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T4
File size: 5,652 Bytes
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import argparse
def main(args):
from dateutil import parser
import numpy as np
import os, time, gzip, json
import glob
folder_with_pdbs_path = args.input_path
save_path = args.output_path
alpha_1 = list("ARNDCQEGHILKMFPSTWYV-")
states = len(alpha_1)
alpha_3 = ['ALA','ARG','ASN','ASP','CYS','GLN','GLU','GLY','HIS','ILE',
'LEU','LYS','MET','PHE','PRO','SER','THR','TRP','TYR','VAL','GAP']
aa_1_N = {a:n for n,a in enumerate(alpha_1)}
aa_3_N = {a:n for n,a in enumerate(alpha_3)}
aa_N_1 = {n:a for n,a in enumerate(alpha_1)}
aa_1_3 = {a:b for a,b in zip(alpha_1,alpha_3)}
aa_3_1 = {b:a for a,b in zip(alpha_1,alpha_3)}
def AA_to_N(x):
# ["ARND"] -> [[0,1,2,3]]
x = np.array(x);
if x.ndim == 0: x = x[None]
return [[aa_1_N.get(a, states-1) for a in y] for y in x]
def N_to_AA(x):
# [[0,1,2,3]] -> ["ARND"]
x = np.array(x);
if x.ndim == 1: x = x[None]
return ["".join([aa_N_1.get(a,"-") for a in y]) for y in x]
def parse_PDB_biounits(x, atoms=['N','CA','C'], chain=None):
'''
input: x = PDB filename
atoms = atoms to extract (optional)
output: (length, atoms, coords=(x,y,z)), sequence
'''
xyz,seq,min_resn,max_resn = {},{},1e6,-1e6
for line in open(x,"rb"):
line = line.decode("utf-8","ignore").rstrip()
if line[:6] == "HETATM" and line[17:17+3] == "MSE":
line = line.replace("HETATM","ATOM ")
line = line.replace("MSE","MET")
if line[:4] == "ATOM":
ch = line[21:22]
if ch == chain or chain is None:
atom = line[12:12+4].strip()
resi = line[17:17+3]
resn = line[22:22+5].strip()
x,y,z = [float(line[i:(i+8)]) for i in [30,38,46]]
if resn[-1].isalpha():
resa,resn = resn[-1],int(resn[:-1])-1
else:
resa,resn = "",int(resn)-1
# resn = int(resn)
if resn < min_resn:
min_resn = resn
if resn > max_resn:
max_resn = resn
if resn not in xyz:
xyz[resn] = {}
if resa not in xyz[resn]:
xyz[resn][resa] = {}
if resn not in seq:
seq[resn] = {}
if resa not in seq[resn]:
seq[resn][resa] = resi
if atom not in xyz[resn][resa]:
xyz[resn][resa][atom] = np.array([x,y,z])
# convert to numpy arrays, fill in missing values
seq_,xyz_ = [],[]
try:
for resn in range(min_resn,max_resn+1):
if resn in seq:
for k in sorted(seq[resn]): seq_.append(aa_3_N.get(seq[resn][k],20))
else: seq_.append(20)
if resn in xyz:
for k in sorted(xyz[resn]):
for atom in atoms:
if atom in xyz[resn][k]: xyz_.append(xyz[resn][k][atom])
else: xyz_.append(np.full(3,np.nan))
else:
for atom in atoms: xyz_.append(np.full(3,np.nan))
return np.array(xyz_).reshape(-1,len(atoms),3), N_to_AA(np.array(seq_))
except TypeError:
return 'no_chain', 'no_chain'
pdb_dict_list = []
c = 0
if folder_with_pdbs_path[-1]!='/':
folder_with_pdbs_path = folder_with_pdbs_path+'/'
init_alphabet = ['A', 'B', 'C', 'D', 'E', 'F', 'G','H', 'I', 'J','K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R', 'S', 'T','U', 'V','W','X', 'Y', 'Z', 'a', 'b', 'c', 'd', 'e', 'f', 'g','h', 'i', 'j','k', 'l', 'm', 'n', 'o', 'p', 'q', 'r', 's', 't','u', 'v','w','x', 'y', 'z']
extra_alphabet = [str(item) for item in list(np.arange(300))]
chain_alphabet = init_alphabet + extra_alphabet
biounit_names = glob.glob(folder_with_pdbs_path+'*.pdb')
for biounit in biounit_names:
my_dict = {}
s = 0
concat_seq = ''
concat_N = []
concat_CA = []
concat_C = []
concat_O = []
concat_mask = []
coords_dict = {}
for letter in chain_alphabet:
xyz, seq = parse_PDB_biounits(biounit, atoms=['N','CA','C','O'], chain=letter)
if type(xyz) != str:
concat_seq += seq[0]
my_dict['seq_chain_'+letter]=seq[0]
coords_dict_chain = {}
coords_dict_chain['N_chain_'+letter]=xyz[:,0,:].tolist()
coords_dict_chain['CA_chain_'+letter]=xyz[:,1,:].tolist()
coords_dict_chain['C_chain_'+letter]=xyz[:,2,:].tolist()
coords_dict_chain['O_chain_'+letter]=xyz[:,3,:].tolist()
my_dict['coords_chain_'+letter]=coords_dict_chain
s += 1
fi = biounit.rfind("/")
my_dict['name']=biounit[(fi+1):-4]
my_dict['num_of_chains'] = s
my_dict['seq'] = concat_seq
if s < len(chain_alphabet):
pdb_dict_list.append(my_dict)
c+=1
with open(save_path, 'w') as f:
for entry in pdb_dict_list:
f.write(json.dumps(entry) + '\n')
if __name__ == "__main__":
argparser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
argparser.add_argument("--input_path", type=str, help="Path to a folder with pdb files, e.g. /home/my_pdbs/")
argparser.add_argument("--output_path", type=str, help="Path where to save .jsonl dictionary of parsed pdbs")
args = argparser.parse_args()
main(args)
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