Pdb

PdbAbstractReader

Bases: BaseReader

Protein Data Bank entries' primary citation abstract reader.

Source code in llama-index-integrations/readers/llama-index-readers-pdb/llama_index/readers/pdb/base.py

class PdbAbstractReader(BaseReader):
    """Protein Data Bank entries' primary citation abstract reader."""

    def __init__(self) -> None:
        super().__init__()

    def load_data(self, pdb_ids: List[str]) -> List[Document]:
        """Load data from RCSB or EBI REST API.

        Args:
            pdb_ids (List[str]): List of PDB ids \
                for which primary citation abstract are to be read.
        """
        results = []
        for pdb_id in pdb_ids:
            title, abstracts = get_pdb_abstract(pdb_id)
            primary_citation = abstracts[title]
            abstract = primary_citation["abstract"]
            abstract_text = "\n".join(
                ["\n".join([str(k), str(v)]) for k, v in abstract.items()]
            )
            results.append(
                Document(
                    text=abstract_text,
                    extra_info={"pdb_id": pdb_id, "primary_citation": primary_citation},
                )
            )
        return results

load_data

load_data(pdb_ids: List[str]) -> List[Document]

Load data from RCSB or EBI REST API.

Parameters:

Name	Type	Description	Default
pdb_ids	List[str]	List of PDB ids for which primary citation abstract are to be read.	required

Source code in llama-index-integrations/readers/llama-index-readers-pdb/llama_index/readers/pdb/base.py

def load_data(self, pdb_ids: List[str]) -> List[Document]:
    """Load data from RCSB or EBI REST API.

    Args:
        pdb_ids (List[str]): List of PDB ids \
            for which primary citation abstract are to be read.
    """
    results = []
    for pdb_id in pdb_ids:
        title, abstracts = get_pdb_abstract(pdb_id)
        primary_citation = abstracts[title]
        abstract = primary_citation["abstract"]
        abstract_text = "\n".join(
            ["\n".join([str(k), str(v)]) for k, v in abstract.items()]
        )
        results.append(
            Document(
                text=abstract_text,
                extra_info={"pdb_id": pdb_id, "primary_citation": primary_citation},
            )
        )
    return results