deepfold.data.search.parsers

Parsing various file formats.

Functions

convert_stockholm_to_a3m(stockholm_format[, ...])	Converts MSA in Stockholm format to the A3M format.
deduplicate_stockholm_msa(stockholm_msa)	Remove duplicate sequences (ignoring insertions wrt query).
parse_a3m(a3m_string)	Parses sequences and deletion matrix from a3m format alignment.
parse_e_values_from_tblout(tblout)	Parse target to e-value mapping parsed from Jackhmmer tblout string.
parse_fasta(fasta_string)	Parses FASTA string and returns list of strings with amino-acid sequences.
parse_hhr(hhr_string)	Parses the content of an entire HHR file.
parse_hmmsearch_a3m(query_sequence, a3m_string)	Parses an a3m string produced by hmmsearch.
parse_hmmsearch_sto(query_sequence, sto_string)	Gets parsed template hits from the raw string output by the tool.
parse_stockholm(stockholm_string)	Parses sequences and deletion matrix from stockholm format alignment.
remove_empty_columns_from_stockholm_msa(...)	Removes empty columns (dashes-only) from a Stockholm MSA.
truncate_stockholm_msa(stockholm_msa_path, ...)	Reads + truncates a Stockholm file while preventing excessive RAM usage.

Classes

HitMetadata(pdb_id, chain, start, end, ...)
TemplateHit(index, name, aligned_cols, ...)	Class representing a template hit.