#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""This module contains functions for computing RASP potential
"""
import os
from shutil import copyfile
from rna_tools.tools.mq.lib.wrappers.SubprocessUtils import run_command
from rna_tools.tools.pdb_formatix.PDBFile import PDBFile#resname_check_and_3to1, set_residues_bfactor
from rna_tools.tools.mq.lib.wrappers.base_wrappers import ProgramWrapper
from rna_tools.rna_tools_config import RASP_PATH, RASP_PATH_DIR
# directory where this script is
# files for some commands are also here
DIRECTORY = os.path.dirname(__file__)
[docs]
class RASP(ProgramWrapper):
"""
Wrapper class for running RASP automatically.
"""
program_name = ['rasp_fd', 'rasp_profile_fd']
executable = ['rasp_fd', 'rasp_profile_fd']
def __init__(self, job_id=None):
super(RASP, self).__init__('', '', job_id=job_id, path=RASP_PATH)
[docs]
def run(self, path_to_pdb, global_energy_score=True, potentials=['c3', 'bb', 'bbr', 'all'], handler=True, verbose=False):
"""Compute RASP potential for a single file
``rasp_fd`` generates:
``output_all.txt``::
-9869.61 66447 -0.148534 0 0 0
``rasp_profile_fd`` generates:
``profile_all.txt``::
C 1 R -775.038
C 2 R -1164.22
U 3 R -2054.17
G 4 R -1601.13
[..]
Input:
* path_to_pdb = path to PDB file
* potential_type = all, bbr or c3
* global_energy_score = True/False (See Output), default=True
* hander = True (if you use PYRO)/FALSE otherwise
Output:
* the output depends on global_enery_score value T/F
You might get:
``-9869.61``
``profile [('C', 1, 'R', -775.03800000000001), ('C', 2, 'R', -1164.22) ..``
"""
# step 0
if handler:
copyfile(path_to_pdb, self.sandbox_dir + os.sep + 'query.pdb')
else: # if Pyro needs this because it cannot access file on client
# TODO: make a function decorator with this
f = open(self.sandbox_dir + os.sep + 'query.pdb', 'w')
f.write(path_to_pdb)
f.close()
old_pwd = os.getcwd()
os.chdir(self.sandbox_dir)
pdb_file = PDBFile(pdb_path=os.path.join(self.sandbox_dir, 'query.pdb'))
pdb_file.resname_check_and_3to1()
pdb_file.save(os.path.join(self.sandbox_dir, 'query.pdb'))
self.pdb_fixes = pdb_file.fixes
scores = [] # colect all scores!
if global_energy_score:
# :
# this order is important, should not be changed!!! (based on this order mqaprnadb_load_from.csv reads the data
for potential_type in potentials:
self.log('Running "global_energy_score"')
if run_command(RASP_PATH + os.sep + 'bin' + os.sep + self.executable[0],
['-e', potential_type, '-p', 'query.pdb'],
env={'RASP': RASP_PATH},
stdout_file='output_' + potential_type + '.txt', verbose=verbose):
print('Computing global energy failed')
return -1
else:
f = open('output_' + potential_type + '.txt')
result = [l.split() for l in f.readlines()]
scores += result[0] # ['-1.9657', '144', '-0.0136507', '0.794594', '1.10601', '-2.49573', '-2309.53', '8595', '-0.268707', '-2199.69', '18.6549', '-5.88841', '-5055.01', '19931', '-0.253625', '-4665.96', '44.262', '-8.7896', '-9869.61', '66447', '-0.148534', '0', '0', '0']
#result = float(result[0][2])
f.close()
else:
self.log('Running profile calculation')
if run_command(self.sandbox_dir + os.sep + self.executable[1],
['-e', potential_type, '-p', 'query.pdb'],
env={'RASP': RASP_PATH},
stdout_file='profile_' + potential_type + '.txt'):
print('Computing profile failed')
return -1
else:
f = open('profile_' + potential_type + '.txt')
result = [l.split() for l in f.readlines()]
try:
result = [(int(i[1]), float(i[3])) for i in result]
except IndexError:
result = [(int(i[1]), float(i[2])) for i in result]
f.close()
self.log('Run finished')
os.chdir(old_pwd)
#return '\t'.join(scores)
return scores
#return result or -1 # return -1 if result is 0 or None
[docs]
def colour_by_local_score(self, path_to_pdb, potential_type='all'):
local_scores = self.run(path_to_pdb, potential_type, global_energy_score=False)
local_scores = [float(i[1]) for i in local_scores]
with open(path_to_pdb) as f:
pdb_file = PDBFile(pdb_string=f.read())
pdb_file.set_residues_bfactor(local_scores)
return pdb_file.pdb_string