def _reindexing(mod, sel, verbose=False):
isel = sel.iselection()
ra = reindexing_array(len(sel), flex.size_t(isel).as_int())
atoms = mod.get_atoms()
for i_seq in isel:
atoms[ra[i_seq]].tmp = i_seq
if verbose:
for atom in mod.get_atoms():
print(atom.quote(), atom.i_seq, atom.tmp)
return mod
def reindex_h_parameterization(self, selection, iselection_original,
n_atoms, h_para):
iselection = selection.iselection().as_int()
r_a = list(reindexing_array(n_atoms, iselection))
reindexing_dict = {}
for index, i_seq in enumerate(iselection_original):
reindexing_dict[iselection_original[index]] = r_a[index]
# Change h_parameterization (contains i_seq --> have to be updated)
new_h_parameterization = []
for index, rc in enumerate(h_para):
key = iselection_original[index]
# No entry for non-selected atoms (H or non-H)
if reindexing_dict[key] == n_atoms: continue
# Non-H atoms (if included in selection) have entry None
if rc is None:
new_h_parameterization.append(None)
continue
# For other entries: 2 possibilities
# a) update all i_seqs according to reindexing dictionary
# b) if any neighbors of H is not in selection --> change this
# entry to None (because if neighbor is missing, H cannot be built)
if reindexing_dict[rc.ih] != n_atoms:
rc.ih = reindexing_dict[rc.ih]
else:
new_h_parameterization.append(None)
continue
if reindexing_dict[rc.a0] != n_atoms:
rc.a0 = reindexing_dict[rc.a0]
else:
new_h_parameterization.append(None)
continue
if reindexing_dict[rc.a1] != n_atoms:
rc.a1 = reindexing_dict[rc.a1]
else:
new_h_parameterization.append(None)
continue
if reindexing_dict[rc.a2] != n_atoms:
rc.a2 = reindexing_dict[rc.a2]
else:
new_h_parameterization.append(None)
continue
# a3 only exists for htype "3neigbs"
if rc.a3 != -1:
if reindexing_dict[rc.a3] != n_atoms:
rc.a3 = reindexing_dict[rc.a3]
else:
new_h_parameterization.append(None)
continue
new_h_parameterization.append(rc)
return new_h_parameterization