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)):
top_Qry = 'resname {} and resid {} and ({})'.format(top_Res[i], top_IDs[i], selQry);
#print "\t-top_Qry: {}".format(top_Qry);
Tsel = u.selectAtoms(top_Qry);
COM = Tsel.centerOfMass();
# finding associated BIN
# location of X
x = COM[0]; y = COM[1];
#print "### TOP leaflet [{}]###".format(num_frm);
#print "\tCOM: x={}, y={}".format(x,y);
tmp = stanalyzer.count_intervals2(x, BIN_X);
loc_x = tmp.index(1);
tmp = stanalyzer.count_intervals2(y, BIN_Y);
loc_y = tmp.index(1);
# count the frequency
bin_idx = loc_x * len(BIN_Y) + loc_y;
tmp_topDNST[bin_idx][2] = tmp_topDNST[bin_idx][2] + 1.0;
#print "\tBIN: x={}, y={}, freq={}".format(BIN_top[bin_idx][0], BIN_top[bin_idx][1], tmp_topDNST[bin_idx][2]);
######################
#----> bottom leaflet
######################
btm_Atoms = u.selectAtoms(btm_selQry);
btm_Res = btm_Atoms.resnames();
btm_IDs = btm_Atoms.resids();
if len(btm_Res) > 0:
btm_flag = btm_flag + 1;
else:
adjY = top_tCRDs[j,1] + csize_y;
# adjusting Z axis
if (top_tCRDs[j,2] >= a_mid_z):
adjZ = top_tCRDs[j,2] - csize_z;
else:
adjZ = top_tCRDs[j,2] + csize_z;
tmpCRDs = np.array([adjX, adjY, adjZ]);
dist1 = np.sqrt(np.sum((top_sCRDs[i] - top_tCRDs[j]) ** 2));
dist2 = np.sqrt(np.sum((top_sCRDs[i] - tmpCRDs) ** 2));
dist = min([dist1, dist2]);
tmp = np.array(stanalyzer.count_intervals2(dist, BIN));
tmp_topDNST = tmp_topDNST + tmp;
if btm_flag == 2:
#print "---> bottom leaflet calculation"
for i in range(len(btm_sCRDs)):
for j in range(len(btm_tCRDs)):
# adjusting X axis
if (btm_tCRDs[j,0] >= a_mid_x):
adjX = btm_tCRDs[j,0] - csize_x;
else:
adjX = btm_tCRDs[j,0] + csize_x;
# adjusting Y axis
if (btm_tCRDs[j,1] >= a_mid_y):
adjY = btm_tCRDs[j,1] - csize_y;
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)):
top_Qry = 'resname {} and resid {} and ({})'.format(top_Res[i], top_IDs[i], selQry);
#print "\t-top_Qry: {}".format(top_Qry);
Tsel = u.selectAtoms(top_Qry);
COM = Tsel.centerOfMass();
# finding associated BIN
# location of X
x = COM[0]; y = COM[1];
#print "### TOP leaflet [{}]###".format(num_frm);
#print "\tCOM: x={}, y={}".format(x,y);
tmp = stanalyzer.count_intervals2(x, BIN_X);
loc_x = tmp.index(1);
tmp = stanalyzer.count_intervals2(y, BIN_Y);
loc_y = tmp.index(1);
# count the frequency
bin_idx = loc_x * len(BIN_Y) + loc_y;
tmp_topDNST[bin_idx][2] = tmp_topDNST[bin_idx][2] + 1.0;
#print "\tBIN: x={}, y={}, freq={}".format(BIN_top[bin_idx][0], BIN_top[bin_idx][1], tmp_topDNST[bin_idx][2]);
######################
#----> bottom leaflet
######################
btm_Atoms = u.selectAtoms(btm_selQry);
btm_Res = btm_Atoms.resnames();
btm_IDs = btm_Atoms.resids();
if len(btm_Res) > 0:
btm_flag = btm_flag + 1;
# adjusting Z axis
if (top_tCRDs[j, 2] >= a_mid_z):
adjZ = top_tCRDs[j, 2] - csize_z
else:
adjZ = top_tCRDs[j, 2] + csize_z
tmpCRDs = np.array([adjX, adjY, adjZ])
dist1 = np.sqrt(
np.sum((top_sCRDs[i] - top_tCRDs[j])**2))
dist2 = np.sqrt(
np.sum((top_sCRDs[i] - tmpCRDs)**2))
dist = min([dist1, dist2])
tmp = np.array(
stanalyzer.count_intervals2(dist, BIN))
tmp_topDNST = tmp_topDNST + tmp
if btm_flag == 2:
#print "---> bottom leaflet calculation"
for i in range(len(btm_sCRDs)):
for j in range(len(btm_tCRDs)):
# adjusting X axis
if (btm_tCRDs[j, 0] >= a_mid_x):
adjX = btm_tCRDs[j, 0] - csize_x
else:
adjX = btm_tCRDs[j, 0] + csize_x
# adjusting Y axis
if (btm_tCRDs[j, 1] >= a_mid_y):
adjY = btm_tCRDs[j, 1] - csize_y
