Much faster coordinate building from angles. fastbuild is more than 300 times faster with autograd on than the default routines for a 437 residue protein (and scales better). It uses parallel matrix operations and a logarithmic building of the backbone. Should be straightforward to define alternative sidechain geometries.
This is a pure python implementation. A C++ implementation only improved speed about 10% and I decided that wasn't worth the extra complexity and opacity to pytorch tools.
Todos
[ ] Need to implement backward pass of MakeSCCoords. Once this is done, switching to use this custom autograd function should improve speed by an additional 3X
[ ] Need to fill in all the necessary information to build sidechain hydrogens in sc_all_atom_build_info. This is essential in order to get the desired orders of magnitude speed ups when constructing full protein for openmm
[ ] Need to deal with terminal atoms (e.g. OXT). In theory this can be implemented in the existing framework by creating C and N terminal residue types with their own sidechain definitions, but since it's only a couple residues a manual solution is probably acceptable, if less elegant.
[ ] Tests need to be written.
[ ] Batched versions of these functions might provide some additional performance benefit.
Questions
[ ] Why can't sidechainnet angles be appropriately oriented to begin with (instead of having to shift by pi?)
Status
[ ] Ready to go. Seriously, swap this in ASAP (need hydrogens) so training can be that much faster.
jonathanking
commented
2 years ago
Description
Much faster coordinate building from angles. fastbuild is more than 300 times faster with autograd on than the default routines for a 437 residue protein (and scales better). It uses parallel matrix operations and a logarithmic building of the backbone. Should be straightforward to define alternative sidechain geometries.
This is a pure python implementation. A C++ implementation only improved speed about 10% and I decided that wasn't worth the extra complexity and opacity to pytorch tools.
Todos
Questions
Status