fatmacankara commited on
Commit
2d335db
·
1 Parent(s): af56dfe

Update code/add_3Dalignment.py

Browse files
Files changed (1) hide show
  1. code/add_3Dalignment.py +4 -14
code/add_3Dalignment.py CHANGED
@@ -10,13 +10,13 @@ from Bio import Align
10
  import gzip
11
  from pathlib import Path
12
  from Bio.Align import substitution_matrices
 
13
  aligner = Align.PairwiseAligner()
14
  import requests
15
  from Bio.PDB import PDBParser, PPBuilder
16
  from io import StringIO
17
 
18
 
19
- from Bio.PDB.Polypeptide import *
20
 
21
 
22
  def convert_non_standard_amino_acids(sequence):
@@ -260,13 +260,7 @@ def get_alignments_3D(identifier, model_num, pdb_path, pdbSequence, source, chai
260
  atomSequence += threeToOne(line[17:20].strip())
261
  coords.append([line[31:38].strip(), line[39:46].strip(), line[47:54].strip()])
262
  resnums_for_sasa.append(line[22:26].strip())
263
- print('In 3D Alignments')
264
- print('atomSequence')
265
- print(atomSequence)
266
- print('coords')
267
- print(coords)
268
- print('resnums_for_sasa')
269
- print(resnums_for_sasa)
270
  aligner.mode = 'local'
271
  aligner.substitution_matrix = substitution_matrices.load("BLOSUM62")
272
  aligner.open_gap_score = -11
@@ -275,14 +269,10 @@ def get_alignments_3D(identifier, model_num, pdb_path, pdbSequence, source, chai
275
 
276
 
277
  atomSequence = convert_non_standard_amino_acids(atomSequence)
278
- print('HERE LASTLY')
279
- print(pdbSequence)
280
- print(atomSequence)
281
- print(aligner.align(pdbSequence, atomSequence))
282
  alignments = aligner.align(pdbSequence, atomSequence)
283
  alignments = (list(alignments))
284
- print('alignments')
285
- print(alignments)
286
  return alignments, coords, resnums_for_sasa
287
  elif mode==2:
288
  atomSequence = ''
 
10
  import gzip
11
  from pathlib import Path
12
  from Bio.Align import substitution_matrices
13
+ from Bio.PDB.Polypeptide import *
14
  aligner = Align.PairwiseAligner()
15
  import requests
16
  from Bio.PDB import PDBParser, PPBuilder
17
  from io import StringIO
18
 
19
 
 
20
 
21
 
22
  def convert_non_standard_amino_acids(sequence):
 
260
  atomSequence += threeToOne(line[17:20].strip())
261
  coords.append([line[31:38].strip(), line[39:46].strip(), line[47:54].strip()])
262
  resnums_for_sasa.append(line[22:26].strip())
263
+
 
 
 
 
 
 
264
  aligner.mode = 'local'
265
  aligner.substitution_matrix = substitution_matrices.load("BLOSUM62")
266
  aligner.open_gap_score = -11
 
269
 
270
 
271
  atomSequence = convert_non_standard_amino_acids(atomSequence)
272
+
 
 
 
273
  alignments = aligner.align(pdbSequence, atomSequence)
274
  alignments = (list(alignments))
275
+
 
276
  return alignments, coords, resnums_for_sasa
277
  elif mode==2:
278
  atomSequence = ''