def calcInitDist():
"""Calculates the "initial distance" based on the first frame of the coordinate file."""
global RUNANALYSIS
global PRMTOPPATH
global COORDPATH
global STARTDIST
global PROTEINATOM
global LIGANDATOM
if not RUNANALYSIS:
log("Calculating initial distance.\n")
with open(COORDPATH + "/initial.pdb") as pdb:
STARTDIST = atomDist(list(pdb), LIGANDATOM, PROTEINATOM)
else: # analysis
STARTDIST = min([
float(name.split('/')[-1]) for name in glob("%s/*.*" % WORKDIR)
if os.path.isdir(os.path.join(WORKDIR, name))
])
if not RUNANALYSIS:
log(BLUE + "Initial distance is " + MAGENTA + "%.3f" % STARTDIST +
BLUE + ". " + END)
if MAXDIST is not None:
log(BLUE + "Analysis endpoint will be " + MAGENTA + "%.3f" %
(MAXDIST + STARTDIST) + BLUE + " angstroms.\n" + END)
else:
log('\n')
def calcInitDist():
"""Calculates the "initial distance" based on the first frame of the coordinate file."""
global RUNANALYSIS
global PRMTOPPATH
global COORDPATH
global STARTDIST
global PROTEINATOM
global LIGANDATOM
if not RUNANALYSIS:
log("Calculating initial distance.\n")
with open(COORDPATH + "/initial.pdb") as pdb:
STARTDIST = atomDist(list(pdb), LIGANDATOM, PROTEINATOM)
else: # analysis
STARTDIST = min([float(name.split('/')[-1]) for name in glob("%s/*.*" % WORKDIR)
if os.path.isdir(os.path.join(WORKDIR, name))])
if not RUNANALYSIS:
log(BLUE + "Initial distance is " + MAGENTA + "%.3f" % STARTDIST + BLUE + ". " + END)
if MAXDIST is not None:
log(BLUE + "Analysis endpoint will be " + MAGENTA + "%.3f" %
(MAXDIST + STARTDIST) + BLUE + " angstroms.\n" + END)
else:
log('\n')
def calcDist(frame):
"""Calculate the distance for a certain frame. Returns (frame, distance)."""
with open("frame_%i.pdb" % frame) as pdb:
dist = atomDist(list(pdb), LIGANDATOM, PROTEINATOM)
log("Frame %i has distance %.3f\n" % (frame, dist))
return frame, dist
def calcDist(frame):
"""Calculate the distance for a certain frame. Returns (frame, distance)."""
with open("frame_%i.pdb" % frame) as pdb:
dist = atomDist(list(pdb), LIGANDATOM, PROTEINATOM)
log("Frame %i has distance %.3f\n" % (frame, dist))
return frame, dist
