Return Vec3Array corresponding to zeros of given shape.

Compute Norm of Vec3Array, clipped to epsilon.

Compute cross product between 'self' and 'other'.

Compute dot product between 'self' and 'other'.

Create a deep copy of this trajectory instance. Creates a new Trajectory instance with identical data but independent from th

prep inputs for TrDesign

deepcopy dictionary

given input [pos]itions (a string of segment ranges seperated by comma, for example: "1,3-4,10-15"), return list of indices to constrain.

plot predictions

get alignment matrix for two sets of coodinates

Unwrap Protenix's single-element list serialization. Protenix's ``save_json`` converts tensors via ``.tolist()``. A shape-[1] tensor becomes

output the loss (for entire trajectory)

Apply affine to a point. Args: point: List of 3 tensors to apply affine. extra_dims: Number of dimensions at the end of the transfor

compute f_i/f_ij/f_ijk given msa

Return unit vector with optional clipping.

Apply rotations 'm' to vectors 'v'.

run model to get outputs, losses and gradients

set sequence params and bias ----------------------------------- -seq=str or seq=[str,str] or seq=array(shape=(L,20) or shape=(?,L,20))

robust function for updating dictionary

Module projecting a Rigid Object. For this Module the Rotation is parametrized as a quaternion, If 'full_quat' is True a 4 vector is produced

extract features from pdb

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

set weights ------------------- note: model.restart() resets the weights to their defaults use model.set_weights(..., set_defaults=Tr

uncrop features

Thread-safe increment of failure counts in tracking CSV. Increments failure counts for specific failure types using thread-safe

Create a rigid 4x4 transformation matrix from two axes and transl.

given coordinates a-b-c-d, return dihedral

compute norm of vector

process features

prep model

Applies Rot3Array to point.

set info for alphafold-multimer

Identify interface hotspot residues between binder and target. Analyzes a protein complex structure to identify binder residues that are

Returns inverse of Rot3Array.

Extracts loop associated with a prefix from mmCIF data as a list. Reference for loop_ in mmCIF: http://mmcif.wwpdb.org/docs/tutorials/mechanics

predict structure for input sequence (if provided)

save pdb coordinates (if filename provided, otherwise return as string) - get_best: False to get the last sampled sequence - save_all: Tr

Return a new quat affine with a different scale for translation.

Set the target directory for trajectory storage. Specifies which directory category this trajectory should be saved to based

decide which model params to use

get 6D features (see TrRosetta paper)

Execute AlphaFold3 structure prediction via Singularity container. Runs AF3 inference using the provided input JSON and configuration settin

single pass through the model

Multiply rotation matrix by a vector.

Generate MSA via ColabFold API with timeout protection. Uses ProcessPoolExecutor to enforce a timeout on MSA generation. If timeout is e

Remove unnecessary information from PDB files for clean processing. Filters PDB files to retain only essential structural information by

Copy residues to new chain with sequential renumbering. Creates a new chain containing copies of the input residues with residue numbers