Implemetation of Kabsch algoritm for finding the best rotation matrix --------------------------------------------------------------------------- x

Implemetation of Kabsch algoritm for finding the best rotation matrix --------------------------------------------------------------------------- x

copy the value of t and u into t0,u0 */

takes the mean of the elements of x that are not masked the mean is taken along the shared leading dims of m equivalent to: x[m].mean(tuple(ra

Takes a list of tensors with the following dimensions: [(d_11, ..., d_1K), (d_21, ..., d_2K), ..., (d_N1,

heuristic run of dynamic programing iteratively to find the best alignment input: initial rotation matrix t, u vectors x and y, d0 output: best alignm

Args: c_in: Input channel dimension c_hidden: Hidden channel dimension no

calculate approximate TM-score given rotation matrix */

compute the score quickly in three iterations

scores: [b, n] cutoff_len: [b, 1] stochastic: bool, whether to add noise to select top_k or not returns: mask: [b, n], with 1

Comprehensive TMscore search engine input: two vector sets: x, y an alignment invmap0[] between x and y simplify_step: 1 or 40 or other integers sco

Convert a PDB chain object into a AlphaFold Protein instance. Forked from alphafold.common.protein.from_pdb_string WARNING: All non-standard

Input: score[1:len1, 1:len2], and gap_open * Output: j2i[1:len2] \in {1:len1} U {-1} * path[0:len1, 0:len2]=1,2,3, from diagonal, horizontal, vert

Entry function for TM-align. Return TM-score calculation status: * 0 - full TM-score calculation * 1 - terminated due to exception * 2-7 -

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

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

* @brief Helper function to close a file descriptor. * * Inspects @a fd and calls <b>close</b>(3) if it has a non-negative value. * *

x: ... NH where NH is number of codebook heads A longtensor of codebook indices, containing values from 0

Runs a forward pass given input sequences. Args: sequences (Union[str, List[str]]): A list of sequences to make predictions for.

1, collect those residues with dis<d; 2, calculate TMscore

Function that sets seed for pseudo-random number generators in: pytorch, numpy, python.random In addition, sets the following environment variable

split a long string into vectors by whitespace * line - input string * line_vec - output vector * delimiter - delimiter */

strip white space at the begining or end of string */

strip white space at the begining or end of string */

Initialize metadata.

Computes FAPE loss. Args: pred_frames: [*, N_frames] Rigid object of predicted frames target_frames: [*,