#list of lists of strings.
name_lists = [[map_to_atom_sel(mnames) for mnames in mapping_list]
for mapping_list in mapping_atom_names_system]
############################### run ########################################
### pull in trajectories
trj = md.load(input_dir + input_traj, top=input_dir + input_top)
#the types of each molecule in the trajectory.
molecule_types = [lipid_types.index(r.name) for r in trj.top.residues]
#actual map command
cg_trj = cg.map_molecules(trj=trj,
selection_list=name_lists,
bead_label_list=label_lists,
molecule_types=molecule_types,
transfer_labels=True)
cg_trj.save(output_dir + output_traj)
cg_trj[0].save(output_dir + output_top)
############################### check results ###############################
# reloading results from disk.
cg_traj = cg_trj.load(output_dir + output_traj, top=output_dir + output_top)
ref_cg_traj = cg_trj.load(reference_dir + reference_traj,
top=reference_dir + reference_top)
result = check.md_content_equality(cg_traj, ref_cg_traj)
]
#names of cg beads created.
label_lists = ['DPH', 'DPM', 'DPT']
############################### run ########################################
### pull in trajectories
trj = md.load(input_dir + input_traj, top=input_dir + input_top)
#the types of each molecule in the trajectory.
molecule_types = [lipid_types.index(r.name) for r in trj.top.residues]
#actual map command
cg_trj = cg.map_molecules(trj=trj,
selection_list=[name_lists],
bead_label_list=[label_lists],
molecule_types=molecule_types)
cg_trj.save(output_dir + output_traj)
cg_trj[0].save(output_dir + output_top)
#actual map command
cg_id_trj = cg.map_identical_molecules(trj=trj,
selection_list=name_lists,
bead_label_list=label_lists)
cg_id_trj.save(output_dir + output_id_traj)
cg_id_trj[0].save(output_dir + output_id_top)
############################### check results ###############################
# reloading results from disk.
#names of cg beads created.
label_lists = ['DPH', 'DPM', 'DPT']
############################### run ########################################
### pull in trajectories
trj = md.load(input_dir + input_traj, top=input_dir + input_top)
#the types of each molecule in the trajectory.
molecule_types = [lipid_types.index(r.name) for r in trj.top.residues]
#actual map command
cg_trj = cg.map_molecules(trj=trj,
selection_list=[name_lists],
bead_label_list=[label_lists],
molecule_types=molecule_types,
split_shared_atoms=False)
cg_trj.save(output_dir + output_traj)
cg_trj[0].save(output_dir + output_top)
############################### check results ###############################
# reloading results from disk.
cg_traj = cg_trj.load(output_dir + output_traj, top=output_dir + output_top)
ref_cg_traj = cg_trj.load(reference_dir + reference_traj,
top=reference_dir + reference_top)
result = check.md_content_equality(cg_traj, ref_cg_traj)
sys.exit(check.check_result_to_exitval(result))
############################### run native ###############################
### pull in trajectories
trj = md.load(input_dir + input_traj,top=input_dir + input_top)
#the types of each molecule in the trajectory.
molecule_types = [lipid_types.index(r.name) for r in trj.top.residues]
#preprocess trajectory content by adding new parts
for a in trj.top.atoms: a.charge = 0
#actual map command
cg_trj = cg.map_molecules( trj = trj,
selection_list = [ name_lists ],
bead_label_list = [ label_lists ],
molecule_types = molecule_types,
mapping_function = 'center')
cg_trj.save(output_dir + output_traj_native)
cg_trj[0].save(output_dir + output_top_native)
############################### run null mass ############################
### pull in trajectories
trj = md.load(input_dir + input_traj,top=input_dir + input_top)
#the types of each molecule in the trajectory.
molecule_types = [lipid_types.index(r.name) for r in trj.top.residues]
#preprocess trajectory content by adding new parts
############################### run null mass ############################
### pull in trajectories
trj = md.load(input_dir + input_traj,top=input_dir + input_top)
#the types of each molecule in the trajectory.
molecule_types = [lipid_types.index(r.name) for r in trj.top.residues]
#preprocess trajectory content by adding new parts
for a in trj.top.atoms: a.element = Element.getBySymbol('H')
#actual map command
call_params = cg.map_molecules( trj = trj,
selection_list = [ name_lists ],
bead_label_list = [ label_lists ],
molecule_types = molecule_types,
mapping_function = 'com',
return_call = True)
cg_trj = cg.cg_by_index(call_params[0],call_params[1],call_params[2],
mapping_function=call_params[3]['mapping_function'])
cg_trj.save(output_dir + output_traj_null_mass)
cg_trj[0].save(output_dir + output_top_null_mass)
############################### check results ###############################
# reloading results from disk.
cg_traj_null_mass = cg_trj.load(output_dir + output_traj_null_mass,
top=output_dir + output_top_null_mass)