Unique key to lookup bonds.

Unique key to lookup bonds.

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

Filter a distribution of logits using top-k and/or nucleus (top-p) filtering Args: logits: logits distribution shape (vocabulary size)

Align structures in a ChemGraph batch to a reference, e.g. for RMSD computation. This uses the sparse formulation of pytorch geometric. If the

Move the molecule center to zero for sparse position tensors. Args: pos: [N, 3] batch positions of atoms in the molecule in sparse batch

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

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

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

Performs a nested concatenation of feature dicts. Args: np_dicts: list of dicts with the same structure. Each dict must have

read list of entries from 'name' to 'chain_list'. * dir_opt is the folder name (prefix). * suffix_opt is the file name extension (suffix_opt). *

read list of entries from 'name' to 'chain_list'. * dir_opt is the folder name (prefix). * suffix_opt is the file name extension (suffix_opt). *

Computes several checks for structural violations.

Args: coords_list: list of length batch_size, each item is a list of floats in shape L x 3 x 3 to describe a backbone

Given a list (Tensor) of non-masked residues get new start and end index for motif placed in scaffold.

Initializes multi-GPU-friendly python command line logger.

x: long tensor of indices for constructing codebook, but actually not utilized in all the experiments. returns big endian bits

secondary stucture assignment for protein: * 1->coil, 2->helix, 3->turn, 4->strand */

Returns the pbd (file) string from the model given the model output.

Right pads dimension of numpy array. Args: x: numpy like array to pad. max_len: desired length after padding pad_idx: dim