#!/usr/bin/env python
import os
import uuid
from ample.util import ample_util, pdb_edit
[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)
[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
