#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""This module contains functions for computing 3dRNAscore
Install::
make # make clean if you don't have clean
At Mac there is a problem (201128, 211103)::
(py37) [mx] example$ ../bin/3dRNAscore -s:l score.in >score.txt
[1] 69818 segmentation fault ../bin/3dRNAscore -s:l score.in > score.txt
"""
import os
from shutil import copyfile
from rna_tools.tools.mq.lib.wrappers.SubprocessUtils import run_command
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 RNAscore_PATH
# directory where this script is
# files for some commands are also here
#try:
#except NameError:
DIRECTORY = os.path.dirname(__file__)
[docs]
class RNAscore(ProgramWrapper):
"""
Wrapper class for running 3dRNAscore
"""
program_name = '/bin/3dRNAscore'
def __init__(self, job_id=None):
super(RNAscore, self).__init__('', '', job_id=job_id)
[docs]
def run(self, path_to_pdb, verbose=1):
copyfile(path_to_pdb, self.sandbox_dir + os.sep + 'query.pdb')
old_pwd = os.getcwd()
#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
os.chdir(self.sandbox_dir)
err = ''
out = ''
self.log('3dRNAscore::start for %s' % self.sandbox_dir + '/query.pdb')
if run_command(RNAscore_PATH + os.sep + self.program_name,
['-s', self.sandbox_dir + '/query.pdb'],
env={'RNAscore': RNAscore_PATH},
stdout_file=self.sandbox_dir + '/output.txt', stderr_file=self.sandbox_dir + '/err.txt', verbose=verbose):
err = open(self.sandbox_dir + '/err.txt').read().strip()
print('3dRNAscore::err', err)
result = -1
else:
f = open(self.sandbox_dir + '/output.txt')
result = float(f.read())
f.close()
self.log('3dRNAscore::err %s' % err)
self.log('3dRNAscore::result %s' % str(result))
self.log('3dRNAscore::Run finished')
os.chdir(old_pwd)
return result # return -1 if result is 0 or None
[docs]
def main():
wrapper = RNAscore()
try:
result = wrapper.run('../test' + os.sep + '1a9n.pdb')
if result:
print(result)
except Exception as e:
print(e)
finally:
#wrapper.cleanup()
pass
if '__main__' == __name__:
main()