search
AlphafoldOptions
dataclass
Options for the AlphaFold sub-search.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
limit
|
NonNegativeInt
|
Maximum number of AlphaFold entries to return. Use '0' to skip the AlphaFold sub-search. |
10000
|
InteractionPartnerOptions
dataclass
Options for the interaction partners sub-search.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
seed
|
Annotated[set[str], Parameter(negative='')]
|
UniProt ID to use as interaction partner seed. The search will be expanded to include structure identifiers of the found interaction partners. Can be specified multiple times. |
set()
|
exclude
|
Annotated[set[str], Parameter(negative='')]
|
UniProt ID to exclude as found interaction partners. Can be specified multiple times. |
set()
|
limit
|
PositiveInt
|
Maximum number of interaction partners to return. |
10000
|
PdbeOptions
dataclass
Options for the PDBe sub-search.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
limit
|
NonNegativeInt
|
Maximum number of PDBe entries to return. Use '0' to skip the PDBe sub-search. |
10000
|
min_residues
|
PositiveInt | None
|
Minimum chain length for PDBe. |
None
|
max_residues
|
PositiveInt | None
|
Maximum chain length for PDBe. |
None
|
top_resolution_per_uniprot_accession
|
PositiveInt
|
Best-N PDBe per UniProt. |
5
|
SearchOptions
dataclass
Options for the search workflow.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
query
|
Annotated[Query, Parameter(name='*', group=uniprot_group)]
|
UniProt search query. |
Query()
|
limit_uniprot
|
Annotated[PositiveInt, Parameter(group=uniprot_group)]
|
Maximum number of UniProt accessions to return. |
10000
|
alphafold
|
Annotated[AlphafoldOptions, Parameter(group=alphafold_group)]
|
Options for the AlphaFold sub-search. |
AlphafoldOptions()
|
pdbe
|
Annotated[PdbeOptions, Parameter(group=pdbe_group)]
|
Options for the PDBe sub-search. |
PdbeOptions()
|
interaction
|
Annotated[InteractionPartnerOptions, Parameter(group=interaction_partners_group)]
|
Options for the interaction partners sub-search. |
InteractionPartnerOptions()
|
search(session_dir, /, *, options=None, _=None)
Search for candidate protein structures.
- Searches for UniProt accessions, writes
<session_dir>/uniprot.txt. - If interaction partner seeds are given, searches for interaction partners.
and adds partners to the list of UniProt accessions.
Writes
<session_dir>/interaction_partner_seeds.txt,<session_dir>/complexes.csvand<session_dir>/uniprot_with_interaction_partners.txt. - Searches for AlphaFold structures for the UniProt accessions.
Writes
<session_dir>/alphafold.csv. - Searches for PDBe structures for the UniProt accessions.
Writes
<session_dir>/pdbe.csv. - Searches for PDBe validation quality reports for the found PDBe structures.
Writes
<session_dir>/pdbe-quality.json. - Writes
<session_dir>/ro-crate-metadata.jsonto keep track of used arguments and its output files.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
session_dir
|
Annotated[Path, Parameter(validator=Path(file_okay=False, dir_okay=False))]
|
RO-Crate session directory. |
required |
options
|
SearchOptions | None
|
Search options. |
None
|