def get_nr(nr_file, an):
number_map = {}
nr = get_ls(nr_file)
for line in nr:
l = line.split()
if l[4] in an:
number_map[l[4]] = l[0]
return number_map
def main():
# get atom type and name map
atom_map = get_ls(opts.map_file)
# build description dictionary for each model, as well as cross model reference
mi, mf, cross_an, cross_at = model_dict(atom_map, opts.model_i, opts.model_f)
old_keys = cross_an.keys()
new_keys = cross_an.values()
if opts.nr_i:
n0 = get_nr(opts.nr_i, old_keys)
nf = get_nr(opts.nr_f, new_keys)
# get map from old to new.
map_ndx = {}
for atm in cross_an:
map_ndx[n0[atm]] = nf[cross_an[atm]]
frm = map_ndx.keys()
# pdb or gro conversion just maps atom names (not types)
map_file(opts.f_i, cross_an, opts.write_out, map_ndx, opts.structure_file, opts.itp)
