uclcheminformatics / scaffoldgraph Goto Github PK

❓ Questions & Help

Hi,

Thanks for this so useful library...I have a doubt, when you are building a hierarchy representation, each bar represent the times of one scaffold is repeated in a dataset??? For example in your example: https://github.com/UCLCheminformatics/ScaffoldGraph/blob/master/examples/scaffold_graphs.ipynb for a network representation. How I could the molecule for earch hierarchy class? I want Know the scaffolds most repeated in the dataset.

Thanks!

Pablo

When dealing with bridged rings using ScaffoldNetwork, the output is different from a similar structure with an aliphatic ring. Some nodes are just missing from the network.

❓ Questions & Help

Basically the title, something like this->

The picture is taken from (https://jcheminf.biomedcentral.com/articles/10.1186/s13321-022-00664-x)

Thanks

How can i get smiles from frags in basic function:

scaffold = Chem.Scaffolds.MurckoScaffold.GetScaffoldForMol(mol)
frags = sg.get_next_murcko_fragments(scaffold)
Draw.MolsToGridImage(frags)

❓ Questions & Help

Glad to see our work taken up in a better library. Are you taking contributions tot his project?

❓ Questions & Help

Hi!
Thank you for this really useful and great module! But there is a problem.
When generating scaffold tree, aromatic bonds are removed. Therefore, it is rather complicated to work with the structures returned. Is there a way how to solve this problem?

❓ Questions & Help

Hello~
When I have installed the ipycytoscape module today and updated scaffoldgraph, it seems I still have problem in importing cytoscape from the vis uilt. The error proved to be ' no module named scaffoldgraph.vis.'. I have checked packages in my envs and found there seems truly no vis module. Is there anything wrong with my implementation?
(Maybe I'll choose to use ipycytoscape directly.

❓ Questions & Help

When I using jupyter lab run relation codes to create and visualize a scaffold network, it could not draw the picture like follows:

Could give me some advices to solve this problem? Thank you!

❓ Questions & Help

Found my answer. [Please delete]

this command "scaffoldgraph network biomol.smi biomol.tmp " give an error as shown below.

scaffold-graph: 15:21:29 19315 INFO: Generating Scaffold Network...
scaffold-graph: 15:21:29 19315 CRITICAL: Unknown error: Python argument types in
SmilesMolSupplier.init(SmilesMolSupplier, str, int, int, int, bool, bool)
did not match C++ signature:
init(_object*)
init(_object*, std::__cxx11::basic_string<char, std::char_traits, std::allocator > data, std::__cxx11::basic_string<char, std::char_traits, std::allocator > delimiter=' ', int smilesColumn=0, int nameColumn=1, bool titleLine=True, bool sanitize=True)
scaffold-graph: 15:21:29 19315 INFO: Exiting scaffoldgraph...

But we can read "biomol.smi" using "Chem.SmilesMolSupplier".How to solve this problem?