def analyzeTrajectory(trajFN):
#print "Analyzing trajectory: %s ..." % trajFN
coords = readxtc( trajFN, atomindices = range(128) )
count = 0
for frame in coords:
rms = RMSD.GetDistance( frame, NatState['XYZ'] )
# print rms
if rms >= options.uCut:
return 1
elif rms <= options.fCut:
return 0
else:
continue
return -1
def analyzeTrajectory(trajFN):
# this function will analyze a trajectory for native contacts in the toTestLists
global U_states
global F_states
#print "Analyzing trajectory: %s ..." % trajFN
coords = readxtc( trajFN, atomindices = range(128) )
# Assignment stuff
#AssList = clstr.Assign(Generators=gens['XYZList'],XYZData=array(coords))
#for ass in AssList:
for frame in coords:
ass,rmsd = clstr.Assign(Generators=gens['XYZList'],XYZData=array([frame]))
ass = ass[0]
if ass in U_states:
return 0
elif ass in F_states:
return 1
return -1
def analyzeTrajectory(trajFN):
global options
global natContacts
global cutoff2Dict
# this function will analyze a trajectory for native contacts in the toTestLists
#print "Analyzing trajectory: %s ..." % trajFN
coords = readxtc( trajFN, atomindices = range(128) )
count = 0
for frame in coords:
frameSum = 0.
count += 1
for contact in natContacts:
atomA = contact[0]
atomB = contact[1]
# Need to check the distance between these atoms in all frames:
tempArray = []
coordA = frame[atomA-1]
coordB = frame[atomB-1]
diff = [ (thingA - thingB) for (thingA,thingB) in zip(coordA,coordB) ]
r2 = diff[0]*diff[0] + diff[1]*diff[1] + diff[2]*diff[2]
try: cutoff2 = cutoff2Dict[ (atomA,atomB) ]
except:
try: cutoff2 = cutoff2Dict[ (atomB,atomA) ]
except:
print "Cutoff not found for %d,%d, using default = 1.0" % (atomA,atomB)
cutoff2 = 1
frameSum += ( r2 <= cutoff2 )
frameSum /= float(len(natContacts))
if frameSum <= options.uCut:
return 1
elif frameSum >= options.fCut:
return 0
else:
continue
return -1
