uniprot
PdbResult
dataclass
Result of a PDB search in UniProtKB.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id
|
str
|
PDB ID (e.g., "1H3O"). |
required |
method
|
str
|
Method used for the PDB entry (e.g., "X-ray diffraction"). |
required |
uniprot_chains
|
str
|
Chains in UniProt format (e.g., "A/B=1-42,A/B=50-99"). |
required |
resolution
|
str | None
|
Resolution of the PDB entry (e.g., "2.0" for 2.0 Å). Optional. |
None
|
Query
dataclass
Search query for UniProtKB.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
taxon_id
|
str | None
|
Taxon ID to filter results by organism (e.g., "9606" for human). |
required |
reviewed
|
bool | None
|
Whether to filter results by reviewed status (True for reviewed, False for unreviewed). |
required |
subcellular_location_uniprot
|
str | None
|
Subcellular location in UniProt format (e.g., "nucleus"). |
required |
subcellular_location_go
|
str | None
|
Subcellular location in GO format (e.g., "GO:0005634" for nucleus). |
required |
molecular_function_go
|
str | None
|
Molecular function in GO format (e.g., "GO:0003674" for molecular_function). |
required |
search4af(uniprot_accs, limit=10000, timeout=1800)
Search for AlphaFold entries in UniProtKB accessions.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
uniprot_accs
|
Iterable[str]
|
UniProt accessions. |
required |
limit
|
int
|
Maximum number of results to return. |
10000
|
timeout
|
int
|
Timeout for the SPARQL query in seconds. |
1800
|
Returns:
| Type | Description |
|---|---|
dict[str, set[str]]
|
Dictionary with protein IDs as keys and sets of AlphaFold IDs as values. |
search4emdb(uniprot_accs, limit=10000, timeout=1800)
Search for EMDB entries in UniProtKB accessions.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
uniprot_accs
|
Iterable[str]
|
UniProt accessions. |
required |
limit
|
int
|
Maximum number of results to return. |
10000
|
timeout
|
int
|
Timeout for the SPARQL query in seconds. |
1800
|
Returns:
| Type | Description |
|---|---|
dict[str, set[str]]
|
Dictionary with protein IDs as keys and sets of EMDB IDs as values. |
search4pdb(uniprot_accs, limit=10000, timeout=1800)
Search for PDB entries in UniProtKB accessions.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
uniprot_accs
|
Iterable[str]
|
UniProt accessions. |
required |
limit
|
int
|
Maximum number of results to return. |
10000
|
timeout
|
int
|
Timeout for the SPARQL query in seconds. |
1800
|
Returns:
| Type | Description |
|---|---|
dict[str, set[PdbResult]]
|
Dictionary with protein IDs as keys and sets of PDB results as values. |
search4uniprot(query, limit=10000, timeout=1800)
Search for UniProtKB entries based on the given query.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
query
|
Query
|
Query object containing search parameters. |
required |
limit
|
int
|
Maximum number of results to return. |
10000
|
timeout
|
int
|
Timeout for the SPARQL query in seconds. |
1800
|
Returns:
| Type | Description |
|---|---|
set[str]
|
Set of uniprot accessions. |