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Altered mr_util to use new parsers
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@hlasimpk
hlasimpk committed May 3, 2017
1 parent 810574c commit 4d58ad6
Showing 1 changed file with 40 additions and 99 deletions.
139 changes: 40 additions & 99 deletions simbad/util/mr_util.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,26 +6,18 @@
import multiprocessing
import os
import pandas
import sys
import types

from simbad.parsers import molrep_parser
from simbad.parsers import phaser_parser
from simbad.parsers import refmac_parser
from simbad.util import anomalous_util
from simbad.util import molrep_util
from simbad.util import mtz_util
from simbad.util import phaser_util
from simbad.util import refmac_util
from simbad.util import simbad_util

# Set up MrBUMP imports
if not "CCP4" in os.environ.keys():
raise RuntimeError('CCP4 not found')
mrbump_incl = os.path.join(os.environ['CCP4'], "share", "mrbump", "include")

sys.path.append(os.path.join(mrbump_incl, 'parsers'))

import parse_molrep
import parse_refmac

__author__ = "Adam Simpkin"
__date__ = "09 Mar 2017"
__version__ = "0.1"
Expand Down Expand Up @@ -259,8 +251,10 @@ def _run_job(self, model):
"""Function to run MR on each model"""
logger.info("Running MR and refinement on %s", model.pdb_code)

# Generate MR input file
self.MR_setup(model)
try:
os.mkdir(self.output_dir)
except OSError:
pass

# Set up MR input paths
mr_pdbin = os.path.join(self.model_dir, '{0}.pdb'.format(model.pdb_code))
Expand All @@ -276,6 +270,12 @@ def _run_job(self, model):

# Run job
if self.mr_program.upper() == 'MOLREP':
# Make output directories
os.mkdir(os.path.join(self.output_dir, model.pdb_code))
os.mkdir(os.path.join(self.output_dir, model.pdb_code, 'mr'))
os.mkdir(os.path.join(self.output_dir, model.pdb_code, 'mr', 'molrep'))
os.mkdir(os.path.join(self.output_dir, model.pdb_code, 'mr', 'molrep', 'refine'))

# Set up class with MOLREP input arguments
molrep = molrep_util.Molrep(self.enant, self.mtz, mr_logfile, mr_pdbin, mr_pdbout, self.space_group,
mr_workdir)
Expand All @@ -288,6 +288,12 @@ def _run_job(self, model):
refmac.run()

elif self.mr_program.upper() == 'PHASER':
# Make output directories
os.mkdir(os.path.join(self.output_dir, model.pdb_code))
os.mkdir(os.path.join(self.output_dir, model.pdb_code, 'mr'))
os.mkdir(os.path.join(self.output_dir, model.pdb_code, 'mr', 'phaser'))
os.mkdir(os.path.join(self.output_dir, model.pdb_code, 'mr', 'phaser', 'refine'))

hklout = os.path.join(mr_workdir, '{0}_mr_output.mtz'.format(model.pdb_code))

# Set up class with PHASER input arguments
Expand Down Expand Up @@ -345,40 +351,6 @@ def get_mtz_info(self, mtz):
self._solvent = self.matthews_coef(self._cell_parameters, self._space_group)
return

def MR_setup(self, model):
"""Code to generate directories for MR and refinement for a model
Parameters
----------
model : class
Class object containing the PDB code for the input model
Returns
-------
file
Output directory for molecular replacement
file
Output directory for refinement
"""

try:
os.mkdir(self.output_dir)
except OSError:
pass

# Create individual directories for every results
if self.mr_program.upper() == "MOLREP":
os.mkdir(os.path.join(self.output_dir, model.pdb_code))
os.mkdir(os.path.join(self.output_dir, model.pdb_code, 'mr'))
os.mkdir(os.path.join(self.output_dir, model.pdb_code, 'mr', 'molrep'))
os.mkdir(os.path.join(self.output_dir, model.pdb_code, 'mr', 'molrep', 'refine'))
elif self.mr_program.upper() == "PHASER":
os.mkdir(os.path.join(self.output_dir, model.pdb_code))
os.mkdir(os.path.join(self.output_dir, model.pdb_code, 'mr'))
os.mkdir(os.path.join(self.output_dir, model.pdb_code, 'mr', 'phaser'))
os.mkdir(os.path.join(self.output_dir, model.pdb_code, 'mr', 'phaser', 'refine'))
return

def multiprocessing(self, results, time_out=60, nproc=2):
"""Code to run MR and refinement in parallel
Expand Down Expand Up @@ -439,16 +411,15 @@ def run(job_queue):
if self.mr_program.lower() == "molrep":
for result in results:
try:
MP = parse_molrep.MolrepLogParser(os.path.join(self.output_dir, result.pdb_code, 'mr',
'molrep', '{0}_mr.log'.format(result.pdb_code)))
MP = molrep_parser.MolrepParser(os.path.join(self.output_dir, result.pdb_code, 'mr', 'molrep',
'{0}_mr.log'.format(result.pdb_code)))
molrep_score = MP.score
molrep_tfscore = MP.tfScore
molrep_tfscore = MP.tfscore

RP = parse_refmac.RefmacLogParser(os.path.join(self.output_dir, result.pdb_code, 'mr',
'molrep', 'refine',
'{0}_ref.log'.format(result.pdb_code)))
final_r_free = RP.finalRfree
final_r_fact = RP.finalRfact
RP = refmac_parser.RefmacParser(os.path.join(self.output_dir, result.pdb_code, 'mr', 'molrep',
'refine', '{0}_ref.log'.format(result.pdb_code)))
final_r_free = RP.final_r_free
final_r_fact = RP.final_r_fact

if self._dano is not None:
AS = anomalous_util.AnomSearch(self.mtz, self.output_dir, self.mr_program)
Expand All @@ -473,41 +444,16 @@ def run(job_queue):
elif self.mr_program.lower() == "phaser":
for result in results:
try:
with open(os.path.join(self.output_dir, result.pdb_code, 'mr',
'phaser', '{0}_mr.log'.format(result.pdb_code)), 'r') as f:
for line in f:
if line.startswith(" SOLU SET") and "TFZ=" in line:
llist = line.split()
llist.reverse()
for i in llist:
if "TFZ==" in i and "*" not in i:
phaser_tfz = float(i.replace("TFZ==", ""))
break
if "TFZ=" in i and "TFZ==" not in i and "*" not in i:
phaser_tfz = float(i.replace("TFZ=", ""))
break

for i in llist:
if "LLG==" in i:
phaser_llg = float(i.replace("LLG==", ""))
break
if "LLG=" in i and "LLG==" not in i:
phaser_llg = float(i.replace("LLG=", ""))
break

for i in llist:
if "RFZ==" in i:
phaser_rfz = float(i.replace("RFZ==", ""))
break
if "RFZ=" in i and "RFZ==" not in i:
phaser_rfz = float(i.replace("RFZ=", ""))
break

RP = parse_refmac.RefmacLogParser(os.path.join(self.output_dir, result.pdb_code, 'mr',
'phaser', 'refine',
'{0}_ref.log'.format(result.pdb_code)))
final_r_free = RP.finalRfree
final_r_fact = RP.finalRfact
PP = phaser_parser.PhaserParser(os.path.join(self.output_dir, result.pdb_code, 'mr', 'phaser',
'{0}_mr.log'.format(result.pdb_code)))
phaser_tfz = PP.tfz
phaser_llg = PP.llg
phaser_rfz = PP.rfz

RP = refmac_parser.RefmacParser(os.path.join(self.output_dir, result.pdb_code, 'mr', 'phaser',
'refine', '{0}_ref.log'.format(result.pdb_code)))
final_r_free = RP.final_r_free
final_r_fact = RP.final_r_fact

if self._dano is not None:
AS = anomalous_util.AnomSearch(self.mtz, self.output_dir, self.mr_program)
Expand Down Expand Up @@ -545,16 +491,11 @@ def solution_found(self, model):
bool
Solution found <True|False>
"""
# Set default values if no results found
final_r_fact = 1
final_r_free = 1

RP = parse_refmac.RefmacLogParser(os.path.join(self.output_dir, model.pdb_code, 'mr',
self.mr_program, 'refine',
'{0}_ref.log'.format(model.pdb_code)))
RP = refmac_parser.RefmacParser(os.path.join(self.output_dir, model.pdb_code, 'mr', self.mr_program, 'refine',
'{0}_ref.log'.format(model.pdb_code)))

final_r_free = RP.finalRfree
final_r_fact = RP.finalRfact
final_r_free = RP.final_r_free
final_r_fact = RP.final_r_fact

if final_r_fact < 0.45 and final_r_free < 0.45:
return True
Expand Down

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