fit_domains_in_chimerax.py

#!/usr/bin/env python3
# # -*- coding: utf-8 -*-

"""
@Authors Max Tong & HB
@Require ChimeraX 1.5 and up with proper excecutable
"""
# Usage
# python fit_domains_in_chimerax pdb_dir output_dir input_map map_level resolution search numProc
# Write a file for the best fit correlation for each domain as a summary

import sys,os,time
from shutil import which
from datetime import datetime
script_dir=os.path.dirname(os.path.realpath(__file__))
import subprocess, multiprocessing

def print_usage ():
	print("usage: fit_domains_in_chimerax.py inputDir outputDir inputMap mapLevel resolution searchNo noProcessor")
	print("eg: fit_domains_in_chimerax.py single_domains solutions ref.mrc 0.0394 5 200 10")
	sys.exit()
	
def execute(cmd):
	print(f'start {cmd}', datetime.now())
	return subprocess.call(cmd,shell=True)

if __name__ == "__main__":

	if len(sys.argv) < 7:
		print_usage()

	
	pdb_dir = sys.argv[1]
	output_dir = sys.argv[2]
	input_map = sys.argv[3]
	map_level = sys.argv[4]
	resolution = sys.argv[5]
	search = sys.argv[6]

	if len(sys.argv) == 7:
		threads = 10; # Default 10 threads
	else:
		threads = int(sys.argv[7])
	
	# Check operating system
	useMacOs = 0
	print("Platform: " + sys.platform)

	if sys.platform == 'darwin': #MacOS
		useMacOs = 1
		print ("No capability to generate picture on MacOS!!!")
		
	chimerax_path = "chimerax"
	if useMacOs == 1:
		chimerax_path = "/Applications/ChimeraX-1.5.app/Contents/MacOS/ChimeraX"
	
	# Check if ChimeraX path is correct	
	if os.path.exists(chimerax_path) == 0 and which(chimerax_path) is None:
		print(f"The file '{chimerax_path}' does not exist.")
		print("Modify the script for the path of ChimeraX version from 1.5 and above.")
		exit(0)
	
	os.makedirs(output_dir, exist_ok=True)

	# Initiate a log file
	log_file = output_dir + '/fit_logs.txt'
	log = open(log_file, "w")
	# log.write("#{}\n".format(datetime.now().strftime("%m/%d/%Y, %H:%M:%S")))
	log.write("\nDomain, NoRes, Best_Corr, Second_Best_Corr, Diff, Worst_Corr, Range, P_val_best_fit, Corr_about_mean, Eta0, Pvalue, BH_adjusted_Pvalue\n")
	# log.write("\n")
	log.close()

	list = os.listdir(pdb_dir)
	cmds=[]
	for pdb in os.listdir(pdb_dir):
		if pdb.endswith((".pdb", ".cif")):
			# Add them to the command list
			cmds.append(f'{chimerax_path} --nogui --offscreen --cmd \"runscript {script_dir}/fit_in_chimerax.py {pdb_dir}/{pdb} {output_dir} {input_map} {map_level} {resolution} {search}" --exit')

	with multiprocessing.Pool(processes=threads) as pool:
		results = pool.map(execute, cmds)

	# Find best domain based on largest change in fit correlation between first and second hit
	import pandas as pd
	df = pd.read_csv(log_file, sep='\s*,\s*', engine='python')
	df.info()
	df.dropna()
	print(df)
	#for col in df.columns:
		#print(col)
	df.sort_values(['BH_adjusted_Pvalue', 'Corr_about_mean'], ascending=[True, False], inplace=True)
	# df.sort_values(by = "Diff", inplace=True, ascending=False)

	#print(df)
	df.to_csv(output_dir + '/fit_logs_revised.csv', index=False)