Big smiles #358
Big smiles #358
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…molecule including edges.
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@pckroon thanks for the comments! I don't understand your worry about the parser maintenance. This is a wrapper around pysmiles that lives in the polyply repro. So maintenance only goes as far as your polyply commitments go. |
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That's the standard I aim for when reviewing ;) |
Co-authored-by: Peter C Kroon <pckroon@users.noreply.github.com>
| hcount = VALENCES[element][0] -\ | ||
| self.meta_molecule.molecule.degree(node) + 1 |
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The VALENCES[element][0] doesn't always work. You need to select the smallest valence that is larger than the current number of bonds present.
Also, why +1?
| if stop < len(pattern) and pattern[stop] == '|': | ||
| # eon => end of next |
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| # add the new residue | ||
| # new we add new residue as often as required |
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| # new we add new residue as often as required | |
| # now we add new residue as often as required |
| prev_node = anchor | ||
| # the outermost loop goes over how often a the branch has to be | ||
| # added to the existing sequence | ||
| for idx in range(0,int(pattern[eon_a+2:eon_b])-1): |
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Create a variable repetition_number or something to aid readability
| for idx in range(0,int(pattern[eon_a+2:eon_b])-1): | |
| repetition_number = int(pattern[eon_a+2:eon_b])-1 | |
| for idx in range(0, repetition_number): |
Also, why -1?
| mol_graph.nodes[node]['hcount'] = hcount - len(mol_graph.nodes[node]['bonding']) | ||
| # get the degree | ||
| ele = mol_graph.nodes[0]['element'] | ||
| # hcoung is the valance minus the degree minus |
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| # hcoung is the valance minus the degree minus | |
| # hcount is the valence minus the degree minus |
| # nx.draw_networkx(meta_mol.molecule, with_labels=True, labels=nx.get_node_attributes(meta_mol.molecule, 'element')) | ||
| # plt.show() |
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| # nx.draw_networkx(meta_mol.molecule, with_labels=True, labels=nx.get_node_attributes(meta_mol.molecule, 'element')) | |
| # plt.show() |
| for node in mol_graph.nodes: | ||
| if mol_graph.nodes[node].get('bonding', False): | ||
| # get the degree | ||
| ele = mol_graph.nodes[0]['element'] |
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line 290 needs to be updated to node instead of just taking 0
Implements parsing capabilities for an adopted BigSmiles format. This format allows to specify both the residue graph well as any all-atom molecule utilising a string-based description similar to a smile.