def widget_msg(self, msg, options):
#e improved timestamp?
#e use html for color etc? [some callers put this directly in the msg, for now]
_quote_html = options.pop(
'quote_html', False
) #bruce 060126 new feature, improving on message_no_html interface ##k
if _quote_html:
msg = quote_html(msg)
_color = options.pop('color', None)
if _color:
#bruce 060126 new feature; for now only permits 4 fixed color name strings;
# should someday permit any color name (in any format) or object (of any kind) #e
funcs = {
'green': greenmsg,
'orange': orangemsg,
'red': redmsg,
'gray': graymsg
}
func = funcs[
_color] # any colorname not in this dict is an exception (ok for now)
msg = func(msg)
_compact_stack = options.pop('compact_stack', "") #bruce 060720
if _compact_stack:
msg += graymsg("; history.message() call stack: %s" %
quote_html(_compact_stack))
# any unrecognized options are warned about below
self._print_msg(msg)
if options:
msg2 = "fyi: bug: widget_msg got unsupported options: %r" % options
print msg2 # too important to only print in the history file --
# could indicate that not enough info is being saved there
self._print_msg(msg2)
return
def widget_msg(self, msg, options):
#e improved timestamp?
#e use html for color etc? [some callers put this directly in the msg, for now]
_quote_html = options.pop('quote_html', False) #bruce 060126 new feature, improving on message_no_html interface ##k
if _quote_html:
msg = quote_html(msg)
_color = options.pop('color', None)
if _color:
#bruce 060126 new feature; for now only permits 4 fixed color name strings;
# should someday permit any color name (in any format) or object (of any kind) #e
funcs = {'green':greenmsg, 'orange':orangemsg, 'red':redmsg, 'gray':graymsg}
func = funcs[_color] # any colorname not in this dict is an exception (ok for now)
msg = func(msg)
_compact_stack = options.pop('compact_stack', "") #bruce 060720
if _compact_stack:
msg += graymsg("; history.message() call stack: %s" % quote_html(_compact_stack))
# any unrecognized options are warned about below
self._print_msg(msg)
if options:
msg2 = "fyi: bug: widget_msg got unsupported options: %r" % options
print msg2 # too important to only print in the history file --
# could indicate that not enough info is being saved there
self._print_msg(msg2)
return
def widget_html(self): ###@@@ experimental. This sort of works...
###e also escape < > and & ? not appropriate when self.text contains html, as it sometimes does!
# maybe it's best in the long run to just require the source messages to escape these if they need to.
# if not, we'll need some sort of hueristic to escape them except when part of well-formatted tags.
return graymsg(self.widget_text_header(
)) + self.text #e could remove graymsg when what's inside it is ""
def graymsg(self, msg, **kws): #bruce 080201
"""
Shorthand for self.message(graymsg(msg), <options>).
"""
self.message(graymsg(msg), **kws)
return
def _kill_Pl_and_rebond_neighbors_0(atom):
# Note: we optimize for the common case (nothing wrong, conversion happens)
### NOTE: many of the following checks have probably also been done by
# calling code before we get here. Optimize this sometime. [bruce 080408]
bonds = atom.bonds
# change these during the loop
bad = False
saw_plus = saw_minus = False
num_bondpoints = 0
neighbors = []
direction = None # KLUGE: set this during loop, but use it afterwards too
for bond in bonds:
other = bond.other(atom)
neighbors += [other]
element = other.element
direction = bond.bond_direction_from(atom)
if direction == 1:
saw_plus = True
elif direction == -1:
saw_minus = True
if element is Singlet:
num_bondpoints += 1
elif element.symbol in ('Ss3', 'Ss5'):
# [in the 080408 copy, will often be one of each!]
pass
else:
bad = True
continue
if not (len(bonds) == 2 and saw_minus and saw_plus and num_bondpoints < 2):
bad = True
if bad:
summary_format = \
"Warning: dna updater left [N] Pl5 pseudoatom(s) unconverted"
env.history.deferred_summary_message( redmsg(summary_format) ) # orange -> red [080408]
return
del saw_plus, saw_minus, num_bondpoints, bad
# Now we know it is either Ss-Pl-Ss or X-Pl-Ss,
# with fully set and consistent bond_directions.
# But we'd better make sure the neighbors are not already bonded!
#
# (This is weird enough to get its own summary message, which is red.
# Mild bug: we're not also counting it in the above message.)
#
# (Note: there is potentially slow debug code in rebond which is
# redundant with this. It does a few other things too that we don't
# need, so if it shows up in a profile, just write a custom version
# for this use. ### OPTIM)
n0, n1 = neighbors
del neighbors
b0, b1 = bonds
del bonds # it might be mutable and we're changing it below,
# so be sure not to use it again
if find_bond(n0, n1):
summary_format = \
"Error: dna updater noticed [N] Pl5 pseudoatom(s) whose neighbors are directly bonded"
env.history.deferred_summary_message( redmsg(summary_format) )
return
# Pull out the Pl5 and directly bond its neighbors,
# reusing one of the bonds for efficiency.
# (This doesn't preserve its bond_direction, so set that again.)
# Kluge: the following code only works for n1 not a bondpoint
# (since bond.bust on an open bond kills the bondpoint),
# and fixing that would require inlining and modifying a
# few Atom methods,
# so to avoid this case, reverse everything if needed.
if n1.element is Singlet:
direction = - direction
n0, n1 = n1, n0
b0, b1 = b1, b0
# Note: bonds.reverse() might modify atom.bonds itself,
# so we shouldn't do it even if we didn't del bonds above.
# (Even though no known harm comes from changing an atom's
# order of its bonds. It's not reviewed as a problematic
# change for an undo snapshot, though. Which is moot here
# since we're about to remove them all. But it still seems
# safer not to do it.)
pass
## # save atom_posn before modifying atom (not known to be needed), and
# set atom.atomtype to avoid bugs in reguess_atomtype during atom.kill
# (need to do that when it still has the right number of bonds, I think)
## atom_posn = atom.posn()
atom.atomtype # side effect: set atomtype
old_nbonds_neighbor1 = len(n1.bonds) # for assert
old_nbonds_neighbor0 = len(n0.bonds) # for assert
b1.bust(make_bondpoints = False) # n1 is now missing one bond; so is atom
# note: if n1 was a Singlet, this would kill it (causing bugs);
# see comment above, where we swap n1 and n0 if needed to prevent that.
b0.rebond(atom, n1) # now n1 has enough bonds again; atom is missing both bonds
assert len(atom.bonds) == 0, "Pl %r should have no bonds but has %r" % (atom, atom.bonds)
assert not atom.killed()
assert len(n1.bonds) == old_nbonds_neighbor1
assert len(n0.bonds) == old_nbonds_neighbor0
## # KLUGE: we know direction is still set to the direction of b1 from atom
## # (since b1 was processed last by the for loop above),
## # which is the overall direction from n0 thru b0 to atom thru b1 to n1,
## # so use this to optimize recording the Pl info below.
## # (Of course we really ought to just rewrite this whole conversion in Pyrex.)
##
## ## assert direction == b1.bond_direction_from(atom) # too slow to enable by default
##
## # not needed, rebond preserves it:
## ## b0.set_bond_direction_from(n0, direction)
## ## assert b0.bond_direction_from(n0) == direction # too slow to enable by default
##
## # now save the info we'll need later (this uses direction left over from for-loop)
##
## if n0.element is not Singlet:
## _save_Pl_info( n0, direction, atom_posn)
##
## if n1.element is not Singlet:
## _save_Pl_info( n1, - direction, atom_posn) # note the sign on direction
# get the Pl atom out of the way
atom.kill()
## # (let's hope this happened before an Undo checkpoint ever saw it --
## # sometime verify that, and optimize if it's not true)
if 0: # for now; bruce 080413 356pm
# summarize our success -- we'll remove this when it becomes the default,
# or condition it on a DEBUG_DNA_UPDATER flag ###
debug_flags.DEBUG_DNA_UPDATER # for use later
summary_format = \
"Note: dna updater removed [N] Pl5 pseudoatom(s) while converting to PAM3+5"
env.history.deferred_summary_message( graymsg(summary_format) )
return
def _convert_Pl5(atom):
"""
If atom's neighbors have the necessary structure
(Ss-Pl-Ss or X-Pl-Ss, with fully set and consistent bond_directions),
save atom's coordinates on its Ss neighbors,
arrange for them to postprocess that info later,
and then kill atom, replacing its bonds with a direct bond
between its neighbors (same bond_direction).
Summarize results (ok or error) to history.
"""
### NOTE: the code starting from here has been copied and modified
#### into a new function in pam3plus5_ops.py by bruce 080408.
assert atom.element is Pl5 # remove when works
# could also assert no dna updater error
# Note: we optimize for the common case (nothing wrong, conversion happens)
bonds = atom.bonds
# change these during the loop
bad = False
saw_plus = saw_minus = False
num_bondpoints = 0
neighbors = []
direction = None # KLUGE: set this during loop, but use it afterwards too
for bond in bonds:
other = bond.other(atom)
neighbors += [other]
element = other.element
direction = bond.bond_direction_from(atom)
if direction == 1:
saw_plus = True
elif direction == -1:
saw_minus = True
if element is Singlet:
num_bondpoints += 1
elif element.symbol in ('Ss3', 'Ss5'):
pass
else:
bad = True
continue
if not (len(bonds) == 2 and saw_minus and saw_plus and num_bondpoints < 2):
bad = True
if bad:
summary_format = \
"Warning: dna updater left [N] Pl5 pseudoatom(s) unconverted"
env.history.deferred_summary_message( orangemsg(summary_format) )
return
del saw_plus, saw_minus, num_bondpoints, bad
# Now we know it is either Ss-Pl-Ss or X-Pl-Ss,
# with fully set and consistent bond_directions.
# But we'd better make sure the neighbors are not already bonded!
#
# (This is weird enough to get its own summary message, which is red.
# Mild bug: we're not also counting it in the above message.)
#
# (Note: there is potentially slow debug code in rebond which is
# redundant with this. It does a few other things too that we don't
# need, so if it shows up in a profile, just write a custom version
# for this use. ### OPTIM)
n0, n1 = neighbors
del neighbors
b0, b1 = bonds
del bonds # it might be mutable and we're changing it below,
# so be sure not to use it again
if find_bond(n0, n1):
summary_format = \
"Error: dna updater noticed [N] Pl5 pseudoatom(s) whose neighbors are directly bonded"
env.history.deferred_summary_message( redmsg(summary_format) )
return
# Pull out the Pl5 and directly bond its neighbors,
# reusing one of the bonds for efficiency.
# (This doesn't preserve its bond_direction, so set that again.)
# Kluge: the following code only works for n1 not a bondpoint
# (since bond.bust on an open bond kills the bondpoint),
# and fixing that would require inlining and modifying a
# few Atom methods,
# so to avoid this case, reverse everything if needed.
if n1.element is Singlet:
direction = - direction
n0, n1 = n1, n0
b0, b1 = b1, b0
# Note: bonds.reverse() might modify atom.bonds itself,
# so we shouldn't do it even if we didn't del bonds above.
# (Even though no known harm comes from changing an atom's
# order of its bonds. It's not reviewed as a problematic
# change for an undo snapshot, though. Which is moot here
# since we're about to remove them all. But it still seems
# safer not to do it.)
pass
# save atom_posn before modifying atom (not known to be needed),
# and set atom.atomtype to avoid bugs in reguess_atomtype during atom.kill
# (need to do that when it still has the right number of bonds, I think)
atom_posn = atom.posn()
atom.atomtype # side effect: set atomtype
old_nbonds_neighbor1 = len(n1.bonds) # for assert
old_nbonds_neighbor0 = len(n0.bonds) # for assert
b1.bust(make_bondpoints = False) # n1 is now missing one bond; so is atom
b0.rebond(atom, n1) # now n1 has enough bonds again; atom is missing both bonds
assert len(atom.bonds) == 0, "Pl %r should have no bonds but has %r" % (atom, atom.bonds)
assert not atom.killed()
assert len(n1.bonds) == old_nbonds_neighbor1
assert len(n0.bonds) == old_nbonds_neighbor0
# KLUGE: we know direction is still set to the direction of b1 from atom
# (since b1 was processed last by the for loop above),
# which is the overall direction from n0 thru b0 to atom thru b1 to n1,
# so use this to optimize recording the Pl info below.
# (Of course we really ought to just rewrite this whole conversion in Pyrex.)
## assert direction == b1.bond_direction_from(atom) # too slow to enable by default
# not needed, rebond preserves it:
## b0.set_bond_direction_from(n0, direction)
## assert b0.bond_direction_from(n0) == direction # too slow to enable by default
# now save the info we'll need later (this uses direction left over from for-loop)
if n0.element is not Singlet:
_save_Pl_info( n0, direction, atom_posn)
if n1.element is not Singlet:
_save_Pl_info( n1, - direction, atom_posn) # note the sign on direction
# get the Pl atom out of the way
atom.kill()
# (let's hope this happened before an Undo checkpoint ever saw it --
# sometime verify that, and optimize if it's not true)
# summarize our success -- we'll remove this when it becomes the default,
# or condition it on a DEBUG_DNA_UPDATER flag ###
debug_flags.DEBUG_DNA_UPDATER # for use later
summary_format = \
"Note: dna updater converted [N] Pl5 pseudoatom(s)"
env.history.deferred_summary_message( graymsg(summary_format) )
return
def widget_html(self): ###@@@ experimental. This sort of works...
###e also escape < > and & ? not appropriate when self.text contains html, as it sometimes does!
# maybe it's best in the long run to just require the source messages to escape these if they need to.
# if not, we'll need some sort of hueristic to escape them except when part of well-formatted tags.
return graymsg(self.widget_text_header()) + self.text #e could remove graymsg when what's inside it is ""
def graymsg(self, msg, **kws): #bruce 080201
"""
Shorthand for self.message(graymsg(msg), <options>).
"""
self.message(graymsg(msg), **kws)
return
