Update code/add_3Dalignment.py

code/add_3Dalignment.py

@@ -213,7 +213,6 @@ def get_coords(annot, alignments, coords, resnums_for_sasa, mode):
 
 
 def get_alignments_3D(identifier, model_num, pdb_path, pdbSequence, source, chain, pdbID, mode, path_3D_alignment,file_format = 'gzip'):
-    st.write('HERE')
     pdbSequence = convert_non_standard_amino_acids(pdbSequence)
     if mode == 1:
         if source == 'PDB':
@@ -272,41 +271,3 @@ def get_alignments_3D(identifier, model_num, pdb_path, pdbSequence, source, chai
         alignments = (list(alignments))
 
         return alignments, coords, resnums_for_sasa
-    elif mode==2:
-
-            atomSequence = ''
-            coords = []
-            resnums_for_sasa = []
-            if file_format == 'txt':
-                with open(name, encoding="utf8") as f:
-                    for line in f.readlines():
-                        if line[0:4].strip() == 'ATOM' and line[13:15].strip() == 'CA':
-                            atomSequence += threeToOne(line[17:20].strip())
-                            coords.append([line[31:38].strip(), line[39:46].strip(), line[47:54].strip()])
-                            resnums_for_sasa.append(line[22:26].strip())
-                        elif line[0:4].strip() == 'ATOM' and line[13:15].strip() == 'CA' and line[21] == ' ':
-                            atomSequence += threeToOne(line[17:20].strip())
-                            coords.append([line[31:38].strip(), line[39:46].strip(), line[47:54].strip()])
-                            resnums_for_sasa.append(line[22:26].strip())
-            elif file_format == 'gzip':
-                with gzip.open(pdb_path, mode='rb') as f:
-                    for line in f:
-                        line = line.decode()
-                        if line[0:4].strip() == 'ATOM' and line[13:15].strip() == 'CA':
-                            atomSequence += threeToOne(line[17:20].strip())
-                            coords.append([line[31:38].strip(), line[39:46].strip(), line[47:54].strip()])
-                            resnums_for_sasa.append(line[22:26].strip())
-                        elif line[0:4].strip() == 'ATOM' and line[13:15].strip() == 'CA' and line[21] == ' ':
-                            atomSequence += threeToOne(line[17:20].strip())
-                            coords.append([line[31:38].strip(), line[39:46].strip(), line[47:54].strip()])
-                            resnums_for_sasa.append(line[22:26].strip())
-            #f = open(Path(path_3D_alignment / f'{identifier}_{str(model_num)}_3Dalignment.txt'),"w")
-            aligner.mode = 'local'
-            aligner.substitution_matrix = substitution_matrices.load("BLOSUM62")
-            aligner.open_gap_score = -11
-            aligner.extend_gap_score = -1
-            atomSequence = convert_non_standard_amino_acids(atomSequence)
-            alignments = aligner.align(pdbSequence, atomSequence)
-            alignments = (list(alignments))
-
-            return alignments, coords, resnums_for_sasa