def _bond_bare_strandAtoms_with_orig_axisAtoms(
self, axis_and_strand_atomPairs_to_bond):
"""
Create bonds between the bare strand atoms of the new dna with the
corresponding axis atoms of the original dna. This method should be
called ONLY from self._replace_overlapping_axisAtoms_of_new_dna() where
we remove the axis atoms of new dna that overlap the ones in old dna.
We need to re-bond the bare strand atoms as a result of this replacment,
with the axis atoms of the old dna.
@param axis_and_strand_atomPairs_to_bond: A list containing pairs of the
axis and strand atoms that will be bonded together. It is of the
format [(atm1, atm2) , ....]
Where,
atm1 is always axisAtom of original dna
atm2 is always bare strandAtom of new dna
@type axis_and_strand_atomPairs_to_bond: list
@see: self._replace_overlapping_axisAtoms_of_new_dna() which calls this.
"""
#@REVIEW/ TODO: Make sure that we are not bondingan axis atom with a
#5' or 3' bondpoint of the strand atom.Skip the pair if its one and
#the same atom (?) This may not be needed because of the other
#code but is not obvious , so better to make sure in this method
#-- Ninad 2008-04-11
for atm1, atm2 in axis_and_strand_atomPairs_to_bond:
#Skip the pair if its one and the same atom.
if atm1 is not atm2:
for s1 in atm1.singNeighbors():
if atm2.singNeighbors():
s2 = atm2.singNeighbors()[0]
bond_at_singlets(s1, s2, move=False)
#REVIEW 2008-04-10 if 'break' is needed -
break
def _make_bonds_1(self, assy = None):
"""
Make bonds -- part 1.
(Actually make the bonds using bond_at_singlets,
call assy.changed() if you make any bonds,
and record some info in several attrs of self.)
"""
if assy == None:
assy = self.o.assy
self.bondable_pairs_atoms = []
self.merged_chunks = []
singlet_found_with_multiple_bonds = False # True when there are singlets with multiple bonds.
self.total_bonds_made = 0 # The total number of bondpoint pairs that formed bonds.
singlets_not_bonded = 0 # Number of bondpoints not bonded.
# print self.bondable_pairs
# This first section of code bonds each bondable pair of singlets.
for s1, s2 in self.bondable_pairs:
# Make sure each singlet of the pair has only one way of bonding.
# If either singlet has more than one ways to bond, we aren't going to bond them.
if self.ways_of_bonding[s1.key] == 1 and self.ways_of_bonding[s2.key] == 1:
# Record the real atoms in case I want to undo the bond later (before general Undo exists)
# Currently, this undo feature is not implemented here. Mark 050325
a1 = s1.singlet_neighbor()
a2 = s2.singlet_neighbor()
self.bondable_pairs_atoms.append( (a1,a2) ) # Add this pair to the list
bond_at_singlets(s1, s2, move = False) # Bond the singlets.
assy.changed() # The assy has changed.
else:
singlet_found_with_multiple_bonds = True
self.singlet_found_with_multiple_bonds = singlet_found_with_multiple_bonds
def pasteBond(self, sing):
"""
If self.pastable has an unambiguous hotspot,
paste a copy of self.pastable onto the given singlet;
return (the copy, description) or (None, whynot)
"""
self.update_pastable()
pastable = self.pastable
# as of 050316 addmol can change self.pastable! See comments in
#pasteFree.
# bruce 041123 added return values (and guessed docstring).
# bruce 050121 using subr split out from this code
ok, hotspot_or_whynot = find_hotspot_for_pasting(pastable)
if not ok:
whynot = hotspot_or_whynot
return None, whynot
hotspot = hotspot_or_whynot
if isinstance(pastable, Chunk):
numol = pastable.copy_single_chunk(None)
#bruce 080314 use new name copy_single_chunk
# bruce 041116 added (implicitly, by default) cauterize = 1
# to mol.copy() above; change this to cauterize = 0 here if
# unwanted, and for other uses of mol.copy in this file.
# For this use, there's an issue that new singlets make it harder to
# find a default hotspot! Hmm... I think copy should set one then.
# So now it does [041123].
hs = numol.hotspot or numol.singlets[0] #e should use
#find_hotspot_for_pasting again
bond_at_singlets(hs, sing) # this will move hs.molecule (numol) to
#match
# bruce 050217 comment: hs is now an invalid hotspot for numol,
# and that used to cause bug 312, but this is now fixed in getattr
# every time the
# hotspot is retrieved (since it can become invalid in many other
# ways too),so there's no need to explicitly forget it here.
if self.pickit():
numol.pickatoms()
#bruce 060412 worries whether pickatoms is illegal or
#ineffective (in both pasteBond and pasteFree)
# given that numol.part is presumably not yet set (until after
#addmol). But these seem to work
# (assuming I'm testing them properly), so I'm not changing
#this. [Why do they work?? ###@@@]
self.o.assy.addmol(numol) # do this last, in case it computes bbox
return numol, "copy of %r" % pastable.name
elif isinstance(pastable, Group):
msg = "Pasting a group with hotspot onto a bond point " \
"is not implemented"
return None, msg
def pasteBond(self, sing):
"""
If self.pastable has an unambiguous hotspot,
paste a copy of self.pastable onto the given singlet;
return (the copy, description) or (None, whynot)
"""
self.update_pastable()
pastable = self.pastable
# as of 050316 addmol can change self.pastable! See comments in
#pasteFree.
# bruce 041123 added return values (and guessed docstring).
# bruce 050121 using subr split out from this code
ok, hotspot_or_whynot = find_hotspot_for_pasting(pastable)
if not ok:
whynot = hotspot_or_whynot
return None, whynot
hotspot = hotspot_or_whynot
if isinstance(pastable, Chunk):
numol = pastable.copy_single_chunk(None)
#bruce 080314 use new name copy_single_chunk
# bruce 041116 added (implicitly, by default) cauterize = 1
# to mol.copy() above; change this to cauterize = 0 here if
# unwanted, and for other uses of mol.copy in this file.
# For this use, there's an issue that new singlets make it harder to
# find a default hotspot! Hmm... I think copy should set one then.
# So now it does [041123].
hs = numol.hotspot or numol.singlets[0] #e should use
#find_hotspot_for_pasting again
bond_at_singlets(hs,sing) # this will move hs.molecule (numol) to
#match
# bruce 050217 comment: hs is now an invalid hotspot for numol,
# and that used to cause bug 312, but this is now fixed in getattr
# every time the
# hotspot is retrieved (since it can become invalid in many other
# ways too),so there's no need to explicitly forget it here.
if self.pickit():
numol.pickatoms()
#bruce 060412 worries whether pickatoms is illegal or
#ineffective (in both pasteBond and pasteFree)
# given that numol.part is presumably not yet set (until after
#addmol). But these seem to work
# (assuming I'm testing them properly), so I'm not changing
#this. [Why do they work?? ###@@@]
self.o.assy.addmol(numol) # do this last, in case it computes bbox
return numol, "copy of %r" % pastable.name
elif isinstance(pastable, Group):
msg = "Pasting a group with hotspot onto a bond point " \
"is not implemented"
return None, msg
def _bond_axisNeighbors_with_orig_axisAtoms(self,
axis_and_axis_atomPairs_to_bond
):
"""
The operation that replaces the overlapping axis atoms of the new dnas
with the corresponding axis atoms of the original dna could leave out
some neighboring axis atoms of the *new dna* without bonds. So those
need to be bonded with the axis atom of the original dna which replaced
their neighbor. This method does that job.
@param axis_and_axis_atomPairs_to_bond: A list containing pairs of the
axis atom of original dna and axis atom on the new dna (which was
a neighbor of the atom deleted in the replacement operation and
was bonded to it) . Thies eatoms will be bonded with each other.
It is of the format [(atm1, atm2) , ....]
Where,
atm1 is always axisAtom of original dna which replaced the
overlapping axis atom of new dna (and thereby broke
bond between that atom's axis neighbors )
atm2 is always axis Atom of new dna , that was a neighbor to
an axis atom, say 'A', replaced by original dna axis atom
(because 'A' was overlapping) and was previously
bonded to 'A'.
"""
for atm1, atm2 in axis_and_axis_atomPairs_to_bond:
#Skip the pair if its one and the same atom.
if atm1 is atm2:
continue
#the following check (atm1.singNeighbors()) < 1....)doesn't work in
#some cases! So explicitly checking the length of the bondpoint
#neighbors of the atom in the for loop afterwords.
##if len(atm1.singNeighbors()) < 1 or len(atm2.singNeighbors()) < 1:
##continue
#Loop through bondpoints of atm1
for s1 in atm1.singNeighbors():
#bond point neigbors of atm2
if atm2.singNeighbors():
s2 = atm2.singNeighbors()[0]
bond_at_singlets(s1, s2, move = False)
break
def _bond_axisNeighbors_with_orig_axisAtoms(self,
axis_and_axis_atomPairs_to_bond
):
"""
The operation that replaces the overlapping axis atoms of the new dnas
with the corresponding axis atoms of the original dna could leave out
some neighboring axis atoms of the *new dna* without bonds. So those
need to be bonded with the axis atom of the original dna which replaced
their neighbor. This method does that job.
@param axis_and_axis_atomPairs_to_bond: A list containing pairs of the
axis atom of original dna and axis atom on the new dna (which was
a neighbor of the atom deleted in the replacement operation and
was bonded to it) . Thies eatoms will be bonded with each other.
It is of the format [(atm1, atm2) , ....]
Where,
atm1 is always axisAtom of original dna which replaced the
overlapping axis atom of new dna (and thereby broke
bond between that atom's axis neighbors )
atm2 is always axis Atom of new dna , that was a neighbor to
an axis atom, say 'A', replaced by original dna axis atom
(because 'A' was overlapping) and was previously
bonded to 'A'.
"""
for atm1, atm2 in axis_and_axis_atomPairs_to_bond:
#Skip the pair if its one and the same atom.
if atm1 is atm2:
continue
#the following check (atm1.singNeighbors()) < 1....)doesn't work in
#some cases! So explicitly checking the length of the bondpoint
#neighbors of the atom in the for loop afterwords.
##if len(atm1.singNeighbors()) < 1 or len(atm2.singNeighbors()) < 1:
##continue
#Loop through bondpoints of atm1
for s1 in atm1.singNeighbors():
#bond point neigbors of atm2
if atm2.singNeighbors():
s2 = atm2.singNeighbors()[0]
bond_at_singlets(s1, s2, move = False)
break
def _bond_bare_strandAtoms_with_orig_axisAtoms(self,
axis_and_strand_atomPairs_to_bond):
"""
Create bonds between the bare strand atoms of the new dna with the
corresponding axis atoms of the original dna. This method should be
called ONLY from self._replace_overlapping_axisAtoms_of_new_dna() where
we remove the axis atoms of new dna that overlap the ones in old dna.
We need to re-bond the bare strand atoms as a result of this replacment,
with the axis atoms of the old dna.
@param axis_and_strand_atomPairs_to_bond: A list containing pairs of the
axis and strand atoms that will be bonded together. It is of the
format [(atm1, atm2) , ....]
Where,
atm1 is always axisAtom of original dna
atm2 is always bare strandAtom of new dna
@type axis_and_strand_atomPairs_to_bond: list
@see: self._replace_overlapping_axisAtoms_of_new_dna() which calls this.
"""
#@REVIEW/ TODO: Make sure that we are not bondingan axis atom with a
#5' or 3' bondpoint of the strand atom.Skip the pair if its one and
#the same atom (?) This may not be needed because of the other
#code but is not obvious , so better to make sure in this method
#-- Ninad 2008-04-11
for atm1, atm2 in axis_and_strand_atomPairs_to_bond:
#Skip the pair if its one and the same atom.
if atm1 is not atm2:
for s1 in atm1.singNeighbors():
if atm2.singNeighbors():
s2 = atm2.singNeighbors()[0]
bond_at_singlets(s1, s2, move = False)
#REVIEW 2008-04-10 if 'break' is needed -
break
def _bond_two_strandAtoms(self, atm1, atm2):
"""
Bonds the given strand atoms (sugar atoms) together. To bond these atoms,
it always makes sure that a 3' bondpoint on one atom is bonded to 5'
bondpoint on the other atom.
@param atm1: The first sugar atom of PAM3 (i.e. the strand atom) to be
bonded with atm2.
@param atm2: Second sugar atom
@see: self.joinNeighboringStrands() which calls this
TODO 2008-10-26: This method is originally from
B_DNA_PAM3_SingleStrand class. It is modified further to account for
color change after bonding the two strand atoms. It needs to
be refactored and moved to a dna_helper package. [-- Ninad comment]
"""
#Moved from B_Dna_PAM3_SingleStrand_Generator to here, to fix bugs like
#2711 in segment resizing-- Ninad 2008-04-14
assert atm1.element.role == 'strand' and atm2.element.role == 'strand'
#Initialize all possible bond points to None
five_prime_bondPoint_atm1 = None
three_prime_bondPoint_atm1 = None
five_prime_bondPoint_atm2 = None
three_prime_bondPoint_atm2 = None
#Initialize the final bondPoints we will use to create bonds
bondPoint1 = None
bondPoint2 = None
#Find 5' and 3' bondpoints of atm1 (BTW, as of 2008-04-11, atm1 is
#the new dna strandend atom See self._fuse_new_dna_with_original_duplex
#But it doesn't matter here.
for s1 in atm1.singNeighbors():
bnd = s1.bonds[0]
if bnd.isFivePrimeOpenBond():
five_prime_bondPoint_atm1 = s1
if bnd.isThreePrimeOpenBond():
three_prime_bondPoint_atm1 = s1
#Find 5' and 3' bondpoints of atm2
for s2 in atm2.singNeighbors():
bnd = s2.bonds[0]
if bnd.isFivePrimeOpenBond():
five_prime_bondPoint_atm2 = s2
if bnd.isThreePrimeOpenBond():
three_prime_bondPoint_atm2 = s2
#Determine bondpoint1 and bondPoint2 (the ones we will bond). See method
#docstring for details.
if five_prime_bondPoint_atm1 and three_prime_bondPoint_atm2:
bondPoint1 = five_prime_bondPoint_atm1
bondPoint2 = three_prime_bondPoint_atm2
#Following will overwrite bondpoint1 and bondPoint2, if the condition is
#True. Doesn't matter. See method docstring to know why.
if three_prime_bondPoint_atm1 and five_prime_bondPoint_atm2:
bondPoint1 = three_prime_bondPoint_atm1
bondPoint2 = five_prime_bondPoint_atm2
#Do the actual bonding
if bondPoint1 and bondPoint2:
bond_at_singlets(bondPoint1, bondPoint2, move = False)
else:
print_compact_stack("Bug: unable to bond atoms %s and %s: " %
(atm1, atm2) )
#The following fixes bug 2770
#Set the color of the whole dna strandGroup to the color of the
#strand, whose bondpoint, is dropped over to the bondboint of the
#other strandchunk (thus joining the two strands together into
#a single dna strand group) - Ninad 2008-04-09
color = atm1.molecule.color
if color is None:
color = atm1.element.color
strandGroup1 = atm1.molecule.parent_node_of_class(self.assy.DnaStrand)
#Temporary fix for bug 2829 that Damian reported.
#Bruce is planning to fix the underlying bug in the dna updater
#code. Once its fixed, The following block of code under
#"if DEBUG_BUG_2829" can be deleted -- Ninad 2008-05-01
DEBUG_BUG_2829 = True
if DEBUG_BUG_2829:
strandGroup2 = atm2.molecule.parent_node_of_class(
self.assy.DnaStrand)
if strandGroup2 is not None:
#set the strand color of strandGroup2 to the one for
#strandGroup1.
strandGroup2.setStrandColor(color)
strandChunkList = strandGroup2.getStrandChunks()
for c in strandChunkList:
if hasattr(c, 'invalidate_ladder'):
c.invalidate_ladder()
def _bond_two_strandAtoms(self, atm1, atm2):
"""
Bonds the given strand atoms (sugar atoms) together. To bond these atoms,
it always makes sure that a 3' bondpoint on one atom is bonded to 5'
bondpoint on the other atom.
@param atm1: The first sugar atom of PAM3 (i.e. the strand atom) to be
bonded with atm2.
@param atm2: Second sugar atom
@Note: This method is copied from DnaDuplex.py
"""
#Moved from B_Dna_PAM3_SingleStrand_Generator to here, to fix bugs like
#2711 in segment resizing-- Ninad 2008-04-14
assert atm1.element.role == 'strand' and atm2.element.role == 'strand'
#Initialize all possible bond points to None
five_prime_bondPoint_atm1 = None
three_prime_bondPoint_atm1 = None
five_prime_bondPoint_atm2 = None
three_prime_bondPoint_atm2 = None
#Initialize the final bondPoints we will use to create bonds
bondPoint1 = None
bondPoint2 = None
#Find 5' and 3' bondpoints of atm1 (BTW, as of 2008-04-11, atm1 is
#the new dna strandend atom See self._fuse_new_dna_with_original_duplex
#But it doesn't matter here.
for s1 in atm1.singNeighbors():
bnd = s1.bonds[0]
if bnd.isFivePrimeOpenBond():
five_prime_bondPoint_atm1 = s1
if bnd.isThreePrimeOpenBond():
three_prime_bondPoint_atm1 = s1
#Find 5' and 3' bondpoints of atm2
for s2 in atm2.singNeighbors():
bnd = s2.bonds[0]
if bnd.isFivePrimeOpenBond():
five_prime_bondPoint_atm2 = s2
if bnd.isThreePrimeOpenBond():
three_prime_bondPoint_atm2 = s2
#Determine bondpoint1 and bondPoint2 (the ones we will bond). See method
#docstring for details.
if five_prime_bondPoint_atm1 and three_prime_bondPoint_atm2:
bondPoint1 = five_prime_bondPoint_atm1
bondPoint2 = three_prime_bondPoint_atm2
#Following will overwrite bondpoint1 and bondPoint2, if the condition is
#True. Doesn't matter. See method docstring to know why.
if three_prime_bondPoint_atm1 and five_prime_bondPoint_atm2:
bondPoint1 = three_prime_bondPoint_atm1
bondPoint2 = five_prime_bondPoint_atm2
#Copied over from BuildAtoms_GraphicsMode._singletLeftUp_joinStrands()
#The following fixes bug 2770
#Set the color of the whole dna strandGroup to the color of the
#strand, whose bondpoint, is dropped over to the bondboint of the
#other strandchunk (thus joining the two strands together into
#a single dna strand group) - Ninad 2008-04-09
color = atm1.molecule.color
if color is None:
color = atm1.element.color
strandGroup1 = atm1.molecule.parent_node_of_class(self.win.assy.DnaStrand)
strandGroup2 = atm2.molecule.parent_node_of_class(
self.win.assy.DnaStrand)
if strandGroup2 is not None:
#set the strand color of strandGroup2 to the one for
#strandGroup1.
strandGroup2.setStrandColor(color)
strandChunkList = strandGroup2.getStrandChunks()
for c in strandChunkList:
if hasattr(c, 'invalidate_ladder'):
c.invalidate_ladder()
#Do the actual bonding
if bondPoint1 and bondPoint2:
try:
bond_at_singlets(bondPoint1, bondPoint2, move = False)
except:
print_compact_traceback("Bug: unable to bond atoms %s and %s"%(atm1,
atm2))
if strandGroup1 is not None:
strandGroup1.setStrandColor(color)
def _bond_two_strandAtoms(self, atm1, atm2):
"""
Bonds the given strand atoms (sugar atoms) together. To bond these atoms,
it always makes sure that a 3' bondpoint on one atom is bonded to 5'
bondpoint on the other atom.
@param atm1: The first sugar atom of PAM3 (i.e. the strand atom) to be
bonded with atm2.
@param atm2: Second sugar atom
@see: self.joinNeighboringStrands() which calls this
TODO 2008-10-26: This method is originally from
B_DNA_PAM3_SingleStrand class. It is modified further to account for
color change after bonding the two strand atoms. It needs to
be refactored and moved to a dna_helper package. [-- Ninad comment]
"""
#Moved from B_Dna_PAM3_SingleStrand_Generator to here, to fix bugs like
#2711 in segment resizing-- Ninad 2008-04-14
assert atm1.element.role == 'strand' and atm2.element.role == 'strand'
#Initialize all possible bond points to None
five_prime_bondPoint_atm1 = None
three_prime_bondPoint_atm1 = None
five_prime_bondPoint_atm2 = None
three_prime_bondPoint_atm2 = None
#Initialize the final bondPoints we will use to create bonds
bondPoint1 = None
bondPoint2 = None
#Find 5' and 3' bondpoints of atm1 (BTW, as of 2008-04-11, atm1 is
#the new dna strandend atom See self._fuse_new_dna_with_original_duplex
#But it doesn't matter here.
for s1 in atm1.singNeighbors():
bnd = s1.bonds[0]
if bnd.isFivePrimeOpenBond():
five_prime_bondPoint_atm1 = s1
if bnd.isThreePrimeOpenBond():
three_prime_bondPoint_atm1 = s1
#Find 5' and 3' bondpoints of atm2
for s2 in atm2.singNeighbors():
bnd = s2.bonds[0]
if bnd.isFivePrimeOpenBond():
five_prime_bondPoint_atm2 = s2
if bnd.isThreePrimeOpenBond():
three_prime_bondPoint_atm2 = s2
#Determine bondpoint1 and bondPoint2 (the ones we will bond). See method
#docstring for details.
if five_prime_bondPoint_atm1 and three_prime_bondPoint_atm2:
bondPoint1 = five_prime_bondPoint_atm1
bondPoint2 = three_prime_bondPoint_atm2
#Following will overwrite bondpoint1 and bondPoint2, if the condition is
#True. Doesn't matter. See method docstring to know why.
if three_prime_bondPoint_atm1 and five_prime_bondPoint_atm2:
bondPoint1 = three_prime_bondPoint_atm1
bondPoint2 = five_prime_bondPoint_atm2
#Do the actual bonding
if bondPoint1 and bondPoint2:
bond_at_singlets(bondPoint1, bondPoint2, move=False)
else:
print_compact_stack("Bug: unable to bond atoms %s and %s: " %
(atm1, atm2))
#The following fixes bug 2770
#Set the color of the whole dna strandGroup to the color of the
#strand, whose bondpoint, is dropped over to the bondboint of the
#other strandchunk (thus joining the two strands together into
#a single dna strand group) - Ninad 2008-04-09
color = atm1.molecule.color
if color is None:
color = atm1.element.color
strandGroup1 = atm1.molecule.parent_node_of_class(self.assy.DnaStrand)
#Temporary fix for bug 2829 that Damian reported.
#Bruce is planning to fix the underlying bug in the dna updater
#code. Once its fixed, The following block of code under
#"if DEBUG_BUG_2829" can be deleted -- Ninad 2008-05-01
DEBUG_BUG_2829 = True
if DEBUG_BUG_2829:
strandGroup2 = atm2.molecule.parent_node_of_class(
self.assy.DnaStrand)
if strandGroup2 is not None:
#set the strand color of strandGroup2 to the one for
#strandGroup1.
strandGroup2.setStrandColor(color)
strandChunkList = strandGroup2.getStrandChunks()
for c in strandChunkList:
if hasattr(c, 'invalidate_ladder'):
c.invalidate_ladder()