ends up being (where dots indicate arrowheads, to show bond direction):
#
# c d
# . /
# \ .
# Pl1 Pl2
# . \
# / .
# a b
#
# Note: Pl1 stays attached to a, and Pl2 to d. Which two opposite bonds to preserve like that
# is an arbitrary choice -- as long as Make and Remove make the same choice about that,
# they'll reverse each other's effects precisely (assuming the sugars were initially correct as Ss or Sj).
# break the bonds we no longer want
for obj1, obj2 in [(Pl1, b), (Pl2, c)]:
bond = find_bond(obj1.atom, obj2.atom)
bond.bust(make_bondpoints = False)
# make the bonds we want and didn't already have
for obj1, obj2 in [(Pl1, c), (Pl2, b)]:
assert not atoms_are_bonded(obj1.atom, obj2.atom)
###e we should make bond_atoms do this assert itself, or maybe tolerate it (or does it already??)
bond_atoms_faster(obj1.atom, obj2.atom, V_SINGLE)
# set directions of all 4 bonds (even the preserved ones -- it's possible they were not set before,
# if some but not all bonds had directions set in the part of a strand whose directions we look at.)
for obj1, obj2 in [(a, Pl1), (Pl1, c), (d, Pl2), (Pl2, b)]:
bond = find_bond(obj1.atom, obj2.atom)
bond.set_bond_direction_from(obj1.atom, 1)
# WARNING: after that bond rearrangement, don't use our Pl5_recognizers in ways that depend on Pl bonding,
# since it's not well defined whether they think about the old or new bonding to give their answers.
Pl_atoms = Pl1.atom, Pl2.atom
del Pl1, Pl2, twoPls
# transmute base sugars to Sj or Ss as appropriate
if dna_updater_is_enabled():
want = Element_Ss5 #bruce 080320 bugfix
else:
want = make and Element_Sj5 or Element_Ss5
for obj in (a,b,c,d):
obj.atom.Transmute(want)
# Note: we do this after the bond making/breaking so it doesn't add singlets which mess us up.
# move Pl atoms into better positions
# (someday, consider using local minimize; for now, just place them directly between their new neighbor atoms,
# hopefully we leave them selected so user can easily do their own local minimize.)
for pl in Pl_atoms:
pl.setposn( average_value( map( lambda neighbor: neighbor.posn() , pl.neighbors() )))
env.history.message( greenmsg( cmdname + ": ") + quote_html("(%s - %s)" % tuple(Pl_atoms)))
#e need assy.changed()? evidently not.
return # from make_or_remove_crossover
