Jit refactor - Githubissues

willsheffler / worms

Protein Origami via Genetic Fusions

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Jit refactor #3

Open willsheffler opened 6 years ago

willsheffler commented 6 years ago

database

[x] fast cache, no poses
[x] basic queries
[x] jit equivalent of Spliceable / SpliceSite logic

Vertex (was Segment)

[x] build seg data
[x] new indexing for tree-search

Edge (pre-filter)

[x] clash, contact, rms in jit
[ ] visualize filtered pairs
[x] extract segment makeposechains
[ ] is it too slow?

WormFilter aka criteria

[x] find some extensibility path
[ ] Geom, clash, size
[ ] PoseFilter aka DB filter

search

[x] auto reallocating accum array aka vector
[ ] pseudocode
[x] ienter contiguous, add ienter to idxrange array
[x] tree search for linear arrangements

[ ] topology configuration? Just start with linear? Recombination logic?

willsheffler commented 6 years ago

How to do filter extensibility? List of jit func and opt objects? Signature: (head, tail, opts) head/tail named tuple (ncac, ss, rest_ncac)

What do these get added to? Some kind of protocol object?

Maybe namedtuple with call func field or something?