#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
"""
from icecream import ic
import sys
ic.configureOutput(outputFunction=lambda *a: print(*a, file=sys.stderr), includeContext=True)
ic.configureOutput(prefix='> ')
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
"""
keep_hydrogens = False
if verbose: ic(keep_hydrogens)
if keep_hydrogens:
cmd = PHENIX_BIN_PATH + os.sep + 'phenix.clashscore %s keep_hydrogens=True ' % fn
else:
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()