/
create_RostDB_span_dG.py
executable file
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/
create_RostDB_span_dG.py
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#!/usr/bin/env python3.5
"""
scripts for working with the Rost data set structurally
"""
import argparse
import matplotlib.pyplot as plt
import numpy as np
from retrive_natural_TMs_scores import parse_rost_db, find_topo, create_AddMembrane_xml
import shutil
import os
import re
from get_pdb import download_pdb
from MyPDB import parse_PDB, MyPDB, write_PDB, extract_seq
from AASeq import AASeq
import sys
from Logger import Logger
def main():
parser = argparse.ArgumentParser()
parser.add_argument('-mode')
args = vars(parser.parse_args())
if args['mode'] == 'setup':
"""
iterate the Rost data set and make a dir with each with:
1: download each PDB, isolate the correct chain
2: read the spans from Rost PDBTM, create a XML subroutine for add membrane
3: create flags file to run an embedding xml
"""
setup_db(args)
elif args['mode'] == 'dg_dist':
"""
go over all results from running jobs that run the flag files made by setup_db.
gather the ∆G_insertion for every span, and show a hist and some statistics
"""
analyse_span_dg_distribution(args)
else:
print('no mode found')
def analyse_span_dg_distribution(args):
rost_db = parse_rost_db()
all_dgs = []
single_span_dgs, multi_span_dgs = [], []
for k in rost_db.keys():
if k in ['q9u6b8', 'q03nm0', 'p32851', 'p0ab98', 'p0abj3']:
print('skipping %s becuause its wierd' % k)
continue
all_files = os.listdir('%s' % k)
out_file = [a for a in all_files if 'out.' in a][0]
this_entry_dgs = []
for l in open('%s/%s' % (k, out_file), 'r'):
if 'core.scoring.membrane.MPSpanInsertionEnergy' in l:
if 'for span' in l and 'skipping' not in l:
# print(l)
all_dgs.append(float(l.split()[5]))
this_entry_dgs.append(float(l.split()[5]))
if len(this_entry_dgs) == 1:
single_span_dgs += this_entry_dgs
else:
multi_span_dgs += this_entry_dgs
for lst, name in zip([single_span_dgs, multi_span_dgs, all_dgs], ['single', 'multi', 'all']):
print('%s mean %.2f' % (name, np.mean(lst)))
print('%s median %.2f' % (name, np.median(lst)))
print('%s std %.2f' % (name, np.std(lst)))
print('%s entries %i' % (name, len(lst)))
plt.hist(all_dgs, bins=50, color='red', alpha=0.5, label='all')
plt.hist(single_span_dgs, bins=50, stacked=True, color='b', alpha=0.5, label='single')
plt.hist(multi_span_dgs, bins=50, stacked=True, color='g', alpha=0.5, label='multi')
plt.legend()
plt.title('span ∆G destributions')
plt.xlabel('∆G')
plt.ylabel('count')
plt.show()
def setup_db(args):
rost_db = parse_rost_db()
failed = []
logger = Logger('./db_setup.log')
for k, v in rost_db.items():
# if k != 'q9u6b8': continue
logger.create_header('working on %s' % k)
logger.log('seq: %s' % v['seq'])
logger.log('pdb: %s' % v['pdb'])
logger.log('chain: %s' % v['chain'])
logger.log('ts: %s' % v['ts'])
os.mkdir(k)
os.chdir(k)
# get pdb and extract chain
download_pdb({'name': v['pdb'], 'path': './'})
empty_pdb = MyPDB(name=v['pdb'])
pdb = parse_PDB('pdb%s.ent' % v['pdb'])
chain = pdb.chains[v['chain']]
empty_pdb.add_chain(chain)
write_PDB('%s_%s.pdb' % (k, v['chain']), empty_pdb)
pdb_seq = extract_seq(empty_pdb)
rdb_seq = AASeq(v['seq'])
score, start, end = pdb_seq[v['chain']].align(rdb_seq)
logger.log('pdb seq: %s' % pdb_seq[v['chain']].aligned)
logger.log('rst seq: %s' % rdb_seq.aligned)
# get spans and print xml
spans = find_topo(v['ts'])
new_spans = []
for sp in spans:
start = pdb_seq[v['chain']].aligned_position_at_non_aligned(sp[0]) + 1
end = pdb_seq[v['chain']].aligned_position_at_non_aligned(sp[1]) + 1
logger.log('span %i->%i %s moving to %i->%i' %(sp[0], sp[1], sp[2], start, end))
new_spans.append([start, end, sp[2]])
create_AddMembrane_xml(new_spans, '%s_AddMembrane.xml' % v['pdb'])
# create flags file
with open('embed.flags', 'w+') as fout:
fout.write('-parser:protocol /home/labs/fleishman/jonathaw/elazaridis/protocols/embed_in_membrane.xml\n')
fout.write('-s %s\n' % '%s_%s.pdb' % (k, v['chain']))
fout.write('-parser:script_vars add_memb_xml=%s\n' % '%s_AddMembrane.xml' % v['pdb'])
fout.write('-overwrite\n')
fout.write('-score::elec_memb_sig_die\n')
fout.write('-corrections::beta_nov15\n')
fout.write('-score::memb_fa_sol\n')
os.chdir('../')
if __name__ == '__main__':
main()