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mengmeng34 / GraphormerDTI

A graph transformer-based approach for drug-target interaction prediction
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What's the physical meaning of the input drug data? #1

Open junqizeng opened 1 year ago

junqizeng commented 1 year ago

Thanks for your nice work.

After running the code, I saw that each pkl file has preserved 7 attributes for one drug compuond, which are: 'num_atom', 'atom_type', 'bond_type', 'spatial_pos', 'edge_input', 'in_degree', 'out_degree'.

But I'm confused about the physical meaning of some important attributes.

For example, 'num_atom' is the atom number of a drug molecule obviously, 'atom_type' represents the element of a atom I guess, but what does 'bond_type' actually denote? The chemical bond type? How to get or define the bond type in this work?

What's more, 'spatial_pos' is usually a N N 3 tensor, I totally have no idea about the physical meaning of this feature, either.

And 'edge_input' is in the same situation.

Could you please give me some advice?

DisfusionLab commented 2 weeks ago

I confuse either with bond_type attribute