`deeporigin.drug_discovery.structures`¶

Classes¶

Ligand `dataclass` ¶

A class representing a ligand molecule in drug discovery workflows. The Ligand class provides functionality to create, manipulate, and analyze small molecules (ligands) in computational drug discovery. It supports various input formats and provides methods for property prediction, visualization, and file operations.

Attributes:

Name	Type	Description
`identifier`	`Optional[str]`	Ligand identifier (e.g., PubChem ID)
`file_path`	`Optional[str]`	Path to the ligand file
`smiles`	`Optional[str]`	SMILES string representing the ligand
`block_type`	`Optional[str]`	Format of the block content ('mol', 'mol2', 'sdf', 'pdb')
`block_content`	`Optional[str]`	String containing the molecule data
`name`	`Optional[str]`	Optional name of the ligand
`seed`	`Optional[int]`	Random seed for coordinate generation
`xref_protein`	`Optional[str]`	Cross-reference to protein
`xref_ins_code`	`Optional[str]`	Cross-reference insertion code
`xref_residue_id`	`Optional[str]`	Cross-reference residue ID
`xref_protein_chain_id`	`Optional[str]`	Cross-reference protein chain ID
`save_to_file`	`bool`	Whether to save the ligand to file
`properties`	`dict`	Dictionary of ligand properties
`mol`	`Optional[Molecule]`	Direct Molecule object initialization

Examples:

>>> # Create from SMILES
>>> ligand = Ligand.from_smiles("CCO", name="Ethanol")

>>> # Create from SDF file
>>> ligand = Ligand.from_sdf("ligand.sdf")

>>> # Get properties
>>> center = ligand.get_center()
>>> props = ligand.admet_properties()

>>> # Visualize
>>> ligand.visualize()

>>> # Save to file
>>> ligand.write_to_file("output.pdb")

Attributes¶

atom_types `property` ¶

atom_types

available_for_docking `class-attribute` `instance-attribute` ¶

available_for_docking: bool = field(
    init=False, default=True
)

block_content `class-attribute` `instance-attribute` ¶

block_content: str | None = None

block_type `class-attribute` `instance-attribute` ¶

block_type: str | None = None

coordinates `property` ¶

coordinates

file_path `class-attribute` `instance-attribute` ¶

file_path: str | None = None

hac `class-attribute` `instance-attribute` ¶

hac: int = field(init=False, default=0)

identifier `class-attribute` `instance-attribute` ¶

identifier: str | None = None

mol `class-attribute` `instance-attribute` ¶

mol: Molecule | None = None

name `class-attribute` `instance-attribute` ¶

name: str | None = None

properties `class-attribute` `instance-attribute` ¶

properties: dict = field(default_factory=dict)

protonated_smiles `class-attribute` `instance-attribute` ¶

protonated_smiles: str | None = field(
    init=False, default=None
)

save_to_file `class-attribute` `instance-attribute` ¶

save_to_file: bool = False

seed `class-attribute` `instance-attribute` ¶

seed: int | None = None

smiles `class-attribute` `instance-attribute` ¶

smiles: str | None = None

xref_ins_code `class-attribute` `instance-attribute` ¶

xref_ins_code: str | None = None

xref_protein `class-attribute` `instance-attribute` ¶

xref_protein: str | None = None

xref_protein_chain_id `class-attribute` `instance-attribute` ¶

xref_protein_chain_id: str | None = None

xref_residue_id `class-attribute` `instance-attribute` ¶

xref_residue_id: str | None = None

Functions¶

admet_properties ¶

admet_properties() -> str

Predict ADMET properties for the ligand.

Returns:

Name	Type	Description
`str`	`str`	A string containing the predicted ADMET properties.

convert_to_sdf `classmethod` ¶

convert_to_sdf(block_content: str, block_type: str) -> str

Convert a ligand block content to SDF format.

Parameters:

Name	Type	Description	Default
`block_content`	`str`	The block content of the ligand.	required
`block_type`	`str`	The type of the block content.	required

Returns:

Name	Type	Description
`str`	`str`	The ligand block content in SDF format.

draw ¶

draw()

Draw the ligand molecule.

Example:

ligand.draw()

from_block_content `classmethod` ¶

from_block_content(
    block_content: str,
    block_type: str,
    name: str = "",
    save_to_file: bool = False,
    **kwargs: Any
) -> Ligand

Create a Ligand instance from block content.

Parameters:

Name	Type	Description	Default
`block_content`	`str`	String containing the molecule data	required
`block_type`	`str`	Format of the block content ('mol', 'mol2', 'sdf', 'pdb')	required
`name`	`str`	Name of the ligand. Defaults to "".	`''`
`save_to_file`	`bool`	Whether to save the ligand to file. Defaults to False.	`False`
`**kwargs`	`Any`	Additional arguments to pass to the constructor	`{}`

Returns:

Name	Type	Description
`Ligand`	`Ligand`	A new Ligand instance

from_csv `classmethod` ¶

from_csv(
    file_path: str, smiles_column: str = "smiles"
) -> list[Ligand]

Create Ligand instances from a CSV file containing SMILES strings and additional properties.

Parameters:

Name	Type	Description	Default
`file_path`	`str`	The path to the CSV file.	required
`smiles_column`	`str`	The name of the column containing SMILES strings. Defaults to "smiles".	`'smiles'`

Returns:

Type	Description
`list[Ligand]`	list[Ligand]: A list of Ligand instances created from the CSV file.

Raises:

Type	Description
`FileNotFoundError`	If the file does not exist.
`ValueError`	If the CSV does not contain the specified smiles column or if SMILES strings are invalid.

from_identifier `classmethod` ¶

from_identifier(
    identifier: str,
    name: Optional[str] = None,
    save_to_file: bool = False,
    **kwargs: Any
) -> Ligand

Create a Ligand instance from a chemical identifier.

Parameters:

Name	Type	Description	Default
`identifier`	`str`	Chemical identifier (e.g., common name, PubChem name, drug name)	required
`name`	`str`	Name of the ligand. If not provided, uses the identifier. Defaults to "".	`None`
`save_to_file`	`bool`	Whether to save the ligand to file. Defaults to False.	`False`
`**kwargs`	`Any`	Additional arguments to pass to the constructor	`{}`

Returns:

Name	Type	Description
`Ligand`	`Ligand`	A new Ligand instance initialized from the chemical identifier

Example

Create ATP molecule¶

atp = Ligand.from_identifier("ATP", name="ATP")

Create serotonin molecule¶

serotonin = Ligand.from_identifier( ... identifier="serotonin", ... name="Serotonin" ... )

Raises:

Type	Description
`DeepOriginException`	If the identifier cannot be resolved to a valid molecule

from_rdkit_mol `classmethod` ¶

from_rdkit_mol(
    mol: Mol,
    name: str = "",
    save_to_file: bool = False,
    **kwargs: Any
) -> Ligand

Create a Ligand instance from an RDKit Mol object.

Parameters:

Name	Type	Description	Default
`mol`	`Mol`	RDKit molecule object to convert to a Ligand	required
`name`	`str`	Name of the ligand. Defaults to "".	`''`
`save_to_file`	`bool`	Whether to save the ligand to file. Defaults to False.	`False`
`**kwargs`	`Any`	Additional arguments to pass to the constructor	`{}`

Returns:

Name	Type	Description
`Ligand`	`Ligand`	A new Ligand instance initialized from the RDKit molecule

Example

from rdkit import Chem mol = Chem.MolFromSmiles("CCO") ligand = Ligand.from_rdkit_mol(mol, name="Ethanol")

from_sdf `classmethod` ¶

from_sdf(
    file_path: str,
    *,
    sanitize: bool = True,
    removeHs: bool = False
) -> Union[List[Ligand], Ligand]

Create Ligand instances from an SDF file.

Parameters:

Name	Type	Description	Default
`file_path`	`str`	The path to the SDF file.	required

Returns:

Type	Description
`Union[List[Ligand], Ligand]`	list[Ligand]: A list of Ligand instances created from the SDF file.

Raises:

Type	Description
`FileNotFoundError`	If the file does not exist.
`ValueError`	If the file cannot be parsed correctly.

from_smiles `classmethod` ¶

from_smiles(
    smiles: str,
    name: str = "",
    save_to_file: bool = False,
    **kwargs: Any
) -> Ligand

Create a Ligand instance from a SMILES string.

Parameters:

Name	Type	Description	Default
`smiles`	`str`	SMILES string representing the ligand	required
`name`	`str`	Name of the ligand. Defaults to "".	`''`
`save_to_file`	`bool`	Whether to save the ligand to file. Defaults to False.	`False`
`**kwargs`	`Any`	Additional arguments to pass to the constructor	`{}`

Returns:

Name	Type	Description
`Ligand`	`Ligand`	A new Ligand instance

Example

ligand = Ligand.from_smiles( ... smiles="CCO", # Ethanol ... name="Ethanol", ... save_to_file=False ... ) print(ligand.smiles) CCO

get_center ¶

get_center() -> Optional[list[float]]

Get the center of the ligand based on its coordinates.

Returns: - list: The center coordinates of the ligand. - None: If coordinates are not available.

Example:

center = ligand.get_center()
print(center)  # Output: [1.23, 4.56, 7.89]

get_property ¶

get_property(prop_name: str)

Get the value of a property for the ligand molecule.

Parameters: - prop_name (str): Name of the property to retrieve.

Returns: - The value of the property if it exists, otherwise None.

Example:

binding_affinity = ligand.get_property("BindingAffinity")

protonate ¶

protonate(pH: float = 7.4, filter_percentage: float = 1)

Predicts the right protonation of a molecule at given pH value.

Parameters: - entry: A single or multiple ligands represented as SMILES or Ligand instances. - pH: pH value of the solvent for concentration calculation. Default is 7.4. - filter_percentage: Percentage threshold for filtering low concentration states. Default is 1.

Returns: - ProtonationReport: A ProtonationReport instance.

protonate_molecules `classmethod` ¶

protonate_molecules(ligands)

Predicts the right protonation of a molecule at given pH value.

Parameters: - entry: A single or multiple ligands represented as SMILES or Ligand instances. - pH: pH value of the solvent for concentration calculation. Default is 7.4. - filter_percentage: Percentage threshold for filtering low concentration states. Default is 1.

Returns: - ProtonationReport: A ProtonationReport instance.

set_property ¶

set_property(prop_name: str, prop_value)

Set a property for the ligand molecule.

Parameters: - prop_name (str): Name of the property. - prop_value: Value of the property.

Example:

ligand.set_property("BindingAffinity", 5.6)

show ¶

show() -> str

Visualize the current state of the ligand molecule.

Returns: - str: HTML representation of the visualization.

Raises: - Exception: If visualization fails.

Example:

ligand.show()

update_coordinates ¶

update_coordinates(coords: ndarray)

update coordinates of the ligand structure

visualize_ligands `classmethod` ¶

visualize_ligands(ligands: list[Ligand])

Visualize ligands.

Parameters:

Name	Type	Description	Default
`ligands`	`list[Ligand]`	list["Ligand"]: The list of ligands objects to visualize.	required

Raises:

Type	Description
`FileNotFoundError`	If the file does not exist.
`ValueError`	If the file cannot be parsed correctly.

visualize_ligands_from_sdf `classmethod` ¶

visualize_ligands_from_sdf(file_path: str)

Visualize ligands from an SDF file.

Parameters:

Name	Type	Description	Default
`file_path`	`str`	The path to the SDF file.	required

Raises:

Type	Description
`FileNotFoundError`	If the file does not exist.
`ValueError`	If the file cannot be parsed correctly.

write_to_file ¶

write_to_file(
    output_path: str = "", output_format: str = ""
)

Writes the ligand molecule to a file, including all properties.

Parameters: - output_path (str): Path where the ligand will be written.

Raises: - ValueError: If the file extension is unsupported. - Exception: If writing to the file fails.

Example:

ligand.write_to_file('/path/to/output.pdb')

Pocket `dataclass` ¶

A class representing a binding pocket in a protein structure.

Attributes¶

block_content `class-attribute` `instance-attribute` ¶

block_content: str = ''

block_type `class-attribute` `instance-attribute` ¶

block_type: str = ''

color `class-attribute` `instance-attribute` ¶

color: str = 'red'

coordinates `class-attribute` `instance-attribute` ¶

coordinates: Optional[ndarray] = None

file_path `class-attribute` `instance-attribute` ¶

file_path: Optional[Path] = None

index `class-attribute` `instance-attribute` ¶

index: Optional[int] = 0

name `class-attribute` `instance-attribute` ¶

name: Optional[str] = None

pdb_id `class-attribute` `instance-attribute` ¶

pdb_id: Optional[str] = None

props `class-attribute` `instance-attribute` ¶

props: Optional[Dict[str, Any]] = field(
    default_factory=dict
)

structure `class-attribute` `instance-attribute` ¶

structure: Optional[ndarray] = None

Functions¶

from_block `classmethod` ¶

from_block(
    block_content: str,
    block_type: str = "pdb",
    **kwargs: Any
) -> Pocket

Create a Pocket instance from block content.

Parameters:

Name	Type	Description	Default
`block_content`	`str`	The content of the pocket structure.	required
`block_type`	`str`	The format of the block content (default: "pdb").	`'pdb'`
`**kwargs`	`Any`	Additional arguments to pass to the Pocket constructor.	`{}`

Returns:

Name	Type	Description
`Pocket`	`Pocket`	A new Pocket instance.

Example

pocket = Pocket.from_block(pdb_content, block_type="pdb")

from_file `classmethod` ¶

from_file(file_path: str, **kwargs: Any) -> Pocket

Create a Pocket instance from a file.

Parameters:

Name	Type	Description	Default
`file_path`	`str`	Path to the pocket structure file.	required
`**kwargs`	`Any`	Additional arguments to pass to the Pocket constructor.	`{}`

Returns:

Name	Type	Description
`Pocket`	`Pocket`	A new Pocket instance.

Example

pocket = Pocket.from_file("pocket.pdb")

from_name `classmethod` ¶

from_name(name: str, **kwargs: Any) -> Pocket

Create a Pocket instance by searching for a file with the given name in the pockets directory.

Parameters:

Name	Type	Description	Default
`name`	`str`	Name of the pocket to search for.	required
`**kwargs`	`Any`	Additional arguments to pass to the Pocket constructor.	`{}`

Returns:

Name	Type	Description
`Pocket`	`Pocket`	A new Pocket instance.

Example

pocket = Pocket.from_name("binding_site_1")

from_pocket_finder_results `classmethod` ¶

from_pocket_finder_results(
    pocket_finder_results_dir: str | Path,
) -> List[Pocket]

Create a list of Pocket objects from pocket finder results directory.

Parameters:

Name	Type	Description	Default
`pocket_finder_results_dir`	`str \| Path`	Directory containing pocket finder results with PDB files for each pocket and a CSV properties file.	required

Returns:

Type	Description
`List[Pocket]`	List of Pocket objects with properties from the CSV file.

from_structure `classmethod` ¶

from_structure(
    structure: ndarray,
    name: Optional[str] = None,
    **kwargs: Any
) -> Pocket

Create a Pocket instance directly from a structure array.

Parameters:

Name	Type	Description	Default
`structure`	`ndarray`	The structure array.	required
`name`	`Optional[str]`	Name for the pocket.	`None`
`**kwargs`	`Any`	Additional arguments to pass to the Pocket constructor.	`{}`

Returns:

Name	Type	Description
`Pocket`	`Pocket`	A new Pocket instance.

Example

pocket = Pocket.from_structure(atom_array, name="binding_site")

get_center ¶

get_center() -> ndarray

Get the center of the pocket based on its coordinates.

Returns:

Type	Description
`ndarray`	np.ndarray: A numpy array containing the center of the pocket.

get_directory `staticmethod` ¶

get_directory() -> str

Generates and ensures the existence of a directory for pockets.

Returns:

Name	Type	Description
`str`	`str`	The path to the pockets directory.

load_structure ¶

load_structure(structure_file_path: str | Path) -> None

Load a PDB structure from a file path into the structure attribute.

Parameters:

Name	Type	Description	Default
`structure_file_path`	`str \| Path`	Path to the PDB file.	required

load_structure_from_block ¶

load_structure_from_block(
    block_content: str, block_type: str
)

Load a pocket structure from block content.

Parameters: - block_content (str): String containing the pocket data. - block_type (str): Format of the block content ('pdb').

Returns: - AtomArray: Loaded structure.

Raises: - ValueError: If the block type is unsupported.

pocket_props ¶

pocket_props()

get the properties of the pocket

show ¶

show()

show the pocket in a jupyter notebook

update_coordinates ¶

update_coordinates(coords: ndarray)

update coordinates of the pocket structure

write_to_file ¶

write_to_file(output_path: str, output_format: str = 'pdb')

Write the current state of the structure to a PDB file.

Parameters: - file_path (str): Path where the pocket structure will be written.

Example:

pocket.write_to_file('/path/to/output.pdb')

Protein `dataclass` ¶

A class representing a protein structure with various manipulation and analysis capabilities.

Attributes¶

atom_types `class-attribute` `instance-attribute` ¶

atom_types: Optional[ndarray] = None

block_content `class-attribute` `instance-attribute` ¶

block_content: Optional[str] = None

block_type `class-attribute` `instance-attribute` ¶

block_type: str = 'pdb'

coordinates `property` ¶

coordinates

file_path `class-attribute` `instance-attribute` ¶

file_path: Optional[Path] = None

info `class-attribute` `instance-attribute` ¶

info: Optional[dict] = None

name `instance-attribute` ¶

name: str

pdb_id `class-attribute` `instance-attribute` ¶

pdb_id: Optional[str] = None

structure `class-attribute` `instance-attribute` ¶

structure: ndarray = field(repr=False)

Functions¶

dock ¶

dock(*, ligand: Ligand, pocket: Pocket) -> str

Dock a ligand into a specific pocket of the protein.

This method performs molecular docking of a ligand into a specified pocket of the protein structure. It uses the Deep Origin docking to generate a 3D structure of the docked ligand.

Parameters:

Name	Type	Description	Default
`ligand`	`Ligand`	The ligand to dock into the protein pocket.	required
`pocket`	`Pocket`	The specific pocket in the protein where the ligand should be docked.	required

Returns:

Name	Type	Description
`str`	`str`	Path to the SDF file containing the docked ligand structure.

download_protein_by_pdb_id `staticmethod` ¶

download_protein_by_pdb_id(
    pdb_id: str, save_dir: str = ""
) -> str

Download a PDB structure by its PDB ID from RCSB.

extract_metals_and_cofactors ¶

extract_metals_and_cofactors() -> (
    Tuple[list[str], list[str]]
)

Extract metal ions and cofactors from the protein structure.

Returns:

Type	Description
`Tuple[list[str], list[str]]`	Tuple[list[str], list[str]]

find_pockets ¶

find_pockets(
    pocket_count: int = 5, pocket_min_size: int = 30
) -> list[Pocket]

Find potential binding pockets in the protein structure.

This method analyzes the protein structure to identify cavities or pockets that could potentially serve as binding sites for ligands. It uses the Deep Origin pocket finding algorithm to detect and characterize these pockets.

Parameters:

Name	Type	Description	Default
`pocket_count`	`int`	Maximum number of pockets to identify. Defaults to 5.	`5`
`pocket_min_size`	`int`	Minimum size of pockets to consider, measured in cubic Angstroms. Defaults to 30.	`30`

Returns:

Type	Description
`list[Pocket]`	list[Pocket]: A list of Pocket objects, each representing a potential binding site in the protein. Each Pocket object contains: - The 3D structure of the pocket - Properties such as volume, surface area, hydrophobicity, etc. - Visualization parameters (color, etc.)

Examples:

>>> protein = Protein(file="protein.pdb")
>>> pockets = protein.find_pockets(pocket_count=3, pocket_min_size=50)
>>> for pocket in pockets:
...     print(f"Pocket: {pocket.name}, Volume: {pocket.properties.get('volume')} Å³")

from_file `classmethod` ¶

from_file(file_path: str, struct_ind: int = 0) -> Protein

Create a Protein instance from a file.

Parameters:

Name	Type	Description	Default
`file_path`	`str`	Path to the protein PDB file.	required
`struct_ind`	`int`	Index of the structure to select if multiple are present.	`0`

Returns:

Name	Type	Description
`Protein`	`Protein`	A new Protein instance.

Raises:

Type	Description
`FileNotFoundError`	If the file does not exist.
`ValueError`	If the structure cannot be loaded.
`RuntimeError`	If the file cannot be read or processed.

from_pdb_id `classmethod` ¶

from_pdb_id(pdb_id: str, struct_ind: int = 0) -> Protein

Create a Protein instance from a PDB ID.

Parameters:

Name	Type	Description	Default
`pdb_id`	`str`	PDB ID of the protein to download.	required
`struct_ind`	`int`	Index of the structure to select if multiple are present.	`0`

Returns:

Name	Type	Description
`Protein`	`Protein`	A new Protein instance.

Raises:

Type	Description
`ValueError`	If the PDB ID is invalid or the structure cannot be loaded.
`RuntimeError`	If the download fails.

get_center_by_residues ¶

get_center_by_residues(residues: list[str]) -> ndarray

Get the center of the protein structure based on specific residues.

Parameters:

Name	Type	Description	Default
`residues`	`list[str]`	List of residue names to include in the calculation.	required

get_directory `staticmethod` ¶

get_directory() -> str

Get the directory for storing protein files.

list_chain_names ¶

list_chain_names() -> list[str]

List all unique chain IDs in the protein structure.

Returns:

Type	Description
`list[str]`	list[str]: A list of unique chain IDs.

list_hetero_names ¶

list_hetero_names(exclude_water=True) -> list[str]

List all unique hetero residue names in the protein structure.

Parameters:

Name	Type	Description	Default
`exclude_water`	`bool`	Whether to exclude water molecules from the list.	`True`

Returns:

Type	Description
`list[str]`	list[str]: A list of unique ligand residue names (excluding water).

load_structure_from_block `staticmethod` ¶

load_structure_from_block(
    block_content: str, block_type: str
) -> ndarray

Load a protein structure from block content.

remove_hetatm ¶

remove_hetatm(
    keep_resnames: Optional[list[str]] = None,
    remove_metals: Optional[list[str]] = None,
) -> None

Remove HETATM records from the protein structure, with options to retain specified residues or exclude certain metals.

Parameters¶

keep_resnames : Optional[list[str]] A list of residue names (strings) to keep in the structure even if they are HETATM records. exclude_metals : Optional[list[str]] A list of metal names (strings) to exclude from removal. These metals will be retained in the structure.

Notes¶

By default, a predefined list of metals is considered for removal unless specified in exclude_metals.
If keep_resnames is provided, those residues (along with any metals not excluded) will be retained even if they are HETATM records.
The method updates the current protein object in place.

Example:

    protein = Protein(structure)
    protein.remove_hetatm(keep_resnames=['HOH'], exclude_metals=['ZN'])

remove_resnames ¶

remove_resnames(
    exclude_resnames: Optional[list[str]] = None,
) -> None

Remove specific residue names from the protein structure in place.

Parameters:

Name	Type	Description	Default
`exclude_resnames`	`Optional[list[str]]`	List of residue names to exclude.	`None`

remove_water ¶

remove_water() -> None

Remove water molecules from the protein structure in place.

Example:

protein.remove_water()

select_chain ¶

select_chain(chain_id: str) -> Optional[Protein]

Select a specific chain by its ID and return a new Protein object.

Parameters: - chain_id (str): Chain ID to select.

Returns: - Protein: A new Protein object containing the selected chain.

Raises: - ValueError: If the chain ID is not found.

Example:

chain_a = protein.select_chain('A')

select_chains ¶

select_chains(chain_ids: list[str]) -> Protein

Select specific chains from the protein structure.

Parameters:

Name	Type	Description	Default
`chain_ids`	`list[str]`	List of chain IDs to select.	required

select_structure `staticmethod` ¶

select_structure(structure: ndarray, index: int) -> ndarray

Select a specific structure by index.

show ¶

show(
    pockets: Optional[list[Pocket]] = None,
    sdf_file: Optional[str] = None,
)

Visualize the protein structure in a Jupyter notebook using MolStar viewer.

This method provides interactive 3D visualization of the protein structure with optional highlighting of binding pockets and docked ligands. The visualization is rendered directly in Jupyter notebooks using the MolStar viewer.

Parameters:

Name	Type	Description	Default
`pockets`	`Optional[list[Pocket]]`	List of Pocket objects to highlight in the visualization. Each pocket will be displayed with its defined color and transparency. Defaults to None.	`None`
`sdf_file`	`Optional[str]`	Path to an SDF file containing docked ligand structures. When provided, the ligands will be displayed alongside the protein structure. Defaults to None.	`None`

Examples:

Visualize protein structure only¶

>>> protein = Protein(file="protein.pdb")
>>> protein.show()

Visualize protein with highlighted pockets¶

>>> pockets = protein.find_pockets(pocket_count=3)
>>> protein.show(pockets=pockets)

Visualize protein with docked ligands¶

>>> protein.show(sdf_file="docked_ligands.sdf")

Visualize protein with both pockets and docked ligands¶

>>> protein.show(pockets=pockets, sdf_file="docked_ligands.sdf")

Notes

When pockets are provided, they are displayed with semi-transparent surfaces (alpha=0.7) while the protein is shown with a more transparent surface (alpha=0.1)
The protein is displayed in cartoon representation when pockets are shown
When an SDF file is provided, the visualization includes both the protein and the docked ligands in their respective binding poses

to_pdb ¶

to_pdb(file_path: str)

Write the protein structure to a PDB file.

Parameters:

Name	Type	Description	Default
`file_path`	`str`	Path where the PDB file will be written.	required

Example:

protein.to_pdb('/path/to/output.pdb')

update_coordinates ¶

update_coordinates(coords: ndarray)

update coordinates of the protein structure

deeporigin.drug_discovery.structures¶

Classes¶

Ligand dataclass ¶

Attributes¶

atom_types property ¶

available_for_docking class-attribute instance-attribute ¶

block_content class-attribute instance-attribute ¶

block_type class-attribute instance-attribute ¶

coordinates property ¶

file_path class-attribute instance-attribute ¶

hac class-attribute instance-attribute ¶

identifier class-attribute instance-attribute ¶

mol class-attribute instance-attribute ¶

name class-attribute instance-attribute ¶

properties class-attribute instance-attribute ¶

protonated_smiles class-attribute instance-attribute ¶

save_to_file class-attribute instance-attribute ¶

seed class-attribute instance-attribute ¶

smiles class-attribute instance-attribute ¶

xref_ins_code class-attribute instance-attribute ¶

xref_protein class-attribute instance-attribute ¶

xref_protein_chain_id class-attribute instance-attribute ¶

xref_residue_id class-attribute instance-attribute ¶

Functions¶

admet_properties ¶

convert_to_sdf classmethod ¶

draw ¶

from_block_content classmethod ¶

from_csv classmethod ¶

from_identifier classmethod ¶

Create ATP molecule¶

Create serotonin molecule¶

from_rdkit_mol classmethod ¶

from_sdf classmethod ¶

from_smiles classmethod ¶

get_center ¶

get_property ¶

protonate ¶

protonate_molecules classmethod ¶

set_property ¶

show ¶

update_coordinates ¶

visualize_ligands classmethod ¶

visualize_ligands_from_sdf classmethod ¶

write_to_file ¶

Pocket dataclass ¶

Attributes¶

block_content class-attribute instance-attribute ¶

block_type class-attribute instance-attribute ¶

color class-attribute instance-attribute ¶

coordinates class-attribute instance-attribute ¶

file_path class-attribute instance-attribute ¶

index class-attribute instance-attribute ¶

name class-attribute instance-attribute ¶

pdb_id class-attribute instance-attribute ¶

props class-attribute instance-attribute ¶

structure class-attribute instance-attribute ¶

Functions¶

from_block classmethod ¶

from_file classmethod ¶

from_name classmethod ¶

from_pocket_finder_results classmethod ¶

from_structure classmethod ¶

get_center ¶

get_directory staticmethod ¶

load_structure ¶

load_structure_from_block ¶

pocket_props ¶

show ¶

update_coordinates ¶

write_to_file ¶

Protein dataclass ¶

Attributes¶

atom_types class-attribute instance-attribute ¶

block_content class-attribute instance-attribute ¶

block_type class-attribute instance-attribute ¶

coordinates property ¶

file_path class-attribute instance-attribute ¶

info class-attribute instance-attribute ¶

name instance-attribute ¶

`deeporigin.drug_discovery.structures`¶

Ligand `dataclass` ¶

atom_types `property` ¶

available_for_docking `class-attribute` `instance-attribute` ¶

block_content `class-attribute` `instance-attribute` ¶

block_type `class-attribute` `instance-attribute` ¶

coordinates `property` ¶

file_path `class-attribute` `instance-attribute` ¶

hac `class-attribute` `instance-attribute` ¶

identifier `class-attribute` `instance-attribute` ¶

mol `class-attribute` `instance-attribute` ¶

name `class-attribute` `instance-attribute` ¶

properties `class-attribute` `instance-attribute` ¶

protonated_smiles `class-attribute` `instance-attribute` ¶

save_to_file `class-attribute` `instance-attribute` ¶

seed `class-attribute` `instance-attribute` ¶

smiles `class-attribute` `instance-attribute` ¶

xref_ins_code `class-attribute` `instance-attribute` ¶

xref_protein `class-attribute` `instance-attribute` ¶

xref_protein_chain_id `class-attribute` `instance-attribute` ¶

xref_residue_id `class-attribute` `instance-attribute` ¶

convert_to_sdf `classmethod` ¶

from_block_content `classmethod` ¶

from_csv `classmethod` ¶

from_identifier `classmethod` ¶

from_rdkit_mol `classmethod` ¶

from_sdf `classmethod` ¶

from_smiles `classmethod` ¶

protonate_molecules `classmethod` ¶

visualize_ligands `classmethod` ¶

visualize_ligands_from_sdf `classmethod` ¶

Pocket `dataclass` ¶

block_content `class-attribute` `instance-attribute` ¶

block_type `class-attribute` `instance-attribute` ¶

color `class-attribute` `instance-attribute` ¶

coordinates `class-attribute` `instance-attribute` ¶

file_path `class-attribute` `instance-attribute` ¶

index `class-attribute` `instance-attribute` ¶

name `class-attribute` `instance-attribute` ¶

pdb_id `class-attribute` `instance-attribute` ¶

props `class-attribute` `instance-attribute` ¶

structure `class-attribute` `instance-attribute` ¶

from_block `classmethod` ¶

from_file `classmethod` ¶

from_name `classmethod` ¶

from_pocket_finder_results `classmethod` ¶

from_structure `classmethod` ¶

get_directory `staticmethod` ¶

Protein `dataclass` ¶

atom_types `class-attribute` `instance-attribute` ¶

block_content `class-attribute` `instance-attribute` ¶

block_type `class-attribute` `instance-attribute` ¶

coordinates `property` ¶

file_path `class-attribute` `instance-attribute` ¶

info `class-attribute` `instance-attribute` ¶

name `instance-attribute` ¶

pdb_id `class-attribute` `instance-attribute` ¶

structure `class-attribute` `instance-attribute` ¶

download_protein_by_pdb_id `staticmethod` ¶

from_file `classmethod` ¶

from_pdb_id `classmethod` ¶

get_directory `staticmethod` ¶

load_structure_from_block `staticmethod` ¶

select_structure `staticmethod` ¶