Fixed interactive FASTA input on backbone

bioexcel · Jul 28, 2024 · c49c1c2 · c49c1c2
1 parent 022b21d
commit c49c1c2
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Showing 2 changed files with 6 additions and 4 deletions.
diff --git a/biobb_structure_checking/commands/backbone.py b/biobb_structure_checking/commands/backbone.py
@@ -205,7 +205,7 @@ def _backbone_fix_main_chain(strcheck, fix_main_bck, breaks_list, modeller_key,
         return []
 
     # Checking for canonical sequence
-    if not strcheck.strucm.sequence_data.has_canonical:
+    if not strcheck.strucm.sequence_data.has_canonical[0]:
         read_ok = False
         while not read_ok:
             input_line = ParamInput(
@@ -231,7 +231,7 @@ def _backbone_fix_main_chain(strcheck, fix_main_bck, breaks_list, modeller_key,
             strcheck.strucm,
             False
         )
-        strcheck.strucm.sequence_data.match_sequence_numbering()
+        strcheck.strucm.sequence_data.match_sequence_numbering(strcheck.strucm)
 
     to_fix = [
         rpair

diff --git a/biobb_structure_checking/modelling/sequencedata.py b/biobb_structure_checking/modelling/sequencedata.py
@@ -176,8 +176,10 @@ def read_canonical_seqs(self, strucm, cif_warn):
                 if cif_warn:
                     print("Warning: sequence data unavailable on cif data")
                 return True
+        print(self.data)
+
         for mod in strucm.st:
-            if mod not in self.data:
+            if mod.id not in self.data:
                 self.data[mod.id] = {}
             for index, chid in enumerate(chids):
                 for ch_id in chid.split(','):
@@ -205,7 +207,6 @@ def read_canonical_seqs(self, strucm, cif_warn):
                     self.data[mod.id][ch_id]['can'].features.append(
                         SeqFeature(FeatureLocation(1, len(seqs[index])))
                     )
-
                     # for chn in chids[i].split(','):
                     #     if chn in strucm.chain_ids:
                     #         self.data[ch_id]['chains'].append(chn)
@@ -330,6 +331,7 @@ def match_sequence_numbering(self, strucm):
                 # print(f"{self.has_canonical=} {mod.id=}")
                 if ch_id not in self.has_canonical.get(mod.id, []) or not self.has_canonical.get(mod.id, dict()).get(ch_id, []):
                     continue
+                print(ch_data)
                 frgs = ch_data['pdb']['frgs']
                 ch_data['pdb']['match_numbering'] = True
                 for nfrag, frag in enumerate(frgs):