#!/usr/bin/env python
import os
import uuid
from ample.util import ample_util
from ample.util import pdb_edit
# Our imports
[docs]class Csymmatch( object ):
def __init__(self):
self._reset()
return
def _reset(self):
self.logfile=None
self.parsed=False
self.changeOfHand = False
self.changeOfOrigin = None
self.chainShifts = {}
return
[docs] def run(self, refPdb=None, inPdb=None, outPdb=None, connectivityRadius=None, originHand=True, cleanup=False):
"""FOO
"""
self._reset()
self.logfile = outPdb +"_{}.log".format(str(uuid.uuid1()))
cmd= [ 'csymmatch',
"-pdbin-ref",
refPdb,
"-pdbin",
inPdb,
"-pdbout",
outPdb
]
if originHand:
cmd += [ "-origin-hand" ]
if connectivityRadius:
cmd += [ "-connectivity-radius", connectivityRadius ]
retcode = ample_util.run_command(cmd=cmd, logfile=self.logfile, dolog=False)
if retcode != 0: raise RuntimeError, "Error running command: {0}".format( " ".join(cmd) )
if cleanup: os.unlink(self.logfile)
return
[docs] def parseLog(self, logfile=None, cleanup=True):
"""Parse the log"""
if logfile is None:
logfile = self.logfile
assert logfile
capturing=0
currentChain=None
self.chainShifts = {}
for line in open( logfile, 'r' ):
line = line.strip()
if not line: continue
if line.startswith("Chain:"):
capturing=1
f = line.split()
currentChain=f[1]
resStart = int( f[2][:-1] )
resEnd = int( f[3] )
if currentChain not in self.chainShifts:
self.chainShifts[ currentChain ] = []
self.chainShifts[ currentChain ].append( { 'resStart' : resStart, 'resEnd' : resEnd } )
continue
if capturing == 1 or capturing == 2:
capturing += 1 # Symmetry Opterator & Lattice Shift
elif capturing == 3:
capturing += 1
score = float( line.split()[3] )
self.chainShifts[ currentChain ][ -1 ][ 'score' ] = score
elif capturing == 4:
# Singnifies end of chain blocks
continue
if "Change of hand" in line:
# For our work, if there is a change of hand it didn't work
fields = line.split()
if fields[ 4 ] == "YES":
self.changeOfHand = True
if "Change of origin:" in line:
# Find position of brackets
i1 = line.index( "(" )
i2 = line.index( ")" )
oline = line[ i1+1:i2 ]
x,y,z = oline.split(",")
self.changeOfOrigin = [ float(x), float(y), float(z) ]
self.parsed=True
if cleanup: os.unlink(logfile)
return
[docs] def origin(self, logfile=None, failOnChangeOfHand=True):
"""Return the change of origin.
Csymmatch will always return something so we use a changeOfHand as indication of failure
"""
if not self.parsed: self.parseLog()
if failOnChangeOfHand and self.changeOfHand: return False
return self.changeOfOrigin
[docs] def averageScore(self):
if not self.parsed: self.parseLog()
if not len(self.chainShifts): return False
score=0.0
count=0
for chain in self.chainShifts.keys():
for shift in self.chainShifts[ chain ]:
score += shift['score']
count += 1
return score/count
[docs] def wrapModelToNative(self,
mrPdb,
nativePdb,
origin=[0.0,0.0,0.0],
csymmatchPdb=None,
workdir=None,
cleanup=True):
"""Take a pdb and wrap it onto the nativePdb using csymmatch.
If origin is not [0.0,0.0,0.0] we also move the structure onto the new origin before wrapping"""
if workdir is None:
workdir = os.getcwd()
assert os.path.isfile(mrPdb) and os.path.isfile(nativePdb),"Cannot find: {0} or {1}".format(mrPdb,nativePdb)
originMrPdb = None
if origin != [ 0.0, 0.0, 0.0 ]:
ostr="o{}_{}".format(origin, str(uuid.uuid1())).replace(" ","" )
originMrPdb = ample_util.filename_append(filename=mrPdb, astr=ostr, directory=workdir)
pdb_edit.translate(inpdb=mrPdb, outpdb=originMrPdb, ftranslate=origin)
mrPdb = originMrPdb
if csymmatchPdb is None:
csymmatchPdb = ample_util.filename_append(filename=mrPdb, astr="csymmatch_{}".format(str(uuid.uuid1())),
directory=workdir)
self.run(refPdb=nativePdb, inPdb=mrPdb, outPdb=csymmatchPdb, originHand=False, cleanup=cleanup)
if not os.path.isfile( csymmatchPdb ):
raise RuntimeError("Error generating csymmatchPdb")
if cleanup and originMrPdb:
os.unlink(originMrPdb)
return csymmatchPdb
