Source code for rna_tools.tools.mq.ClashScore.ClashScore

#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""This module contains functions for computing NAST potential via Pyro.
"""
from __future__ import print_function

import argparse
import os

from rna_tools.rna_tools_config import PHENIX_BIN_PATH
from rna_tools.tools.mq.lib.wrappers.base_wrappers import ProgramWrapper
from subprocess import Popen, PIPE

# directory where this script is
# files for some commands are also here
DIRECTORY = os.path.dirname(__file__)


[docs]class ClashScore(object): """ClashScore: Wrapper class for running phenix.clashscore """ def __init__(self): pass
[docs] def run(self, fn, verbose=False): """ Args: fn (string): path to a file verbose (bool): be verbose Returns: clashscore (float) Example:: /Applications/phenix-1.18.2-3874/build/bin/phenix.clashscore test/1xjrA.pdb Using electron cloud x-H distances and vdW radii Adding H/D atoms with reduce... Bad Clashes >= 0.4 Angstrom: A 17 A N1 A 34 G N1 :0.430 clashscore = 0.66 test/1xjrA.pdb 0.66 /Applications/phenix-1.18.2-3874/build/bin/phenix.clashscore test/1xjrA_M1.pdb Using electron cloud x-H distances and vdW radii Adding H/D atoms with reduce... Bad Clashes >= 0.4 Angstrom: A 41 G H2' A 42 U OP1 :0.738 A 25 U H6 A 25 U HO2' :0.659 A 46 U H2' A 47 U OP2 :0.656 A 29 A H5'' A 30 U O2' :0.623 (...) A 24 G O2' A 26 A C8 :0.410 A 42 U O2' A 43 G H8 :0.409 A 43 G H2' A 44 A O4' :0.408 A 28 G C8 A 28 G O2' :0.403 clashscore = 15.45 test/1xjrA_M1.pdb 15.45 # so the output is clashscore = 15.45 """ cmd = PHENIX_BIN_PATH + os.sep + 'phenix.clashscore %s ' % fn if verbose: print(cmd) out = Popen([cmd], stderr=PIPE, stdout=PIPE, shell=True) stdout = out.stdout.read().decode().strip() if verbose: print(stdout) out = float(stdout.split('\n')[-1].replace('clashscore = ','')) # this is another #cmd = 'phenix.clashscore_1.8.1-1168 keep_hydrogens=True %s' % name #out2 = float(getoutput(cmd).split('\n')[-1].replace('clashscore = ','')) #return ','.join([str(out), str(out2)]) return out
[docs] def cleanup(self): pass
[docs]def test(): wrapper = ClashScore() fns = ['../test' + os.sep + '1xjrA.pdb', '../test' + os.sep + '1xjrA_M1.pdb', # native, and M1 from rasp decoys '../test' + os.sep + '6TNA.pdb' ] for f in fns: result = wrapper.run(f, True) print(f) print(result) wrapper.cleanup()
if __name__ == '__main__': test()