Module deeporigin.src.utilities.prepare_protein

Functions

def prepare(protein_path: str,
protein_pdb_id: str = '',
protein_extension: str = 'pdb',
metal_resnames: List[str] = None,
cofactor_resnames: List[str] = None,
model_loops: bool = False)

Expand source code

def prepare(
        protein_path: str, 
        protein_pdb_id: str = "", 
        protein_extension: str = "pdb", 
        metal_resnames: List[str] = None, 
        cofactor_resnames: List[str] = None, 
        model_loops: bool = False
    ):
    """
    Prepare a protein structure for docking by processing its PDB file.

    This function sends the protein structure to a server for preparation, which may include
    cleaning the structure, adding missing atoms, and handling metal ions and cofactors.

    Args:
        protein_path (str): Path to the protein structure file
        protein_pdb_id (str, optional): PDB ID of the protein. Defaults to "".
        protein_extension (str, optional): File extension of the protein structure. Defaults to "pdb".
        metal_resnames (List[str], optional): List of metal residue names to preserve. Defaults to None.
        cofactor_resnames (List[str], optional): List of cofactor residue names to preserve. Defaults to None.
        model_loops (bool, optional): Whether to model missing loops. Defaults to False.

    Returns:
        dict: A dictionary containing:
            - prepared_protein_content (str): The prepared protein structure in PDB format
            - raw_protein_path (str): Path to the original protein file
            - protein_extension (str): File extension of the protein structure
            - protein_pdb_id (str): PDB ID of the protein

    Raises:
        May raise exceptions related to file operations or HTTP requests.
    """
    client = Client()
    with open(protein_path, "r") as e:
        data = e.read()

    metal_resnames = ",".join(metal_resnames) if metal_resnames else ""
    cofactor_resnames = ",".join(cofactor_resnames) if cofactor_resnames else ""

    payload = {
        "content": data,
        "pdb_id": protein_pdb_id,
        "extension": protein_extension,
        "metals": metal_resnames,
        "cofactors": cofactor_resnames,
        "model_loops": model_loops,
    }

    response = client.post_request(
        logger=DEFAULT_LOGGER,
        endpoint="docking/prepare",
        data=payload,
    )
    pdb_content = ""
    if response.status_code == 200:
        data = response.json()
        DEFAULT_LOGGER.log_info(data["msg"])

        pdb_content = data["pdb_content"]
    else:
        msg = data.get("msg", "")
        if not msg:
            msg = "Failed to prepare"
        DEFAULT_LOGGER.log_error(msg)

    return {
        "prepared_protein_content": pdb_content,
        "raw_protein_path": protein_path,
        "protein_extension": protein_extension,
        "protein_pdb_id": protein_pdb_id,
    }

Prepare a protein structure for docking by processing its PDB file.

This function sends the protein structure to a server for preparation, which may include cleaning the structure, adding missing atoms, and handling metal ions and cofactors.

Args

protein_path : str

Path to the protein structure file

protein_pdb_id : str, optional

PDB ID of the protein. Defaults to "".

protein_extension : str, optional

File extension of the protein structure. Defaults to "pdb".

metal_resnames : List[str], optional

List of metal residue names to preserve. Defaults to None.

cofactor_resnames : List[str], optional

List of cofactor residue names to preserve. Defaults to None.

model_loops : bool, optional

Whether to model missing loops. Defaults to False.

Returns

dict

A dictionary containing: - prepared_protein_content (str): The prepared protein structure in PDB format - raw_protein_path (str): Path to the original protein file - protein_extension (str): File extension of the protein structure - protein_pdb_id (str): PDB ID of the protein

Raises

May raise exceptions related to file operations or HTTP requests.