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proton.py
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proton.py
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#!/usr/bin/env python
# Copyright 2021 Mehdi Koşaca, Ezgi Karaca
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
import os
import sys
import time
import shutil
import argparse
import uuid
import string
import random
t0 = time.time()
def main(args): #it runs the script depend on the selected algorithm.
try:
res = ''.join(random.choices(string.ascii_letters, k=5))
run_id = str(uuid.uuid4().hex)
os.system("mkdir -p {}".format(run_id))
current_dir = os.getcwd()
os.system("cp -rf {} .".format(args.pdb))
os.system("cp -rf src {}".format(run_id))
os.system("cp -rf {} {}/src".format(args.pdb,run_id))
os.system("cp -rf EvoEF1 {}".format(run_id))
os.chdir("{}/src".format(run_id))
print("Defining the Interface Residues...")
time.sleep(1)
os.system("python interface_residues.py --pdb {} --chain_ID {} --cut_off {}".format(args.pdb,args.chain_ID,args.cut_off))
if args.algorithm == "EvoEF1":
os.chdir("../")
os.system("mkdir -p {}_chain_{}_EvoEF1_output".format(pdb,args.chain_ID))
os.chdir("src")
parameters = open("parameters","w")
print("cut_off:{} IQR:{}".format(args.cut_off,args.IQR),file=parameters)
parameters.close()
shutil.move("parameters", "../{}_chain_{}_EvoEF1_output".format(pdb,args.chain_ID))
shutil.move("{}_chain_{}_interface_aa_list".format(pdb,args.chain_ID), "../{}_chain_{}_EvoEF1_output".format(pdb,args.chain_ID))
shutil.move("{}_pairwise_distance_list".format(pdb), "../{}_chain_{}_EvoEF1_output".format(pdb,args.chain_ID))
print("Mutant structures and their energies are being calculated ...")
time.sleep(3)
os.system("python energy_calculation_EvoEF1.py --pdb {} --chain_ID {} --mutation_list {}_chain_{}_mutation_list".format(args.pdb,args.chain_ID,pdb,args.chain_ID))
os.system("python detect_outliers.py --pdb {} --chain_ID {} --scores_file {}_chain_{}_proton_scores --algorithm EvoEF1 --IQR {}".format(args.pdb,args.chain_ID,pdb,args.chain_ID,args.IQR))
shutil.move("heatmap_df","../{}_chain_{}_EvoEF1_output".format(pdb,args.chain_ID))
shutil.move("{}_chain_{}_depleting_mutations".format(pdb,args.chain_ID), "../{}_chain_{}_EvoEF1_output".format(pdb,args.chain_ID))
shutil.move("{}_chain_{}_enriching_mutations".format(pdb,args.chain_ID), "../{}_chain_{}_EvoEF1_output".format(pdb,args.chain_ID))
shutil.move("{}_chain_{}_stabilizing_depleting_mutations".format(pdb,args.chain_ID), "../{}_chain_{}_EvoEF1_output".format(pdb,args.chain_ID))
shutil.move("{}_chain_{}_stabilizing_enriching_mutations".format(pdb,args.chain_ID), "../{}_chain_{}_EvoEF1_output".format(pdb,args.chain_ID))
shutil.move("{}_chain_{}_proton_scores".format(pdb,args.chain_ID), "../{}_chain_{}_EvoEF1_output".format(pdb,args.chain_ID))
shutil.move("{}.pdb".format(pdb), "../{}_chain_{}_EvoEF1_output".format(pdb,args.chain_ID))
t1 = time.time()
print("Time elapsed: ", t1-t0, "seconds")
os.chdir("../")
os.system("rm -rf EvoEF1")
os.system("rm -rf src")
os.chdir("../")
os.rename(run_id, str(res)+"_"+"{}_chain_{}_EvoEF1_output".format(pdb,args.chain_ID))
shutil.move(str(res)+"_"+"{}_chain_{}_EvoEF1_output".format(pdb,args.chain_ID),"results")
elif args.algorithm == "FoldX":
os.chdir("../")
os.system("mkdir -p {}_chain_{}_FoldX_output".format(pdb,args.chain_ID))
os.chdir("src")
parameters = open("parameters","w")
print("cut_off:{} IQR:{}".format(args.cut_off,args.IQR),file=parameters)
parameters.close()
shutil.move("parameters", "../{}_chain_{}_FoldX_output".format(pdb,args.chain_ID))
shutil.move("{}_chain_{}_interface_aa_list".format(pdb,args.chain_ID), "../{}_chain_{}_FoldX_output".format(pdb,args.chain_ID))
shutil.move("{}_pairwise_distance_list".format(pdb), "../{}_chain_{}_FoldX_output".format(pdb,args.chain_ID))
print("Mutant structures and their energies are being calculated ...")
time.sleep(3)
os.system("python energy_calculation_FoldX.py --pdb {} --chain_ID {} --mutation_list {}_chain_{}_mutation_list".format(args.pdb,args.chain_ID,pdb,args.chain_ID))
os.system("python detect_outliers.py --pdb {} --chain_ID {} --scores_file {}_chain_{}_proton_scores --algorithm FoldX --IQR {}".format(args.pdb,args.chain_ID,pdb,args.chain_ID,args.IQR))
shutil.move("heatmap_df","../{}_chain_{}_FoldX_output".format(pdb,args.chain_ID))
shutil.move("{}_chain_{}_depleting_mutations".format(pdb,args.chain_ID), "../{}_chain_{}_FoldX_output".format(pdb,args.chain_ID))
shutil.move("{}_chain_{}_enriching_mutations".format(pdb,args.chain_ID), "../{}_chain_{}_FoldX_output".format(pdb,args.chain_ID))
shutil.move("{}_chain_{}_stabilizing_depleting_mutations".format(pdb,args.chain_ID), "../{}_chain_{}_FoldX_output".format(pdb,args.chain_ID))
shutil.move("{}_chain_{}_stabilizing_enriching_mutations".format(pdb,args.chain_ID), "../{}_chain_{}_FoldX_output".format(pdb,args.chain_ID))
shutil.move("{}_chain_{}_proton_scores".format(pdb,args.chain_ID), "../{}_chain_{}_FoldX_output".format(pdb,args.chain_ID))
shutil.move("{}.pdb".format(pdb), "../{}_chain_{}_FoldX_output".format(pdb,args.chain_ID))
t1 = time.time()
print("Time elapsed: ", t1-t0, "seconds")
os.chdir("../")
os.system("rm -rf EvoEF1")
os.system("rm -rf src")
os.chdir("../")
os.rename(run_id, str(res)+"_"+"{}_chain_{}_FoldX_output".format(pdb,args.chain_ID))
shutil.move(str(res)+"_"+"{}_chain_{}_FoldX_output".format(pdb,args.chain_ID),"results")
except:
print("PROT-ON encountered an error. All intermediate files will be removed.")
shutil.rmtree(current_dir + "/" + run_id)
if __name__ == "__main__":
parser = argparse.ArgumentParser(description='PROT-ON')
parser.add_argument("--pdb", type=str, help="dimer complex")
parser.add_argument("--chain_ID", type=str, help="chain ID of interest")
parser.add_argument("--algorithm", type=str, default="EvoEF1", help="algorithm for building mutation and calculating the binding affinities. Selection: EvoEF1 or FoldX")
parser.add_argument("--cut_off", type=float, default=5.0, help="cut-off distance for defining the interface")
parser.add_argument("--IQR", type=float, default=1.5, help="IQR range to define the outliers of box-and-whisker plot")
args = parser.parse_args()
chains = []
unique_chains = []
amino_acids = []
if "/" in args.pdb:
pdb = (args.pdb.split("/")[-1])[:-4]
else:
pdb = args.pdb[:-4] #pdb filename without .pdb extension
with open(args.pdb, "r") as pdbfile:
for line in pdbfile:
if line[:4] == "ATOM":
chains.append(line[21])
amino_acids.append(line[16:21])
for x in chains:
if x not in unique_chains:
unique_chains.append(x)
if len(unique_chains) != 2:
print("""
*************************************************************************************
PROT-ON works only with dimers! Please isolate the relevant dimer from your complex.
*************************************************************************************
""")
sys.exit()
else:
pass
chain1 = unique_chains[0]
chain2 = unique_chains[1]
if args.chain_ID == chain1:
pass
elif args.chain_ID == chain2:
pass
else:
print("""
*************************************************************************************
Something is wrong with your input chain ID definition. Please refer to the example:
python interface_residues.py --pdb complex.pdb --chain_ID D --cut_off 5.0
*************************************************************************************
""")
sys.exit(0)
main(args)