if tsdata[0][ts.head_col.step] == 1:
if not ts.has_more_data():
print('Not enough data in .ts file (2)')
sys.exit(2)
tsdata, lines = ts.read_onestep()
if tsdata[0][ts.head_col.e_bridge] == '0.0000000':
struct = dcd.read_onestep()
iatom = 0
for c in chains:
for r in c.residues:
for a in r.atoms:
a.xyz.put_as_list(struct[iatom])
iatom += 1
imodel += 1
pdb.modelID = imodel
pdb.set_remark('ORIGINAL_FILE %s' % (dcd_filename,))
pdb.set_remark('ORIGINAL_FRAME %i' % (i_org,))
for iunit, x in enumerate(tsdata):
if iunit == 0:
tsline = 'TS_all'
else:
tsline = 'TS_%i ' % (iunit,)
for y in x:
tsline += ' ' + y
pdb.set_remark(tsline)
pdb.write_all(chains)
else:
dcd.skip_onestep()
i_org += 1
continue
struct = dcd.read_onestep()
""" Move to the origin """
if args.flg_origin:
com = [0.0, 0.0, 0.0]
for v in struct:
com = [com[i]+v[i] for i in range(3)]
com = [com[i]/float(len(struct)) for i in range(3)]
for i in range(len(struct)):
struct[i] = [struct[i][j] - com[j] for j in range(3)]
iatom = 0
for c in chains:
for r in c.residues:
for a in r.atoms:
a.xyz.put_as_list(struct[iatom])
iatom += 1
movie.modelID = iframe + args.id_offset
movie.set_remark('ORIGINAL_FILE %s' % (args.dcd,))
movie.set_remark('ORIGINAL_FRAME %i' % (i_orig,))
movie.write_all(chains)
i_orig += 1
movie.close()
pdb.close()