def calcDists():
"""In a parallel method, calculate all of the distances for each frame.
Returns a list of (frame, distance)"""
global TOTALFRAMES
os.chdir(OUTPATH)
with open(OUTPATH + "/initial.pdb") as p:
LIGANDATOM, PROTEINATOM, lAtomCoord, pAtomCoord, lCenter, pCenter = \
calcCenterAtoms(list(p))
log("Selected ligand center atom ID " + MAGENTA + "%i" % LIGANDATOM + END +
" at (%.3f, %.3f, %.3f), " %
(lAtomCoord[0], lAtomCoord[1], lAtomCoord[2]) +
"closest to (%.3f, %.3f, %.3f).\n" %
(lCenter[0], lCenter[1], lCenter[2]))
log("Selected protein center atom ID " + MAGENTA + "%i" % PROTEINATOM +
END + " at (%.3f, %.3f, %.3f), " %
(pAtomCoord[0], pAtomCoord[1], pAtomCoord[2]) +
"closest to (%.3f, %.3f, %.3f).\n" %
(pCenter[0], pCenter[1], pCenter[2]))
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
log("Calculating distances.\n")
output = parMap(calcDist, range(1, TOTALFRAMES + 1), n=cpu_count() / 2)
os.chdir(WORKDIR)
return output
def calcDists():
"""In a parallel method, calculate all of the distances for each frame.
Returns a list of (frame, distance)"""
global TOTALFRAMES
os.chdir(OUTPATH)
with open(OUTPATH + "/initial.pdb") as p:
LIGANDATOM, PROTEINATOM, lAtomCoord, pAtomCoord, lCenter, pCenter = \
calcCenterAtoms(list(p))
log("Selected ligand center atom ID " + MAGENTA + "%i" % LIGANDATOM + END +
" at (%.3f, %.3f, %.3f), " % (lAtomCoord[0], lAtomCoord[1], lAtomCoord[2]) +
"closest to (%.3f, %.3f, %.3f).\n" % (lCenter[0], lCenter[1], lCenter[2]))
log("Selected protein center atom ID " + MAGENTA + "%i" % PROTEINATOM + END +
" at (%.3f, %.3f, %.3f), " % (pAtomCoord[0], pAtomCoord[1], pAtomCoord[2]) +
"closest to (%.3f, %.3f, %.3f).\n" % (pCenter[0], pCenter[1], pCenter[2]))
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
log("Calculating distances.\n")
output = parMap(calcDist, range(1, TOTALFRAMES + 1), n=cpu_count() / 2)
os.chdir(WORKDIR)
return output
def determineRestraint():
"""Determine the atom groups used for the center-of-mass restaints and sets them in the PROTEINATOM and LIGANDATOM
lists."""
global PROTEINATOM
global LIGANDATOM
global PRMTOPPATH
global COORDPATH
with open(COORDPATH + "/initial.pdb") as p:
LIGANDATOM, PROTEINATOM, ligandAtomCoord, proteinAtomCoord, ligandCenter, proteinCenter = \
calcCenterAtoms(list(p))
log("Selected ligand center atom ID " + MAGENTA + "%i" % LIGANDATOM + END +
" at (%.3f, %.3f, %.3f), " % (ligandAtomCoord[0], ligandAtomCoord[1], ligandAtomCoord[2]) +
"closest to (%.3f, %.3f, %.3f).\n" % (ligandCenter[0], ligandCenter[1], ligandCenter[2]))
log("Selected protein center atom ID " + MAGENTA + "%i" % PROTEINATOM + END +
" at (%.3f, %.3f, %.3f), " % (proteinAtomCoord[0], proteinAtomCoord[1], proteinAtomCoord[2]) +
"closest to (%.3f, %.3f, %.3f).\n" % (proteinCenter[0], proteinCenter[1], proteinCenter[2]))
def determineRestraint():
"""Determine the atom groups used for the center-of-mass restaints and sets them in the PROTEINATOM and LIGANDATOM
lists."""
global PROTEINATOM
global LIGANDATOM
global PRMTOPPATH
global COORDPATH
with open(COORDPATH + "/initial.pdb") as p:
LIGANDATOM, PROTEINATOM, ligandAtomCoord, proteinAtomCoord, ligandCenter, proteinCenter = \
calcCenterAtoms(list(p))
log("Selected ligand center atom ID " + MAGENTA + "%i" % LIGANDATOM + END +
" at (%.3f, %.3f, %.3f), " %
(ligandAtomCoord[0], ligandAtomCoord[1], ligandAtomCoord[2]) +
"closest to (%.3f, %.3f, %.3f).\n" %
(ligandCenter[0], ligandCenter[1], ligandCenter[2]))
log("Selected protein center atom ID " + MAGENTA + "%i" % PROTEINATOM +
END + " at (%.3f, %.3f, %.3f), " %
(proteinAtomCoord[0], proteinAtomCoord[1], proteinAtomCoord[2]) +
"closest to (%.3f, %.3f, %.3f).\n" %
(proteinCenter[0], proteinCenter[1], proteinCenter[2]))