def _postProcess(self, baseList):
"""
Final tweaks on the DNA chunk, including:
- Transmute Ax3 atoms on each end into Ae3.
- Adjust open bond singlets.
@param baseList: List of basepair chunks that make up the duplex.
@type baseList: list
@note: baseList must contain at least two base-pair chunks.
"""
if len(baseList) < 1:
print_compact_stack("bug? (ignoring) DnaDuplex._postProcess called but "\
"baseList is empty. Maybe dna_updater was "\
"run?: ")
return
start_basepair_atoms = baseList[0].atoms.values()
end_basepair_atoms = baseList[-1].atoms.values()
Ax_caps = filter( lambda atom: atom.element.symbol in ('Ax3'),
start_basepair_atoms)
Ax_caps += filter( lambda atom: atom.element.symbol in ('Ax3'),
end_basepair_atoms)
# Transmute Ax3 caps to Ae3 atoms.
# Note: this leaves two "killed singlets" hanging around,
# one from each Ax3 cap.
#
# REVIEW: is it safe to simply not do this when dna_updater_is_enabled()?
# [bruce 080320 question]
for atom in Ax_caps:
atom.Transmute(Element_Ae3)
# X_List will contain 6 singlets, 2 of which are killed (non-bonded).
# The other 4 are the 2 pair of strand open bond singlets.
X_List = filter( lambda atom: atom.element.symbol in ('X'),
start_basepair_atoms)
X_List += filter( lambda atom: atom.element.symbol in ('X'),
end_basepair_atoms)
# Adjust the 4 open bond singlets.
for singlet in X_List:
if singlet.killed():
# Skip the 2 killed singlets.
continue
adjustSinglet(singlet)
return
def _postProcess(self, baseList):
"""
Final tweaks on the DNA chunk, including:
- Transmute Ax3 atoms on each end into Ae3.
- Adjust open bond singlets.
@param baseList: List of basepair chunks that make up the duplex.
@type baseList: list
@note: baseList must contain at least two base-pair chunks.
"""
if len(baseList) < 1:
print_compact_stack("bug? (ignoring) DnaDuplex._postProcess called but "\
"baseList is empty. Maybe dna_updater was "\
"run?: ")
return
start_basepair_atoms = baseList[0].atoms.values()
end_basepair_atoms = baseList[-1].atoms.values()
Ax_caps = filter(lambda atom: atom.element.symbol in ('Ax3'),
start_basepair_atoms)
Ax_caps += filter(lambda atom: atom.element.symbol in ('Ax3'),
end_basepair_atoms)
# Transmute Ax3 caps to Ae3 atoms.
# Note: this leaves two "killed singlets" hanging around,
# one from each Ax3 cap.
#
# REVIEW: is it safe to simply not do this when dna_updater_is_enabled()?
# [bruce 080320 question]
for atom in Ax_caps:
atom.Transmute(Element_Ae3)
# X_List will contain 6 singlets, 2 of which are killed (non-bonded).
# The other 4 are the 2 pair of strand open bond singlets.
X_List = filter(lambda atom: atom.element.symbol in ('X'),
start_basepair_atoms)
X_List += filter(lambda atom: atom.element.symbol in ('X'),
end_basepair_atoms)
# Adjust the 4 open bond singlets.
for singlet in X_List:
if singlet.killed():
# Skip the 2 killed singlets.
continue
adjustSinglet(singlet)
return
def makeStrandChunkFromBrokenStrand(self, x1, x2): # by Mark
"""
Makes a new strand chunk using the two singlets just created by
busting the original strand, which is now broken. If the original
strand was a ring, no new chunk is created.
The new strand chunk, which includes the atoms between the 3' end of
the original strand and the new 5' end (i.e. the break point), is
added to the same DNA group as the original strand and assigned a
different color.
@param x1: The first of two singlets created by busting a strand
backbone bond. It is either the 3' or 5' open bond singlet,
but we don't know yet.
@type x1: L{Atom}
@param x2: The second of two singlets created by busting a backbone
backbone bond. It is either the 3' or 5' open bond singlet,
but we don't know yet.
@type x2: L{Atom}
@return: The new strand chunk. Returns B{None} if no new strand chunk
is created, as is the case of a ring.
@rtype: L{Chunk}
"""
minimize = debug_pref("Adjust broken strand bondpoints using minimizer?",
#bruce 080415 revised text (to not use the developer-
# jargon-only term "singlet"), changed prefs_key,
# and removed non_debug = True, for .rc2 release,
# since the repositioning bug this worked around
# is now fixed.
Choice_boolean_False,
prefs_key = True,
)
_five_prime_atom = None
_three_prime_atom = None
for singlet in (x1, x2):
adjustSinglet(singlet, minimize = minimize)
open_bond = singlet.bonds[0]
if open_bond.isFivePrimeOpenBond():
_five_prime_atom = open_bond.other(singlet)
else:
_three_prime_atom = open_bond.other(singlet)
# Make sure we have exactly one 3' and one 5' singlet.
# If not, there is probably a direction error on the open bond(s)
# that x1 and/or x2 are members of.
if not _five_prime_atom:
print_compact_stack("No 5' bondpoint.")
return None
if not _three_prime_atom:
print_compact_stack("No 3' bondpoint.")
return None
atomList = self.o.assy.getConnectedAtoms([_five_prime_atom])
if _three_prime_atom in atomList:
# The strand was a closed loop strand, so we're done.
return None # Since no new chunk was created.
# See self.ensure_toplevel_group() docstring for explanation.
self.ensure_toplevel_group()
_group_five_prime_was_in = _five_prime_atom.molecule.dad
if env.prefs[assignColorToBrokenDnaStrands_prefs_key]:
_new_strand_color = getNextStrandColor(_five_prime_atom.molecule.color)
else:
_new_strand_color = _five_prime_atom.molecule.color
return self.makeChunkFromAtomList(atomList,
group = _group_five_prime_was_in,
name = gensym("Strand"),
# doesn't need "DnaStrand" or self.assy,
# since not normally seen by users
# [bruce 080407 comment]
color = _new_strand_color)
def makeStrandChunkFromBrokenStrand(self, x1, x2): # by Mark
"""
Makes a new strand chunk using the two singlets just created by
busting the original strand, which is now broken. If the original
strand was a ring, no new chunk is created.
The new strand chunk, which includes the atoms between the 3' end of
the original strand and the new 5' end (i.e. the break point), is
added to the same DNA group as the original strand and assigned a
different color.
@param x1: The first of two singlets created by busting a strand
backbone bond. It is either the 3' or 5' open bond singlet,
but we don't know yet.
@type x1: L{Atom}
@param x2: The second of two singlets created by busting a backbone
backbone bond. It is either the 3' or 5' open bond singlet,
but we don't know yet.
@type x2: L{Atom}
@return: The new strand chunk. Returns B{None} if no new strand chunk
is created, as is the case of a ring.
@rtype: L{Chunk}
"""
minimize = debug_pref(
"Adjust broken strand bondpoints using minimizer?",
#bruce 080415 revised text (to not use the developer-
# jargon-only term "singlet"), changed prefs_key,
# and removed non_debug = True, for .rc2 release,
# since the repositioning bug this worked around
# is now fixed.
Choice_boolean_False,
prefs_key=True,
)
_five_prime_atom = None
_three_prime_atom = None
for singlet in (x1, x2):
adjustSinglet(singlet, minimize=minimize)
open_bond = singlet.bonds[0]
if open_bond.isFivePrimeOpenBond():
_five_prime_atom = open_bond.other(singlet)
else:
_three_prime_atom = open_bond.other(singlet)
# Make sure we have exactly one 3' and one 5' singlet.
# If not, there is probably a direction error on the open bond(s)
# that x1 and/or x2 are members of.
if not _five_prime_atom:
print_compact_stack("No 5' bondpoint.")
return None
if not _three_prime_atom:
print_compact_stack("No 3' bondpoint.")
return None
atomList = self.o.assy.getConnectedAtoms([_five_prime_atom])
if _three_prime_atom in atomList:
# The strand was a closed loop strand, so we're done.
return None # Since no new chunk was created.
# See self.ensure_toplevel_group() docstring for explanation.
self.ensure_toplevel_group()
_group_five_prime_was_in = _five_prime_atom.molecule.dad
if env.prefs[assignColorToBrokenDnaStrands_prefs_key]:
_new_strand_color = getNextStrandColor(
_five_prime_atom.molecule.color)
else:
_new_strand_color = _five_prime_atom.molecule.color
return self.makeChunkFromAtomList(
atomList,
group=_group_five_prime_was_in,
name=gensym("Strand"),
# doesn't need "DnaStrand" or self.assy,
# since not normally seen by users
# [bruce 080407 comment]
color=_new_strand_color)