def analysis(lUniverses,
lTpr,
lXtc,
sSurface,
lOutput,
lTimeOffsets=[],
sSaveAs='SASAResults'):
makeIndex(lUniverses, sSurface, lOutput)
lSASA = []
npSASA = np.array(lSASA)
lOutputInts = []
for y in range(1, len(lOutput) + 1):
lOutputInts.append(y)
for x in range(len(lTpr)):
cSASA = tools.G_sas(s=lTpr[x],
f=lXtc[x],
n='SASAIndex.ndx',
o='SASA.xvg',
surface=["0"],
output=lOutputInts)
cSASA.run()
wSASA = wrap.XVG()
wSASA.read(filename='SASA.xvg')
npTempSASA = wSASA.array
if x == 0:
npSASA = deepcopy(npTempSASA)
else:
npSASA = np.concatenate((npSASA, npTempSASA), axis=1)
dSASA = createDictionary(lUniverses, npSASA, sSurface, lOutput,
lTimeOffsets)
#save dictionary
pickleMethods.save(dSASA, sSaveAs)
def analysis(lUniverses,
lAtomSelections,
lTimeOffsets=[],
sSaveAs="DihedralResults"):
npDihedral = []
for universe in lUniverses:
lQuartets = []
for x in lAtomSelections:
lQuartets.append(universe.select_atoms(x))
D = Dihedrals.Dihedral(lQuartets)
D.run()
npTempDihedral = D.angles.T
if len(npDihedral) == 0:
npDihedral = deepcopy(npTempDihedral)
else:
npDihedral = np.concatenate((npDihedral, npTempDihedral), axis=1)
dDihedral = {}
for x in range(len(lAtomSelections)):
dDihedral[lAtomSelections[x]] = npDihedral[x]
#Add time points
iTimeStep = int(lUniverses[0].trajectory[1].time -
lUniverses[0].trajectory[0].time)
dDihedral['time'] = []
for y in range(len(lUniverses)):
for x in range(0,
len(lUniverses[y].trajectory) * iTimeStep, iTimeStep):
if ((y - 1) == 0) | ((y - 1) > 0):
dDihedral['time'].append(x + lTimeOffsets[y - 1])
else:
dDihedral['time'].append(x)
pickle.save(dDihedral, sSaveAs)
def analysis(lUniverses,
lGroupSelection,
lTimeOffsets=[],
sSaveAs="GyrationResults"):
Rgyr = []
u = 0
for universe in lUniverses:
lGroups = []
for group in lGroupSelection:
lGroups.append(universe.select_atoms(group))
for ts in universe.trajectory:
tempRgyr = []
if u < 1:
tempRgyr.append(universe.trajectory.time)
else:
tempRgyr.append(universe.trajectory.time + lTimeOffsets[u - 1])
for group in lGroups:
tempRgyr.append(group.radius_of_gyration())
Rgyr.append(tempRgyr)
u += 1
Rgyr = np.array(Rgyr).T
dGyration = {}
dGyration['time'] = Rgyr[0]
for x in range(len(lGroupSelection)):
dGyration[lGroupSelection[x]] = Rgyr[x + 1]
pickle.save(dGyration, sSaveAs)
def analysis(lUniverses,
uRef,
sSelection,
lGroups,
sSaveAs="RMSDResults",
lTimeOffsets=[]):
lRMSD = []
for universe in lUniverses:
R = MDAnalysis.analysis.rms.RMSD(universe,
uRef,
select=sSelection,
groupselections=lGroups,
filename="rmsd.dat")
R.run()
if len(lRMSD) < 1:
lRMSD = R.rmsd.T
else:
lRMSD = np.concatenate((lRMSD.T, R.rmsd), axis=0).T
if len(lTimeOffsets) > 0:
for x in range(len(lTimeOffsets)):
fBegIndex = 0
for i in range(x + 1):
fBegIndex += len(lUniverses[i].trajectory)
for y in range(fBegIndex,
fBegIndex + len(lUniverses[x + 1].trajectory)):
lRMSD[1][y] = lRMSD[1][y] + lTimeOffsets[x]
dRMSD = {}
dRMSD['frame'] = lRMSD[0]
dRMSD['time'] = lRMSD[1]
dRMSD[sSelection] = lRMSD[2]
for x in range(len(lGroups)):
dRMSD[lGroups[x]] = lRMSD[x + 3]
pickle.save(dRMSD, sSaveAs)