#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""This module contains functions for computing RNA3DCNN potential
Output::
Trainable params: 4,282,801
Non-trainable params: 0
_________________________________________________________________
Scores for each nucleotide in /var/folders/yc/ssr9692s5fzf7k165grnhpk80000gp/T/tmptg6jy2ud/query.pdb:
[[ 0.02462262]
[ 0.03271335]
[ 0.06199259]
[ 0.02006263]
[ 0.05937254]
[ 0.12025979]
[ 0.20201728]
[ 0.24463326]
[ 0.43518737]
[ 0.7260638 ]
[ 0.6140108 ]
[ 0.6588027 ]
[ 0.7668936 ]
[ 0.4776191 ]
[ 0.39859247]
[ 0.572009 ]
[ 0.64892375]
[ 0.11587611]
[ 0.0560993 ]
[ 0.05285829]
[ 0.0167731 ]
[ 0.01759553]
[ 0.02143204]
[-0.01818037]]
Total score for /var/folders/yc/ssr9692s5fzf7k165grnhpk80000gp/T/tmptg6jy2ud/query.pdb is 6.3262305
If missing atoms::
Total params: 4,282,801
Trainable params: 4,282,801
Non-trainable params: 0
_________________________________________________________________
There is no atom O5' in residue 620A in chain A in PDB /var/folders/yc/ssr9692s5fzf7k165grnhpk80000gp/T/tmpx87uus6x/query.pdb.
There is no atom O5' in residue 635A in chain B in PDB /var/folders/yc/ssr9692s5fzf7k165grnhpk80000gp/T/tmpx87uus6x/query.pdb.
There is no atom O5' in residue 1750G in chain C in PDB /var/folders/yc/ssr9692s5fzf7k165grnhpk80000gp/T/tmpx87uus6x/query.pdb.
Scores for each nucleotide in /var/folders/yc/ssr9692s5fzf7k165grnhpk80000gp/T/tmpx87uus6x/query.pdb:
[]
Total score for /var/folders/yc/ssr9692s5fzf7k165grnhpk80000gp/T/tmpx87uus6x/query.pdb is 0.0
"""
import os
import re
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 RNA3DCNN_PATH, PYTHON3_PATH
[docs]
class RNA3DCNN(ProgramWrapper):
"""
Wrapper class for RNA3DCNN.
"""
max_seq_len = 100000 # I don't know about any restriction
def __init__(self):
super(RNA3DCNN, self).__init__()
[docs]
def run(self, path_to_pdb, verbose=False):
copyfile(path_to_pdb, self.sandbox_dir + os.sep + 'query.pdb')
old_pwd = os.getcwd()
os.chdir(self.sandbox_dir)
self.log('start for %s' % self.sandbox_dir + '/query.pdb', level="debug")
# 4. To print scores of each nucleotide and total scores, use flag "-local 1"
# 5. To print only total scores, use flag "-local 0"
# For example:<br />
# python Main.py -pl pdblist -model RNA3DCNN_MD.hdf5 -local 0<br />
cmd = PYTHON3_PATH + ' ' + RNA3DCNN_PATH + '/Main.py ' + \
' -pn ' + self.sandbox_dir + '/query.pdb ' + \
' -model ' + RNA3DCNN_PATH + '/RNA3DCNN_MD.hdf5 ' + \
' -local 1 2>> ' + self.sandbox_dir + '/log.txt >>' + self.sandbox_dir + '/log.txt'
if verbose:
print(cmd)
os.system(cmd)
"""
Total params: 4,282,801
Trainable params: 4,282,801
Non-trainable params: 0
_________________________________________________________________
Total score for /var/folders/yc/ssr9692s5fzf7k165grnhpk80000gp/T/tmpO_jRVR/query.pdb is 6.3262305
"""
self.log('Run finished')
output = open(self.sandbox_dir + '/log.txt').read()
score = output.split()[-1]
lscore = re.search('\[\[.*\]\]', output, re.M | re.DOTALL)
try:
lscore = lscore.group().replace('[','').replace(']\n', ',').replace(']]','')
except:
print(output)
return error
# 0.02462262, 0.03271335, 0.06199259, 0.02006263, 0.05937254, 0.12025979,
lscore = [float(x.strip()) for x in lscore.split(',')] # [0.02462262, 0.03271335, ...
if verbose:
print(lscore)
print(score)
os.chdir(old_pwd)
try:
return float(score)
except:
error = 'Error: problem with the file'
with open(self.sandbox_dir + '/log.txt') as f:
error += f.read()
return error
[docs]
def main():
wrapper = RNA3DCNN()
try:
result = wrapper.run('../test' + os.sep + '1a9n.pdb', verbose=True)
if result:
print(result)
except Exception as e:
print(e)
finally:
#wrapper.cleanup()
pass
if '__main__' == __name__:
main()