deepfold.data.search.templates

Building the template features for the DeepFold model.

Functions

build_query_to_hit_index_mapping(...)	Gets mapping from indices in original query sequence to indices in the hit.
create_empty_template_feats(seqlen[, empty])
extract_template_features(mmcif_dict, ...)	Extracts template features from a single HHSearch hit.
get_atom_positions(mmcif_dict, ...)	Gets atom positions and mask from a list of Biopython Residues.
load_mmcif_dict(mmcif_dirpath, pdb_id)	Load mmCIF dict for pdb_id.
load_pdb_obsolete_mapping(pdb_obsolete_filepath)	Parses the data file from PDB that lists which PDB ids are obsolete.

Classes

TemplateFeaturesResult(features, error, warning)
TemplateHitFeaturizer(max_template_hits, ...)	A class for computing template features from template hits.

Exceptions

AlignRatioError	An error indicating that the hit align ratio to the query was too small.
CaDistanceError	An error indicating that a CA atom distance exceeds a threshold.
DateError	An error indicating that the hit date was after the max allowed date.
DuplicateError	An error indicating that the hit was an exact subsequence of the query.
LengthError	An error indicating that the hit was too short.
NoAtomDataInTemplateError	An error indicating that template mmCIF didn't contain atom positions.
NoChainsError	An error indicating that template mmCIF didn't have any chains.
PrefilterError	A base class for template prefilter exceptions.
QueryToTemplateAlignError	An error indicating that the query can't be aligned to the template.
SequenceNotInTemplateError	An error indicating that template mmCIF didn't contain the sequence.
TemplateAtomMaskAllZerosError	An error indicating that template mmCIF had all atom positions masked.