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2d335db
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af56dfe
Update code/add_3Dalignment.py
Browse files- code/add_3Dalignment.py +4 -14
code/add_3Dalignment.py
CHANGED
@@ -10,13 +10,13 @@ from Bio import Align
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import gzip
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from pathlib import Path
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from Bio.Align import substitution_matrices
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aligner = Align.PairwiseAligner()
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import requests
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from Bio.PDB import PDBParser, PPBuilder
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from io import StringIO
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from Bio.PDB.Polypeptide import *
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def convert_non_standard_amino_acids(sequence):
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@@ -260,13 +260,7 @@ def get_alignments_3D(identifier, model_num, pdb_path, pdbSequence, source, chai
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atomSequence += threeToOne(line[17:20].strip())
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coords.append([line[31:38].strip(), line[39:46].strip(), line[47:54].strip()])
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resnums_for_sasa.append(line[22:26].strip())
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print('atomSequence')
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print(atomSequence)
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print('coords')
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print(coords)
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print('resnums_for_sasa')
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print(resnums_for_sasa)
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aligner.mode = 'local'
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aligner.substitution_matrix = substitution_matrices.load("BLOSUM62")
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aligner.open_gap_score = -11
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@@ -275,14 +269,10 @@ def get_alignments_3D(identifier, model_num, pdb_path, pdbSequence, source, chai
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atomSequence = convert_non_standard_amino_acids(atomSequence)
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print(pdbSequence)
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print(atomSequence)
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print(aligner.align(pdbSequence, atomSequence))
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alignments = aligner.align(pdbSequence, atomSequence)
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alignments = (list(alignments))
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print(alignments)
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return alignments, coords, resnums_for_sasa
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elif mode==2:
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atomSequence = ''
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import gzip
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from pathlib import Path
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from Bio.Align import substitution_matrices
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from Bio.PDB.Polypeptide import *
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aligner = Align.PairwiseAligner()
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import requests
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from Bio.PDB import PDBParser, PPBuilder
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from io import StringIO
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def convert_non_standard_amino_acids(sequence):
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atomSequence += threeToOne(line[17:20].strip())
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coords.append([line[31:38].strip(), line[39:46].strip(), line[47:54].strip()])
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resnums_for_sasa.append(line[22:26].strip())
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aligner.mode = 'local'
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aligner.substitution_matrix = substitution_matrices.load("BLOSUM62")
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aligner.open_gap_score = -11
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atomSequence = convert_non_standard_amino_acids(atomSequence)
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alignments = aligner.align(pdbSequence, atomSequence)
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alignments = (list(alignments))
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return alignments, coords, resnums_for_sasa
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elif mode==2:
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atomSequence = ''
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