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Fix firstOnly selection behavior #152

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Fix firstOnly selection behavior #152

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31 changes: 19 additions & 12 deletions findseq.py
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Original file line number Diff line number Diff line change
Expand Up @@ -333,46 +333,53 @@ def findseq(needle, haystack='*', selName=None, het=0, firstOnly=0):
return None

# remove hetero atoms (waters/ligands/etc) from consideration?
hstk = cmd.get_unused_name()
if bool(int(het)):
cmd.select("__h", "br. " + haystack)
cmd.select(hstk, f"byres {haystack}")
else:
cmd.select("__h", "br. " + haystack + " and not het")
cmd.select(hstk, f"byres {haystack} and not het")

# get the AAs in the haystack
IDs = defaultdict(list)
AAs = defaultdict(list)
for obj in cmd.get_object_list():
for atom in cmd.get_model(f"%{obj} and (name ca) and __h").atom:
for atom in cmd.get_model(f"%{obj} and (name ca) and {hstk}").atom:
IDs[(obj, atom.segi, atom.chain)].append(atom.resi)
AAs[(obj, atom.segi, atom.chain)].append(ONE_LETTER[atom.resn])

reNeedle = re.compile(needle.upper())
# make an empty selection to which we add residues
cmd.select(rSelName, 'None')

for key in AAs:
matches = defaultdict(list)
for key in sorted(AAs):
obj, segi, chain = key

if int(firstOnly) and len(matches[obj]) >= 1:
# ignore other chains
continue

chain_sequence = "".join(AAs[key])
it = reNeedle.finditer(chain_sequence)
for i in it:
start, stop = i.span()
resi = "+".join(IDs[key][start:stop])

sel = f'__h and %{obj} and resi {resi}'
sel = f'{hstk} and %{obj} and resi {resi}'

if chain:
sel += f' and chain {chain}'
if segi:
sel += f' and segi {segi}'

sel = f'{rSelName} or ({sel})'
cmd.select(rSelName, sel)
matches[obj].append(sel)

# remove multiple matches in the same chain
if int(firstOnly):
for obj, v in matches.items():
matches[obj] = v[:1]

if int(firstOnly):
break
cmd.select(rSelName, " or ".join(f"({s})" for v in matches.values() for s in v))
cmd.delete(hstk)

cmd.delete("__h")
cnt = cmd.count_atoms(rSelName)
if not cnt:
print("Sequence was not found")
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