def buildContiguousCloseResidueSequences(self):
#7. attempt to show ribbon for contiguous residues in macromolecule
rdict = self.results
res = rdict['macro_close_res']
chs = res.parent.uniq()
ss_res = ResidueSet()
last_ind = 0
chain1 = 1
#output = 0
for c in chs:
num_res = len(c.residues)
if num_res <3:
continue
rr = res.get(lambda x: x.parent==c)
rr.sort()
chain1 = 0
current_seq = ResidueSet() # contiguous residues
current_set = ResidueSet() # all pieces in this chain
skipped_set = ResidueSet() # hole in current contiguous piece
if len(rr)>3: #?? min num residues for ss:at least 3??
#reset all
first = c.residues.index(rr[0])
last = c.residues.index(rr[-1])
for r in c.residues[first:last+1]:
if r==c.residues[-1]:
if r in rr:
if len(current_seq)>3:
current_seq.append(r)
if len(current_seq)>4:
ss_res.extend(current_seq)
if r not in rr: #process hole
skipped_set.append(r) # one hole ok
if len(skipped_set)>=2: # found second hole -> end seq
if len(current_seq)>4:
if not len(current_set):
current_set = current_seq[:]
current_set.sort()
else:
current_set.extend(current_seq)
current_set.sort()
if not len(ss_res):
ss_res = current_set[:]
else:
ss_res.extend(current_set)
skipped_set = ResidueSet()
current_seq = ResidueSet()
else:
#reset skipped_set
if len(skipped_set)<=1 and len(current_seq)>=1: #save RR_R
current_seq.extend(skipped_set) #save hole if there is one
current_seq.append(r) #save this residue
else: #just save it
current_seq.append(r)
skipped_set= ResidueSet()
if len(current_seq)>4:
for r in current_seq:
if r not in ss_res:
ss_res.append(r)
if len(current_set)>4:
for r in current_set:
if r not in ss_res:
ss_res.append(r)
rdict['ss_res'] = ss_res
def buildContiguousCloseResidueSequences(self):
#7. attempt to show ribbon for contiguous residues in macromolecule
rdict = self.results
res = rdict['macro_close_res']
chs = res.parent.uniq()
ss_res = ResidueSet()
last_ind = 0
chain1 = 1
#output = 0
for c in chs:
num_res = len(c.residues)
if num_res <3:
continue
rr = res.get(lambda x: x.parent==c)
rr.sort()
chain1 = 0
current_seq = ResidueSet() # contiguous residues
current_set = ResidueSet() # all pieces in this chain
skipped_set = ResidueSet() # hole in current contiguous piece
if len(rr)>3: #?? min num residues for ss:at least 3??
#reset all
first = c.residues.index(rr[0])
last = c.residues.index(rr[-1])
for r in c.residues[first:last+1]:
if r==c.residues[-1]:
if r in rr:
if len(current_seq)>3:
current_seq.append(r)
if len(current_seq)>4:
ss_res.extend(current_seq)
if r not in rr: #process hole
skipped_set.append(r) # one hole ok
if len(skipped_set)>=2: # found second hole -> end seq
if len(current_seq)>4:
if not len(current_set):
current_set = current_seq[:]
current_set.sort()
else:
current_set.extend(current_seq)
current_set.sort()
if not len(ss_res):
ss_res = current_set[:]
else:
ss_res.extend(current_set)
skipped_set = ResidueSet()
current_seq = ResidueSet()
else:
#reset skipped_set
if len(skipped_set)<=1 and len(current_seq)>=1: #save RR_R
current_seq.extend(skipped_set) #save hole if there is one
current_seq.append(r) #save this residue
else: #just save it
current_seq.append(r)
skipped_set= ResidueSet()
if len(current_seq)>4:
for r in current_seq:
if r not in ss_res:
ss_res.append(r)
if len(current_set)>4:
for r in current_set:
if r not in ss_res:
ss_res.append(r)
rdict['ss_res'] = ss_res
