File size: 2,538 Bytes
ad9fbbf | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 | import os, pickle
import numpy as np
from Bio import pairwise2
from pad_feature import parse_fasta_file
software_path = "./Software/"
def process_dssp(dssp_file):
aa_type = "ACDEFGHIKLMNPQRSTVWY"
SS_type = "HBEGITSC"
rASA_std = [115, 135, 150, 190, 210, 75, 195, 175, 200, 170,
185, 160, 145, 180, 225, 115, 140, 155, 255, 230]
with open(dssp_file, "r") as f:
lines = f.readlines()
seq = ""
dssp_feature = []
p = 0
while lines[p].strip()[0] != "#":
p += 1
for i in range(p + 1, len(lines)):
aa = lines[i][13]
if aa == "!" or aa == "*":
continue
seq += aa
SS = lines[i][16]
if SS == " ":
SS = "C"
SS_vec = np.zeros(9) # The last dim represents "Unknown" for missing residues
SS_vec[SS_type.find(SS)] = 1
PHI = float(lines[i][103:109].strip())
PSI = float(lines[i][109:115].strip())
ACC = float(lines[i][34:38].strip())
ASA = min(100, round(ACC / rASA_std[aa_type.find(aa)] * 100)) / 100
dssp_feature.append(np.concatenate((np.array([PHI, PSI, ASA]), SS_vec)))
return seq, dssp_feature
def match_dssp(seq, dssp, ref_seq):
alignments = pairwise2.align.globalxx(ref_seq, seq)
ref_seq = alignments[0].seqA
seq = alignments[0].seqB
SS_vec = np.zeros(9) # The last dim represent "Unknown" for missing residues
SS_vec[-1] = 1
padded_item = np.concatenate((np.array([360, 360, 0]), SS_vec))
new_dssp = []
for aa in seq:
if aa == "-":
new_dssp.append(padded_item)
else:
new_dssp.append(dssp.pop(0))
matched_dssp = []
for i in range(len(ref_seq)):
if ref_seq[i] == "-":
continue
matched_dssp.append(new_dssp[i])
return matched_dssp
def transform_dssp(dssp_feature):
dssp_feature = np.array(dssp_feature)
angle = dssp_feature[:,0:2]
ASA_SS = dssp_feature[:,2:]
radian = angle * (np.pi / 180)
dssp_feature = np.concatenate([np.sin(radian), np.cos(radian), ASA_SS], axis = 1)
return dssp_feature
def get_dssp(ID, ref_seq):
os.system("{}dssp-2.0.4/mkdssp -i ../datasets/alphafold3pdb/{}.pdb -o ./dssp/{}.dssp".format(software_path, ID, ID))
dssp_seq, dssp_matrix = process_dssp("./dssp/" + ID + ".dssp")
if dssp_seq != ref_seq:
dssp_matrix = match_dssp(dssp_seq, dssp_matrix, ref_seq)
np.save("./dssp/" + ID, transform_dssp(dssp_matrix))
os.system("rm ./dssp/" + ID + ".dssp")
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