Split off a base parser from read_smiles #49
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Also teaches the tests to ignore these "operational" node and edge attributes
fgrunewald
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Nov 22, 2024
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| for node in mol: | ||
| mol.nodes[node].update(parse_atom(mol.nodes[node]['_atom_str'])) | ||
| for idx, jdx, attrs in ring_bonds: | ||
| if mol.nodes[idx].get('rs_isomer'): | ||
| mol.nodes[idx]['rs_isomer'][1].append(jdx) | ||
| if mol.nodes[jdx].get('rs_isomer'): | ||
| mol.nodes[jdx]['rs_isomer'][1].append(idx) | ||
| for edge in mol.edges: | ||
| if mol.edges[edge]['_bond_str']: | ||
| order = bond_to_order[mol.edges[edge]['_bond_str']] | ||
| if not order and not zero_order_bonds: | ||
| mol.remove_edge(*edge) | ||
| continue | ||
| mol.edges[edge]['order'] = order | ||
| elif mol.nodes[edge[0]].get('aromatic') and mol.nodes[edge[1]].get('aromatic'): | ||
| mol.edges[edge]['order'] = default_aromatic_bond | ||
| else: | ||
| mol.edges[edge]['order'] = default_bond | ||
|
|
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If one were to make a bold suggestion: These could be put into functions as well such that one can mix and match a read_smiles interpreter function. Maybe even decorators? Something like an abstract interpret_graph method.
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I like the idea, but I need to think on it a little bit. How to organise the code and such. I suggest leaving that for a next PR
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