def _residueCB(self, trigName, ignore, resChanges): deletions = [dr for dr in resChanges.deleted if dr in self.resMap] if len(deletions) == len(self.resMap): self.demoteToSequence() return # sort deletions into descending order so we can easily # delete from our residue list deletions.sort(lambda r1, r2: cmp(self.resMap[r2], self.resMap[r1])) for dr in deletions: pos = self.resMap[dr] del self.resMap[dr] self.residues[pos] = None typesChanged = False if "type changed" in resChanges.reasons: from resCode import res3to1 ungapped = self.ungapped() for res, pos in self.resMap.items(): if res3to1(res.type) != ungapped[pos]: typesChanged = True self[self.ungapped2gapped(pos) ] = res3to1(res.type) if deletions or typesChanged: self.triggers.activateTrigger(self.TRIG_MODIFY, self)
def insert(self, pos, insertion): if type(insertion) == str: return Sequence.insert(self, pos, insertion) for r, i in self.resMap.items(): if i >= pos: self.resMap[r] = i+1 self.residues.insert(pos, insertion) self.resMap[insertion] = pos from resCode import res3to1 Sequence.insert(self, pos, res3to1(insertion.type)) self.triggers.activateTrigger(self.TRIG_MODIFY, self)
def append(self, item): try: itemList = list(item) except TypeError: itemList = [item] if itemList and isinstance(itemList[0], basestring): return Sequence.extend(self, itemList) base = len(self.residues) for i, res in enumerate(itemList): self.resMap[res] = base + i self.residues.extend(itemList) from resCode import res3to1 Sequence.extend(self, [res3to1(r.type) for r in itemList])
def __setitem__(self, key, val):
if type(val) == str:
return Sequence.__setitem__(self, key, val)
ungapped = self.gapped2ungapped(key)
if ungapped is None:
raise KeyError("Cannot set gap to non-gap")
oldRes = self.residues[ungapped]
if oldRes:
del self.resMap[oldRes]
self.resMap[val] = ungapped
self.residues[ungapped] = val
from resCode import res3to1
Sequence.__setitem__(self, key, res3to1(val.type))
self.triggers.activateTrigger(self.TRIG_MODIFY, self)
def __setslice__(self, i, j, seq): if not isinstance(seq, self.__class__): return Sequence.__setslice__(self, i, j, seq) ungappedI = self._bestUngapped(i) ungappedJ = self._bestUngapped(j) for r in self.residues[ungappedI:ungappedJ]: del self.resMap[r] size = ungappedJ - ungappedI for r, ri in self.resMap.items(): if ri >= ungappedI: self.resMap[r] = ri + len(seq) - max(size, 0) self.residues[ungappedI:ungappedJ] = seq.residues from resCode import res3to1 Sequence.__setslice__(self, i, j, [res3to1(r.type) for r in seq]) self.triggers.activateTrigger(self.TRIG_MODIFY, self)
def r3to1(rType):
from resCode import res3to1
l = res3to1(rType)
if l == 'X':
return rType
return l
def _residueCB(self, trigName, ignore, resChanges):
deletions = [dr for dr in resChanges.deleted
if dr in self.resMap]
if len(deletions) == len(self.residues):
self.demoteToSequence()
return
# sort deletions into descending order so we can easily
# delete from our residue list
deletions.sort(lambda r1, r2:
cmp(self.resMap[r2], self.resMap[r1]))
for dr in deletions:
pos = self.resMap[dr]
Sequence.__delitem__(self, self.ungapped2gapped(pos))
del self.resMap[dr]
del self.residues[pos]
typesChanged = False
if "type changed" in resChanges.reasons:
from resCode import res3to1
ungapped = self.ungapped()
for res, pos in self.resMap.items():
if res3to1(res.type) != ungapped[pos]:
typesChanged = True
self[self.ungapped2gapped(pos)
] = res3to1(res.type)
# identify new residues that should be added to the sequence
candidates = {}.fromkeys([cr for cr in resChanges.created
if cr.molecule == self.molecule
and cr not in self.resMap])
addedSome = False
if candidates:
# find cross-residue bonds that connect candidates/
# current residues
allRes = self.resMap.copy()
allRes.update(candidates)
crossBonds = [b for b in self.molecule.bonds
if b.atoms[0].residue != b.atoms[1].residue
and b.atoms[0].residue in allRes
and b.atoms[1].residue in allRes]
resConn = {}
joined = {}
for cb in crossBonds:
crs = [a.residue for a in cb.atoms]
resConn.setdefault(crs[0], []).append(crs[1])
resConn.setdefault(crs[1], []).append(crs[0])
joined[tuple(crs)] = True
crs.reverse()
joined[tuple(crs)] = True
while True:
addThese = {}
for ar in candidates.keys():
for jr in resConn.get(ar, []):
if jr not in self.resMap:
continue
if len(resConn.get(jr, [])) > 2:
# throw up hands
continue
addThese[ar] = jr
if addThese:
addedSome = True
from resCode import res3to1
for add, prev in addThese.items():
after = cmp(add.id,
prev.id) > 0
where = self.residues.index(
prev) + after
if where == len(self.residues):
seqWhere = len(self)
else:
seqWhere = self.\
ungapped2gapped(where)
self.residues.insert(where, add)
Sequence.insert(self, seqWhere,
res3to1(add.type))
self.resMap[add] = None
del candidates[add]
else:
break
if deletions or typesChanged or addedSome:
self.resMap.clear()
for i, r in enumerate(self.residues):
self.resMap[r] = i
self.triggers.activateTrigger(self.TRIG_MODIFY, self)
def r3to1(rType): from resCode import res3to1 l = res3to1(rType) if l == 'X': return rType return l