update_mmcif_block()

[lobnaOmar20]

is there an alternative for update_mmcif_block() for small structures. It doesn't seem to be in the documentation.
I want to update my label in the existing cif file.

[wojdyr]

You could read CIF file as cif::Document (instead of Structure / SmallStructure) and directly modify strings in tables.

[lobnaOmar20]

Thank you for your reply. That is what I understood from the documentation and I am trying to implement it.

[lobnaOmar20]

Everytime I try to modify the table, or the column I want to modify, I get an error like so

doc = cif.read_file('Datei.cif')
block = doc.sole_block()

table = block.find(['_atom_site_label'])
#print (table[14])

atoms_labels = []
small = gemmi.read_small_structure('supercell_i00011_w8.cif')
for labeli in range(len(small.sites)):
    atoms_labels.append(small.sites[labeli])

for i in range(len(table)):
    table[i] = atoms_labels[i]

AttributeError: setitem

I even tried to delete them
del table[12:15] and re-assign values I get

IndexError: remove_row(): invalid index

[wojdyr]

Table is 2-dimensional, two indices are needed. Instead of table[i] = do table[i][0] =.

Alternatively, you can use Column with a single index:

column = block.find_values('_atom_site_label')
for i in range(len(column)):
    column[i] = atoms_labels[i]

Note that atom_labels must be strings. In the example you are missing .label after small.sites[labeli].

[lobnaOmar20]

Thank you so much for your reply.

I thought if this wasn't working then I will create a new cif file and then write whatever I want.

for this, I used one of your examples in the documentation and then proceeded from there

block_one = d.add_new_block(block.name)
block_one.set_pair('_chemical_name_common', block.find_value('_chemical_name_common'))
block_one.set_pair('_cell_length_a', block.find_value('_cell_length_a'))
block_one.set_pair('_cell_length_b', block.find_value('_cell_length_b'))
block_one.set_pair('_cell_length_c', block.find_value('_cell_length_c'))
block_one.set_pair('_cell_angle_alpha', block.find_value('_cell_angle_alpha'))
block_one.set_pair('_cell_angle_beta', block.find_value('_cell_angle_beta'))
block_one.set_pair('_cell_angle_gamma', block.find_value('_cell_angle_gamma'))

d.write_file('1.cif')

and it is working great. But your solution above will help me even more because in the current case it is not ideal to create another new cif.

Thank you so much once more :)

[lobnaOmar20]

You write brilliant easy simple solutions. It took me some time to get used to Gemmi library. It is working now. Thank you so much I have the new cif file with the labels finally edited.

This Gemmi library is brilliant. It is the best for handling cif files, at least to my understanding. I tried so many other options with Python and I was never happy 'cause they were very complicated to understand. I already study complicated phenomena and I don't want further complications.