def generatePDB(frame):
"""Generate the PDB for a certain frame"""
with open("frame_%i.in" % frame, 'w') as script:
script.write("""parm %s
trajin %s %i %i 1
trajout frame_%i.pdb pdb
""" % (PRMTOPPATH, COORDPATH, frame, frame, frame))
system("cpptraj < frame_%i.in > /dev/null 2> /dev/null" % frame)
with open("frame_%i.pdb" % frame) as pdb:
thisDist = rmsdDist(pdbLines=list(pdb), refCoords=REFCOORDS, segments=SEGMENTS)
log("Frame %i has dist %.3f\n" % (frame, thisDist))
return frame, thisDist
def generatePDBs():
"""In a parallel method, generate all of the PDBs of the trajectory"""
global TOTALFRAMES
global OUTPATH
with directory(OUTPATH):
def generatePDB(frame):
"""Generate the PDB for a certain frame"""
with open("frame_%i.in" % frame, "w") as script:
script.write(
"""parm %s
trajin %s %i %i 1
trajout frame_%i.pdb pdb
"""
% (PRMTOPPATH, COORDPATH, frame, frame, frame)
)
system("cpptraj < frame_%i.in > /dev/null 2> /dev/null" % frame)
with open("frame_%i.pdb" % frame) as pdb:
thisDist = rmsdDist(pdbLines=list(pdb), refCoords=REFCOORDS, segments=SEGMENTS)
log("Frame %i has dist %.3f\n" % (frame, thisDist))
return frame, thisDist
log("Generating PDB files.\n")
distances = parMap(generatePDB, range(1, TOTALFRAMES + 1), n=(cpu_count() / 2), silent=True)
# clash_screen output sorted by ID
distances = sorted(distances, key=itemgetter(0))
# Write output file
with open(DISTPATH, "w") as dist_vs_t:
for frameID, dist in distances:
dist_vs_t.write("%i %.3f\n" % (frameID, dist))
# Name PDB files
copy("frame_1.pdb", "initial.pdb")
for frameID, dist in distances:
os.rename("frame_%i.pdb" % frameID, "%i.pdb" % frameID)
unblocked_system("rm frame_%i.in" % frameID)
unblocked_system("rm reference.pdb")
def generatePDBs():
"""In a parallel method, generate all of the PDBs of the trajectory"""
global TOTALFRAMES
global OUTPATH
with directory(OUTPATH):
def generatePDB(frame):
"""Generate the PDB for a certain frame"""
with open("frame_%i.in" % frame, 'w') as script:
script.write("""parm %s
trajin %s %i %i 1
trajout frame_%i.pdb pdb
""" % (PRMTOPPATH, COORDPATH, frame, frame, frame))
system("cpptraj < frame_%i.in > /dev/null 2> /dev/null" % frame)
with open("frame_%i.pdb" % frame) as pdb:
thisDist = rmsdDist(pdbLines=list(pdb), refCoords=REFCOORDS, segments=SEGMENTS)
log("Frame %i has dist %.3f\n" % (frame, thisDist))
return frame, thisDist
log("Generating PDB files.\n")
distances = parMap(generatePDB, range(1, TOTALFRAMES + 1),
n=(cpu_count() / 2), silent=True)
# clash_screen output sorted by ID
distances = sorted(distances, key=itemgetter(0))
# Write output file
with open(DISTPATH, 'w') as dist_vs_t:
for frameID, dist in distances:
dist_vs_t.write("%i %.3f\n" % (frameID, dist))
# Name PDB files
copy("frame_1.pdb", "initial.pdb")
for frameID, dist in distances:
os.rename("frame_%i.pdb" % frameID, "%i.pdb" % frameID)
unblocked_system("rm frame_%i.in" % frameID)
unblocked_system("rm reference.pdb")
def prep():
"""Sets up variables for the entire script. Also detects whether analysis runs are necessary
and returns a boolean to indicate this."""
global WORKDIR
WORKDIR = os.getcwd()
# Basic verifications
if args.prmtop is None or args.coord is None:
fail(RED + UNDERLINE + "Error:" + END + RED +
" please provide the topology and coordinate files.\n" + END)
if not os.path.splitext(args.coord)[1].lower() == ".nc":
fail(RED + UNDERLINE + "Error:" + END + RED +
" coordinate file extension is invalid. Please specify a binary NetCDF file.\n" + END)
global PRMTOPPATH
global COORDPATH
global OUTPATH
global DISTPATH
global REFPRMTOPPATH
global REFPATH
# Path modifications
if not os.path.isabs(args.prmtop):
PRMTOPPATH = WORKDIR + "/" + args.prmtop
else:
PRMTOPPATH = args.prmtop
if args.refprmtop is None:
REFPRMTOPPATH = PRMTOPPATH
elif args.refprmtop is not None and not os.path.isabs(args.refprmtop):
REFPRMTOPPATH = WORKDIR + "/" + args.refprmtop
else:
REFPRMTOPPATH = args.refprmtop
if not os.path.isabs(args.ref):
REFPATH = WORKDIR + "/" + args.ref
else:
REFPATH = args.ref
if not os.path.isabs(args.coord):
COORDPATH = WORKDIR + "/" + args.coord
else:
COORDPATH = args.coord
if not os.path.isabs(args.out):
OUTPATH = WORKDIR + "/" + args.out
else:
OUTPATH = args.out
if not os.path.isdir(OUTPATH):
os.mkdir(OUTPATH)
if not os.path.isabs(args.dist):
DISTPATH = WORKDIR + "/" + args.dist
else:
DISTPATH = args.dist
global TOTALFRAMES
TOTALFRAMES = 0
global SEGMENTS
if args.segments is None:
SEGMENTS = []
log("Will process all segments.\n")
else:
error = RED + UNDERLINE + "Error:" + END + \
RED + ' please provide a valid segment string.\n' + END
SEGMENTS = eval(args.segments)
if not isinstance(SEGMENTS, list):
fail(error)
for tup in SEGMENTS:
if not isinstance(tup, tuple) or len(tup) != 2 \
or not isinstance(tup[0], int) \
or not isinstance(tup[1], int) or tup[0] > tup[1]:
fail(error)
log("Will process segments ")
for tup in SEGMENTS:
log("%i to %i; " % (tup[0], tup[1]))
log("\n")
