File size: 2,646 Bytes
40e5504 | 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 numpy as np
from Bio import pairwise2
########## Process PDB file ##########
def get_pdb_xyz(pdb_file):
current_pos = -1000
X = []
current_aa = {} # N, CA, C, O, R
for line in pdb_file:
if (line[0:4].strip() == "ATOM" and int(line[22:26].strip()) != current_pos) or line[0:4].strip() == "TER":
if current_aa != {}:
R_group = []
for atom in current_aa:
if atom not in ["N", "CA", "C", "O"]:
R_group.append(current_aa[atom])
if R_group == []:
R_group = [current_aa["CA"]]
R_group = np.array(R_group).mean(0)
X.append([current_aa["N"], current_aa["CA"], current_aa["C"], current_aa["O"], R_group])
current_aa = {}
if line[0:4].strip() != "TER":
current_pos = int(line[22:26].strip())
if line[0:4].strip() == "ATOM":
atom = line[13:16].strip()
if atom != "H":
xyz = np.array([line[30:38].strip(), line[38:46].strip(), line[46:54].strip()]).astype(np.float32)
current_aa[atom] = xyz
return np.array(X)
########## Get DSSP ##########
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(8)
SS_vec[SS_type.find(SS)] = 1
ASA = float(lines[i][34:38].strip())
RSA = min(1, ASA / rASA_std[aa_type.find(aa)]) # relative solvent accessibility
dssp_feature.append(np.concatenate((np.array([RSA]), 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
padded_item = np.zeros(9)
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
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