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edee deeeeef d ee fddZdS )zA module for interacting with the AlphaFold Protein Structure Database.
See the `database website `_ and the `API docs `_.
N)PathLike)Iterator)Optional)Union)urlopen) MMCIFParser) Structure qualifierreturnc c sR d| }t |}t| E dH W d dS 1 s"w Y dS )zGet all AlphaFold predictions for a UniProt accession.
:param qualifier: A UniProt accession, e.g. P00520
:type qualifier: str
:return: The AlphaFold predictions
:rtype: Iterator[dict]
z%https://alphafold.com/api/prediction/N)r jsonloadsreaddecode)r urlresponse r H/var/www/html/myenv/lib/python3.10/site-packages/Bio/PDB/alphafold_db.pyget_predictions s
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prediction directoryc C s8 |du rt }| d }|dd }tt j||S )am Get the path to the mmCIF file for an AlphaFold prediction.
:param prediction: An AlphaFold prediction
:type prediction: dict
:param directory: The directory that stores the mmCIF file, defaults to the current working directory
:type directory: Union[int, str, bytes, PathLike], optional
:return: The path to the mmCIF file
:rtype: str
NcifUrl/)osgetcwdsplitstrpathjoin)r r cif_url file_namer r r _get_mmcif_file_path_for s
r! c C s |du rt }| d }t j|dd t| |}t j|r(td| d |S t| }| }W d n1 s;w Y t |d}|
| W d |S 1 sVw Y |S )a Download the mmCIF file for an AlphaFold prediction.
Downloads the file to the current working directory if no destination is specified.
:param prediction: An AlphaFold prediction
:type prediction: dict
:param directory: The directory to write the mmCIF data to, defaults to the current working directory
:type directory: Union[int, str, bytes, PathLike], optional
:return: The path to the mmCIF file
:rtype: str
Nr T)exist_okzFile z# already exists, skipping download.wb) r r makedirsr! r existsprintr r
openwrite)r r r file_pathr datafiler r r download_cif_for5 s"
r, mmcif_parserc c s` |du rt }|du rt }t| D ]}t||}tj|s&t||}|| |V qdS )aG Get the PDB structures for a UniProt accession.
Downloads the mmCIF files to the directory if they are not present.
:param qualifier: A UniProt accession, e.g. P00520
:type qualifier: str
:param mmcif_parser: The mmCIF parser to use, defaults to ``MMCIFParser()``
:type mmcif_parser: MMCIFParser, optional
:param directory: The directory to store the mmCIF data, defaults to the current working directory
:type directory: Union[int, str, bytes, PathLike], optional
:return: An iterator over the PDB structures
:rtype: Iterator[PDBStructure]
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mmcif_pathr r r get_structural_models_forW s
r0 )N)NN)__doc__r r r collections.abcr typingr r urllib.requestr Bio.PDB.MMCIFParserr Bio.PDB.Structurer StructuralModelr dictr bytesr! r, r0 r r r r sL
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