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schrodinger / coordgenlibs

Schrodinger-developed 2D Coordinate Generation
BSD 3-Clause "New" or "Revised" License
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Some coordgen templates don't match themselves #52

Open d-b-w opened 4 years ago

d-b-w commented 4 years ago

There are some coordgen templates that don't match themselves! If I import the coordgen templates.mae file into Maestro and display the structures in the 2D viewer, the 2D view clearly doesn't match the input template.

This affects templates (0 indexed):

 [1, 8, 19, 20, 22, 43, 53, 65, 66, 67]

Here's an example. White is the coordinates generated by coordgen, black is the template structure:

coordgen_bad_template

Furthermore, some of the templates match other templates instead of themselves! This means that that some templates will never be used, and so only part of the template is actually honored. This affects templates (0 indexed):

[18, 27]
ZontaNicola commented 4 years ago

this happens because we now try to first open one ring and generate the rest of the coordinates and when we can't do that resort to templates. I'm actually happy with the result in this case but I do think that it'd be worth to search for templates as a first step instead and have a look at how that impacts performance

greglandrum commented 4 years ago

If it doesn't have a big performance impact, it seems like the "expected" behavior would indeed be to check the templates first.

Are templates allowed to match parts of a set of fused rings? I could imagine that leading to awkward depictions if we apply the templates first.