schrodinger.livedesign.biologics.fasta module¶
- schrodinger.livedesign.biologics.fasta.create_single_entity_fasta_header(headers_map: Dict[schrodinger.application.bioluminate.antibody.io.csv_reader.Headers, int]) str¶
Create the leading string that identifies a file as a single-entity fasta and provides the necessary mapping for specialized construct registration
- Parameters
headers_map – a dictionary keyed by Header enum which connects an antibody chain to an index in the subsequent fasta entries in the file
- Returns
a string which tags a fasta as having special format and specifies which entry corresponds to which antibody chain
- schrodinger.livedesign.biologics.fasta.is_registrable_fasta(bio_data_str: str) bool¶
Check if a string is in a registrable fasta format, either as a standard fasta or as a special single-entity fasta
- Parameters
bio_data_str – a string containing biological data
- Returns
True, if the string contains registrable fasta data
- schrodinger.livedesign.biologics.fasta.is_single_entity_fasta(bio_data_str: str) bool¶
Check if the string contains a single-entity fasta
- Parameters
bio_data_str – a string containing biological data
- Returns
True if the string represents a single-entity fasta
- schrodinger.livedesign.biologics.fasta.is_multi_entity_fasta(bio_data_str: str) bool¶
Check if the string contains a typical fasta
- Parameters
bio_data_str – a string containing biological data
- Returns
True if the string represents a standard fasta
- schrodinger.livedesign.biologics.fasta.get_fasta_helm_models(fasta_str: str) Iterator[schrodinger.protein.helm._helm_parser.HelmModel]¶
Yield all helm models generated by the parsing of the fasta data. If single-entity, this will include one entry for each sequence, as well as entries for any recognized combined constructs :param fasta_str: a string containing fasta data :return: an iterator of helm models, one for each identified entity
- schrodinger.livedesign.biologics.fasta.parse_multi_entity_fasta(fasta_str: str) Iterator[schrodinger.protein.helm._helm_parser.HelmModel]¶
Parse the fasta string as a standard fasta, with one HelmModel per sequence
- Parameters
fasta_str – a string containing fasta data
- Returns
an iterator of helm models, one for each sequence
- schrodinger.livedesign.biologics.fasta.get_single_chain_helm_model(seq: str) schrodinger.protein.helm._helm_parser.HelmModel¶
Create a HelmModel for a single simple peptide
- Parameters
seq – the sequence of the peptide to add
- Returns
a simple helm model with the given peptide sequence
- schrodinger.livedesign.biologics.fasta.parse_single_entity_fasta(annotated_fasta_str: str) Iterator[schrodinger.protein.helm._helm_parser.HelmModel]¶
Parse the single-entity-formatted fasta string as an antibody, with one HelmModel for each single-chain or multi-chain entity identified
- Parameters
annotated_fasta_str – fasta string with a first line that maps each entry index to an antibody CSV header name
- Returns
an iterator of helm models, one for each hierarchical entity in the construct
- schrodinger.livedesign.biologics.fasta.get_annotation_line_mappings(annotation_line: str) Dict[schrodinger.application.bioluminate.antibody.io.csv_reader.Headers, int]¶
- schrodinger.livedesign.biologics.fasta.validate_mappings(mappings: Dict[schrodinger.application.bioluminate.antibody.io.csv_reader.Headers, int])¶
- schrodinger.livedesign.biologics.fasta.is_valid_ab_header_combination(headers: Set[schrodinger.application.bioluminate.antibody.io.csv_reader.Headers]) bool¶
Check if headers exactly match one of the valid header sets for antibody ingestion :param headers: a list of column headers for sequence fields :return: True if the headers fit at least one antibody type