def onSearch(self, query):
self.should_stop = False
self.found_something = False
# Transform whitespace-separated query into OR-regex.
regex = re.compile(
'|'.join(tools.get_pattern(word) for word in query.split()),
re.IGNORECASE)
for dir in self.get_search_paths() + [consts.dirBaseUsr]:
# Check if search has been aborted during filtering
if self.should_stop:
break
# Only search in home folder if we haven't found anything yet.
if dir == consts.dirBaseUsr and self.found_something:
break
results = self.search_dir(dir, query)
# Check if search has been aborted during searching
if results is None or self.should_stop:
break
dirs, files = self.filter_results(results, dir, regex)
if not self.should_stop and (dirs or files):
self.found_something = True
modules.postMsg(consts.MSG_EVT_SEARCH_APPEND, {
'results': (dirs, files),
'query': query
})
modules.postMsg(consts.MSG_EVT_SEARCH_END)
def onSearch(self, query):
self.should_stop = False
self.found_something = False
# Transform whitespace-separated query into OR-regex.
regex = re.compile('|'.join(tools.get_pattern(word)
for word in query.split()), re.IGNORECASE)
for dir in self.get_search_paths() + [consts.dirBaseUsr]:
# Check if search has been aborted during filtering
if self.should_stop:
break
# Only search in home folder if we haven't found anything yet.
if dir == consts.dirBaseUsr and self.found_something:
break
results = self.search_dir(dir, query)
# Check if search has been aborted during searching
if results is None or self.should_stop:
break
dirs, files = self.filter_results(results, dir, regex)
if not self.should_stop and (dirs or files):
self.found_something = True
modules.postMsg(consts.MSG_EVT_SEARCH_APPEND,
{'results': (dirs, files), 'query': query})
modules.postMsg(consts.MSG_EVT_SEARCH_END)
def ss_motif(args):
# sanity checks
files = args.files
print "# Finding 3D Single Strand Motifs..."
# assert args.bulges < 3, "# FATAL: cannot do bulges > 2"
ref_pdb = reader.Pdb(args.reference, res_mode=args.res_mode)
ref_len = len(ref_pdb.model.sequence)
ref_mat = (ref_pdb.model.get_gmat(args.cutoff)).reshape(-1)
if args.seq == None:
query = "N" * ref_len
else:
assert len(args.seq) == ref_len, "# FATAL: query structure and sequence length mismatch!"
query = args.seq
pattern = tools.get_pattern(query)
# OK...
fh = open(args.name, "w")
fh.write("# This is a baRNAba run.\n")
for k in sorted(args.__dict__):
s = "# " + str(k) + " " + str(args.__dict__[k]) + "\n"
fh.write(s)
for i in xrange(0, len(files)):
cur_pdb = reader.Pdb(files[i], res_mode=args.res_mode)
cur_pdb.set_xtc(args.xtc)
cur_len = len(cur_pdb.model.sequence)
if cur_len < ref_len:
continue
# return indeces matching query
indeces = tools.get_idx(cur_pdb.model.sequence, query, args.bulges)
idx = 0
while idx >= 0:
gmats = [(cur_pdb.model.get_gmat(args.cutoff, index)).reshape(-1) for index in indeces]
dists = distance.cdist([ref_mat], gmats) / np.sqrt(ref_len)
below_t = (dists < args.treshold).nonzero()[1]
for ss in below_t:
seq = "_".join([cur_pdb.model.sequence_id[p] for p in indeces[ss]])
string = "%8.5f %s %i - %s \n" % (dists[0, ss], files[i], idx, seq)
fh.write(string)
idx = cur_pdb.read()
fh.close()
