def _C_ordered_bases(self):
"""
[compute method for self.ordered_bases]
Return our two bases (as Base5_recognizer objects, which may or may not be .in_helix),
in an order consistent with backbone bond direction,
which we require to be locally defined in a consistent way.
@warning: value will be None (not a sequence) if a RecognizerError was
raised.
"""
if self.unordered_bases is None:
raise RecognizerError("doesn't have two bases")
bases = list(
self.unordered_bases
) # we might destructively reverse this later, before returning it
nn = bases[0].atom, bases[1].atom
# reverse bases if bond directions go backwards, or complain if not defined or not consistent
# (Note: the following code is mostly generic for pairs of directional bonds,
# so we might package it up into a utility function someday.)
# BTW, in the future we should improve this as follows:
# - find directional-bond strands in both directions, including at least one bond not altered
# when making/unmaking a crossover, and ending on the first bond with direction defined,
# or when you have to end due to error (too far away to stop us) or end of strand.
# - require that this gave you a direction and was not inconsistent.
# - when making the crossover later, actually set all those directions you passed over
# (not just those of your new bonds).
dir1 = bond_direction(nn[0], self.atom) # -1 or 0 or 1
dir2 = bond_direction(self.atom, nn[1])
dirprod = dir1 * dir2
if dirprod < 0:
# both directions are set, and they're inconsistent
raise RecognizerError("inconsistent bond directions")
# including self.atom in the message would be redundant -- compute method glue will annotate with self ###DOIT
elif dirprod > 0:
# both directions are set, consistently
if dir1 < 0:
bases.reverse()
else: # dirprod == 0
# at most one direction is set (need a warning if one is set and one not? assume not, for now)
dir = dir1 + dir2
if dir < 0:
bases.reverse()
elif dir == 0:
# both directions are unset
raise RecognizerError(
"backbone bond direction is locally undefined")
###REVIEW: this should not prevent offering "Make Crossover", only doing it successfully.
return bases
def _filter_neighbor_atompairs(self, atom_dict):
"""
@see: self._find_crossover_atompairs_between_atom_dicts()
"""
new_atom_dict = {}
atomPairsList = []
for atm in atom_dict.values():
for neighbor in atm.neighbors():
if atom_dict.has_key(id(neighbor)):
if self._final_crossover_atoms_dict.has_key(id(atm)) and \
self._final_crossover_atoms_dict.has_key(id(neighbor)):
continue #skip this iteration
if self.graphicsMode.DEBUG_DRAW_ALL_POTENTIAL_CROSSOVER_SITES:
if not new_atom_dict.has_key(id(neighbor)):
new_atom_dict[id(neighbor)] = neighbor
if not new_atom_dict.has_key(id(atm)):
new_atom_dict[id(atm)] = atm
#@@BUG: What if both neighbors of atm are in atom_dict_1??
#In that case, this code creates two separate tuples with
#'atm' as a common atom in each.
#MAKE SURE TO append atoms in the same order as
#their bond_direction. Example, if the bond is atm --> neighbor
#append them as (atm, neighbor) . If bond is from
#neighbor > atm, append them as (neighbor, atm).
#Possible BUG: This method DOES NOT handle case with
#bond_direction = 0 (simply assumes a random order)
if bond_direction(atm, neighbor) == - 1:
atomPairsList.append((neighbor, atm))
else:
atomPairsList.append((atm, neighbor))
return new_atom_dict, atomPairsList
def _filter_neighbor_atompairs(self, atom_dict):
"""
@see: self._find_crossover_atompairs_between_atom_dicts()
"""
new_atom_dict = {}
atomPairsList = []
for atm in atom_dict.values():
for neighbor in atm.neighbors():
if atom_dict.has_key(id(neighbor)):
if self._final_crossover_atoms_dict.has_key(id(atm)) and \
self._final_crossover_atoms_dict.has_key(id(neighbor)):
continue #skip this iteration
if self.graphicsMode.DEBUG_DRAW_ALL_POTENTIAL_CROSSOVER_SITES:
if not new_atom_dict.has_key(id(neighbor)):
new_atom_dict[id(neighbor)] = neighbor
if not new_atom_dict.has_key(id(atm)):
new_atom_dict[id(atm)] = atm
#@@BUG: What if both neighbors of atm are in atom_dict_1??
#In that case, this code creates two separate tuples with
#'atm' as a common atom in each.
#MAKE SURE TO append atoms in the same order as
#their bond_direction. Example, if the bond is atm --> neighbor
#append them as (atm, neighbor) . If bond is from
#neighbor > atm, append them as (neighbor, atm).
#Possible BUG: This method DOES NOT handle case with
#bond_direction = 0 (simply assumes a random order)
if bond_direction(atm, neighbor) == -1:
atomPairsList.append((neighbor, atm))
else:
atomPairsList.append((atm, neighbor))
return new_atom_dict, atomPairsList
def _C_ordered_bases(self):
"""
[compute method for self.ordered_bases]
Return our two bases (as Base5_recognizer objects, which may or may not be .in_helix),
in an order consistent with backbone bond direction,
which we require to be locally defined in a consistent way.
@warning: value will be None (not a sequence) if a RecognizerError was
raised.
"""
if self.unordered_bases is None:
raise RecognizerError("doesn't have two bases")
bases = list(self.unordered_bases) # we might destructively reverse this later, before returning it
nn = bases[0].atom, bases[1].atom
# reverse bases if bond directions go backwards, or complain if not defined or not consistent
# (Note: the following code is mostly generic for pairs of directional bonds,
# so we might package it up into a utility function someday.)
# BTW, in the future we should improve this as follows:
# - find directional-bond strands in both directions, including at least one bond not altered
# when making/unmaking a crossover, and ending on the first bond with direction defined,
# or when you have to end due to error (too far away to stop us) or end of strand.
# - require that this gave you a direction and was not inconsistent.
# - when making the crossover later, actually set all those directions you passed over
# (not just those of your new bonds).
dir1 = bond_direction(nn[0], self.atom) # -1 or 0 or 1
dir2 = bond_direction(self.atom, nn[1])
dirprod = dir1 * dir2
if dirprod < 0:
# both directions are set, and they're inconsistent
raise RecognizerError("inconsistent bond directions")
# including self.atom in the message would be redundant -- compute method glue will annotate with self ###DOIT
elif dirprod > 0:
# both directions are set, consistently
if dir1 < 0:
bases.reverse()
else: # dirprod == 0
# at most one direction is set (need a warning if one is set and one not? assume not, for now)
dir = dir1 + dir2
if dir < 0:
bases.reverse()
elif dir == 0:
# both directions are unset
raise RecognizerError("backbone bond direction is locally undefined")
###REVIEW: this should not prevent offering "Make Crossover", only doing it successfully.
return bases
