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natedey / RINRUS

Residue Interaction Network ResidUe Selector
MIT License
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From all possibilities of backbone atoms in res_atoms.dat - need to include logic for simple trims #22

Open natedey opened 2 years ago

natedey commented 2 years ago

RINRUS can't currently handle the situation where the only backbone atoms interacting with seed are the carbon alpha and it's hydrogen. If this is the case, then there are two outcomes: 1) If the sidechain is included in the model, we wouldn't want to add additional backbone, because the C_alpha trimmed to CH3R would be captured in the sidechain fragment 2) If the sidechain isn't included in the model, there needs to be some default trimming behavior based on if neighboring residues are in the model or will eventually be added.

natedey commented 1 year ago

Need group to go through res_atoms.dat and find situations where only CA or HA are in a line. How does RINRUS behave? We need some context to see how RINRUS behaves or misbehaves and have a few concrete examples. Then we should be able to figure out what (if anything) needs to be fixed.

natedey commented 1 year ago

both of my examples have HA only and they seem to build correctly. We need to track down an example of CA only then. Anyone find anything?

tsantaloci commented 11 months ago

The solution I had for GLY may of solved this issue too. We should check