Generate an unpaired MSA for the given sequence using colabfold_search. Args: sequence (str): The sequence to generate an MSA for.

Compute AbLang gradient for the hallucination loop. Args: seq: logits dict (with key 'logits') or raw array, shape (..

compute autoregressive mask, given order of positions

Extract Predicted Aligned Error metrics from the best model iteration. Retrieves the Predicted Aligned Error (PAE) and interface PAE (iPAE) v

Extract confidence metrics from the best model iteration. Calculates the predicted Local Distance Difference Test (pLDDT) and interface p

compute weight per sequence

Extract protein sequences from PDB file organized by chain. Parses a PDB file and extracts the amino acid sequence for each chain, conver

Unique key to lookup bonds.

run model to get outputs, losses and gradients

I = { [[required]] 'X' = (L,4,3) 'mask' = (L,) 'residue_index' = (L,) 'chain_idx' = (L,) '

score sequence

set [opt]ions ------------------- note: model.restart() resets the [opt]ions to their defaults use model.set_opt(..., set_defaults=Tr

set/reset optimizer ---------------------------------- supported optimizers include: [adabelief, adafactor, adagrad, adam, adamw, fr

Update additional analysis metrics and metadata. Updates supplementary metrics that don't fall into trajectory or filtering c

Iterate a function `f` `count` times, with non-shared parameters.

Build token IDs, soft input embeddings, and AA positions from sequence logits. Common setup shared by all three gradient variants (unmasked C

Gets the bin centers from the bin edges. Args: breaks: [num_bins - 1] the error bin edges. Returns: bin_centers: [num_bins] the error bin

Calculate mean LIS for each subunit pair. Args: transformed_pae: The PAE matrix after LIS transformation. subunit_sizes: A l

Return (arr2d, had_batch) where arr2d has shape (L, K).

dgram to contacts

dgram to contacts

logits to score/sequence_recovery

Load AbLang model (lazy, cached).

mutate random position

given coordinates a-b-c, return angle

compute CB placement from N, CA, C

given coordinates a-b, return length or distance

compute pairwise distance

compute RMSD of distance matrices

Computes the relative indices for each residue with respect to the original sequence.

animate the trajectory - use [s]tart and [e]nd to define range to be animated - use dpi to specify the resolution of animation - colo

Apply Rigid3Array transform to point.

Calculate secondary structure percentages from counts. Converts raw counts of secondary structure elements to percentages with proper han

Define chi-angle rigid groups via one-hot representations.

optimize logits

semigreedy search

optimize softmax(logits/temp)

Compute distogram from amino acid positions. Arguments: positions: [N_res, 3] Position coordinates. num_bins: The number of bins in the dist

soft positions to dgram converter

convert dictionary to string for print out

Construct Rot3Array from components of quaternion.

Construct Rot3Array from two Vectors. Rot3Array is constructed such that in the corresponding frame 'e0' lies on the positive x-Axis and 'e1'

compute autoregressive mask, given order of positions

Get CB coordinates (CA for GLY)

get contact map from distogram

Get key atoms to check for each residue type Returns list of important atoms for VDW contacts

parse TrRosetta params into dictionary

Apply inverse of transformation to a point. Args: transformed_point: List of 3 tensors to apply affine extra_dims: Number of dimensi

pad input features