Error with getVoxelDescriptors: protein has less bonds than atoms about moleculekit HOT 6 CLOSED

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Ok this is a trivial bug. Thanks for picking it up. It's in the assumption that you cannot have less bonds than atoms while of course you can have one less bond than atoms. I will fix the bond check.

As for the PDB it's a funny workaround you found. The bond guesser returns undirected bonds (one per pair) but when we write to PDB we write them directed (two per pair, both ways). So then you have double the bonds and it passes the check.

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Fixed here: 53681e9

If you want to use the fix either wait for a new release or use directly the moleculekit source code from github. Or you can disable the validity checks for that molecule so that it doesn't complain.

Thanks again for the bug report and sorry for the delayed response as I was out on holidays.

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That's an interesting bug. Thank you Stefan.

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This is very interesting, now I want to voxelize the active pocket of a protein. However, this protein pocket is a very small PDB file (from PDBbind2016), which results in 5 separate amino acid segments in this PDB file (which leads to the number of my bonds must be less than residue-1) . Now I want to skip the validity check of the numerator, how should I do it?

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https://software.acellera.com/moleculekit/moleculekit.tools.voxeldescriptors.html#moleculekit.tools.voxeldescriptors.getVoxelDescriptors

validityChecks = False

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