iframe = 0
while dcd.has_more_data() :
data = dcd.read_onestep_np()
##########################################################
### Wrapping the molecule to do bestfit
# Find most lateral coordinates
max_xyz, min_xyz, L = find_max_min_PBC(data[ID_DOM_INI_FIT:ID_DOM_END_FIT+1])
if L[0] > BOXSIZE or L[1] > BOXSIZE or L[2] > BOXSIZE:
print(('Warning: (1) L exceeds BOXSIZE at frame %i' % iframe))
mtx_move = mtx_crd_transform()
#mtx_move.reset()
mtx_move.translation(0.5*L[0] - max_xyz[0],
0.5*L[1] - max_xyz[1],
0.5*L[2] - max_xyz[2])
mtx_move.do_to_ndarray(data)
##########################################################
### Align to the reference PDB
(post, rmsd, ier, rot, center_ref, center_pre) = py_bestfit.bestfit(ref, data.T,
ref_idx, pre_idx)
data = post.T
# 2 BIOMTx
# 3 N
row = int(lsp[2][5:])
#print ('row', row)
if row != row_pre + 1:
print('Error row %i is expected but %i loaded' %
(row_pre + 1, row))
sys.exit(2)
mtx_id = int(lsp[3])
#print ('id', mtx_id)
if row == 1:
mtx = mtx_crd_transform()
mtx.mtx[row - 1, 0] = float(lsp[4])
mtx.mtx[row - 1, 1] = float(lsp[5])
mtx.mtx[row - 1, 2] = float(lsp[6])
mtx.mtx[row - 1, 3] = float(lsp[7])
if row == 3:
matrices[mtx_id] = mtx
assembly_units.append(mtx_id)
if row == 3:
row_pre = 0
else:
row_pre = row
#Ste7(189-471)の重心(CAのみで計算）が原点に重なるように並進
com = Coord()
n_com = 0
for (i,r) in enumerate(chains[1].residues):
if (i+1)>=189 and (i+1)<=471:
for a in r.atoms:
if a.name.find("CA") != -1:
com += a.xyz
n_com += 1
if n_com != 283:
print("ERROR: n_com = ",n_com)
sys.exit(2)
com /= n_com
trans_com = mtx_crd_transform()
trans_com.translation(-com.x, -com.y, -com.z)
for c in chains:
for r in c.residues:
for a in r.atoms:
a.xyz.transform(trans_com.mtx)
print("重心を原点へ")
print("Q:",Q.get_as_tuple())
print("N:",N.get_as_tuple())
##########################################################
#重心を固定したまま、QをZ軸上へ持っていく。
#Qと原点を結ぶ線Lと垂直な、xy平面上の軸を表す単位ベクトルR
header = dcd.get_header()
dcd_out.set_header(header)
dcd_out.write_header()
nmp = header.nmp_real
while dcd.has_more_data() :
data = dcd.read_onestep()
##########################################################
#重心(CAのみで計算）が原点に重なるように並進
com = [0.0] * 3
n_com = ID_DOM_END - ID_DOM_INI + 1
for i in range(ID_DOM_INI, ID_DOM_END+1):
com[0] += data[i][0]
com[1] += data[i][1]
com[2] += data[i][2]
com = [-x/float(n_com) for x in com]
trans_com = mtx_crd_transform()
trans_com.translation(com[0],com[1],com[2])
#for i in xrange(nmp):
# data[i][0:3] = trans_com.do_to_array(data[i])
trans_com.do_to_data(data)
dcd_out.write_onestep(data)
dcd.close()
dcd_out.close()