Enums§
- AAAtom
- Typed atom37 slots; discriminants match
ATOM37_NAMESindices. - Residue
Constants§
- ALPHABET
- One-letter code alphabet for the 20 standard amino acids plus UNK.
Functions§
- aa1to_
int - Convert a 1-letter amino acid code to an integer index (0–20, UNK→20).
- aa3to1
- Convert a 3-letter amino acid code to a 1-letter code.
- calculate_
cb - Get Pseudo CB
- cat_
neighbors_ nodes - compute_
nearest_ neighbors - Retrieve the nearest Neighbor of a set of coordinates. Usually used for CA carbon distance.
- create_
backbone_ mask_ 37 - Input coords. Output 1 <batch x 1 > Tensor representing whether each residue has all 4 backbone atoms. note that the internal ordering is different between backbone only [N/CA/C/O] and all-atom [N/CA/C/CB/O]….
- cross_
product - Custom Cross-Product Fn.
- gather_
edges - Gather_edges
Features
[B,N,N,C]at Neighbor indices[B,N,K]=> Neighbor features[B,N,K,C] - gather_
nodes - Gather Nodes
- gather_
nodes_ t - get_
nearest_ neighbours - Per-residue ligand atom context: the
number_of_ligand_atomsligand atoms nearest each residue’s Cβ. - int_
to_ aa1 - Convert an integer index (0–20) to a 1-letter amino acid code.
- linear_
last_ dim - Apply a [
Linear] across the last dimension of a tensor of any rank. - linspace
- linspace_
f32 - topk_
last_ dim