Group entries of an iterable by n

Number a Bio.PDB chain with a Ig or Tcr numbering scheme.

Apply the Chothia numbering scheme for light chains Rules should be implemented using two strings - the state string and the region stri

Run the sequences in sequence list against a precompiled hmm_database. Those sequence that have a significant hit with a bit score over a th

Check whether a sequence is a protein sequence or if someone has submitted something nasty.

Search PATH for executable files with the given name. On newer versions of MS-Windows, the PATHEXT environment variable will be set t

entry function for NWalign * invmap_only - whether to return seqxA and seqyA or to return invmap * 0: only return seqxA and seqyA

Returns SeqRecord objects for each chain in a PDB file. The sequences are derived from the SEQRES lines in the PDB file header, not the atoms

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

Check to see if the domains are overlapping. @param dom1: @param dom2: @return: True or False

Wolfguy's L1 annotation is based on recognising the length and the sequence pattern defined by a set of rules. If the length has not been cha

Take a hit hsp and turn the alignment into a state vector with sequence indices

@param query: hmmer query object from Biopython @param bit_score_threshold: the threshold for which to consider a hit a hit. T

Add regions to the selection.

Annotate chain with regions. The loaded numbering scheme is used

Given a numbered sequence annotate which region each residue belongs to. The numbering scheme can be one chothia, kabat, imgt or martin

calculate approximate TM-score given rotation matrix */

:param h: [bs * n_node, input_size] :param edge_index: list of [n_edge], [n_edge] :param radial: [n_edge, n_channel, n_channe

calculate dynamic programming matrix using gotoh algorithm * S - cumulative scorefor each cell * P - string representation for path *

As the length of CDR3 gets long (over 30ish) an alignment that does not include the J region becomes more favourable. This leads to really lo

Compile a remark report that is parsable

Memory efficient with complexity of O(Nn) where n is the largest number of nodes in the batch

Converts amino acid three letter code to one letter codes. '' is returned if a coversion cannot be made.

coord: [bs * n_node, n_channel, d] edge_index: list of [n_edge], [n_edge] coord_diff: [n_edge, n_channel, d] edge_fea

:param coord: [bs * n_node, n_channel, d] :param edge_index: list of [n_edge], [n_edge] :param coord_diff: [n_edge, n_channel

Function to align two sequences by checking if one is in the other. This function will conserve gaps.

:param source: [n_edge, input_size] :param target: [n_edge, input_size] :param radial: [n_edge, n_channel, n_channel]

extract pairwise sequence alignment from residue index vectors, * assuming that "sequence" contains two empty strings. * return length of alignmen

Extract the sequence of the chain (amino acids only)

Given a fasta file. yield tuples of header, sequence https://www.biostars.org/p/710/

locate the cell with highest alignment score. reset path after * the cell to zero */

Annotate the pairs of domains in the structure using the distance between the interface cysteine residue CA atoms.

Consider the case where there is one or more missing residues flanked by identical residues: QETGGGGGGNCP QETGG-GGGNCP The align

Args: R: Frame basis matrices, (N, L, 3, 3_index). t: Frame external (absolute) coordinates, (N, L, 3).

Args: R: Frame basis matrices, (N, L, 3, 3_index). t: Frame external (absolute) coordinates, (N, L, 3).

automatically generate side chain according to statistics

:param X: [n_all_node, n_channel, 3] :param S: [n_all_node] :param L: list of cdr types :param offsets: [batch_size +

:param X: [n_all_node, n_channel, 3] :param S: [n_all_node] :param L: list of cdr types :param offsets: [batch_size +

Get the length of an hmm given a species and chain type. This tells us how many non-insertion positions there could possibly be in a domain

Args: pos14: (N, L, 14, 3) atom_mask: (N, L, 14)

Get the region in which the position belongs given the chain, numbering scheme and definition. **Note** this function does not know about in