trj = "{0}{1}".format(base_path, trajectoryFile[idx])
print "Reading PSF: " + psf
print "Reading DCD: " + trj
u = Universe(psf, trj)
print "{0} is done!".format(idx)
# read based on frame
for ts in u.trajectory:
# tclock = cnt;
cnt = cnt + 1
if (cnt % frmInt) == 0:
# ======= Centeralization =========
if cntQry != "no":
# print "Centeralization..."
# stanalyzer.centerByCOM(ts, u, cntQry);
stanalyzer.centerByRes2(ts, u, cntQry, 1, cntAxs)
# 1st residue is always chosen for centering membrane
# print "DONE!"
# ==================================
tmp_time = float(cnt) * float(num_ps) - float(num_ps)
STMP.append(tmp_time)
print "[{0}ps]selecting atoms...".format(tmp_time)
selAtoms = u.selectAtoms(selQry)
print "DONE!"
if len(selAtoms) > 1:
# get coordinates
CRDs = selAtoms.coordinates()
MASS = selAtoms.masses()
ELEC = stanalyzer.getAtomNumber(selAtoms.names())
for ts in u.trajectory:
# flag for top and bottom leaflet
top_flag = 0; btm_flag = 0;
cnt = cnt + 1;
if (cnt % ST_frmInt) == 0:
num_frm = num_frm + 1.0;
#######################################################
############## Write your code below ##################
#######################################################
#======= Centeralization =========
if (cntQry != 'no') :
stanalyzer.centerByRes2(ts, u, cntQry, 1, cntAxs); # 1st residue is always chosen for centering membrane
#==================================
#############################################
#### Calculating top and bottom layer #######
#############################################
####################
#----> top leaflet
####################
#print "#top_selQry = {}".format(top_selQry);
top_Atoms = u.selectAtoms(top_selQry);
top_Res = top_Atoms.resnames();
top_IDs = top_Atoms.resids();
if len(top_Res) > 0:
top_flag = top_flag + 1;
for i in range(len(top_Res)):
# reading trajectory
trj = '{0}{1}'.format(base_path, trajectoryFile[idx]);
print 'Reading PSF: ' + psf
print 'Reading DCD: ' + trj
u = Universe(psf, trj);
# read based on frame
for ts in u.trajectory:
cnt = cnt + 1;
if (cnt % frmInt) == 0:
#======= Centeralization =========
if (cntQry != 'no') :
#print "Centeralization..."
#stanalyzer.centerByCOM(ts, u, cntQry);
stanalyzer.centerByRes2(ts, u, cntQry, 1, cntAxs); # 1st residue is always chosen for centering membrane
#print "DONE!"
#==================================
tmp_time = float(cnt) * float(num_ps) - float(num_ps);
STMP.append(tmp_time);
#print "[{0}ps]selecting atoms...".format(tmp_time);
selAtoms = u.selectAtoms(selQry);
CRDs = selAtoms.coordinates();
#print "DONE!"
posZ = [];
negZ = [];
if len(selAtoms) > 1:
# finding 'P' haivng positive value in 'z' axis
for p_idx in CRDs:
z = p_idx[2];
allCRDs = allAtoms.coordinates()
print '{0} is done!'.format(idx)
# read based on frame
for ts in u.trajectory:
# reading system size at each frame
sysX = ts.dimensions[0]
sysY = ts.dimensions[1]
sysZ = ts.dimensions[2]
#======= Centeralization =========
if (cntQry != 'no'):
#print "Centeralization..."
#stanalyzer.centerByCOM(ts, u, cntQry);
stanalyzer.centerByRes2(ts, u, cntQry, 1, cntAxs)
# 1st residue is always chosen for centering membrane
#print "DONE!"
#==================================
tmp_time = float(cnt) * float(num_ps) - float(num_ps)
# defining unit vector
if taxis == 'X':
top_cut = sysX * 0.165
btm_cut = -1.0 * top_cut
top_selQry = "segid {} and resname {} and (prop x > {})".format(
segID, resName, top_cut)
btm_selQry = "segid {} and resname {} and (prop x < {})".format(
segID, resName, btm_cut)
elif taxis == 'Y':
