`deeporigin.drug_discovery.Ligand`¶

Bases: Entity

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.

After running :class:~deeporigin.drug_discovery.molprops.Molprops, predicted ADMET values are available on dedicated attributes (log_s, log_d, log_p, herg, cyp, ames, has_pains, pains_fragments) as well as in :attr:properties.

The RDKit molecule must be passed as the keyword-only argument mol (typically via :meth:from_smiles, :meth:from_rdkit_mol, or similar factory methods).

Attributes¶

ames `class-attribute` `instance-attribute` ¶

ames: dict[str, Any] | None = None

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

canonical_smiles `property` ¶

canonical_smiles: str

Canonical (RDKit) SMILES for this ligand.

Notes: - Canonicalization is RDKit-specific. - Returns implicit-H SMILES by default (explicit Hs removed). - Preserves stereochemistry if present.

contains_boron `property` ¶

contains_boron: bool

Check if the ligand contains boron atoms.

Currently, ligands with boron atoms are not supported for docking.

Returns:

Name	Type	Description
`bool`	`bool`	True if the ligand contains boron atoms, False otherwise.

coordinates `property` ¶

coordinates

cyp `class-attribute` `instance-attribute` ¶

cyp: dict[str, Any] | None = None

formal_charge `property` ¶

formal_charge: int

Compute the formal charge of the ligand molecule.

Returns:

Name	Type	Description
`int`	`int`	The sum of formal charges of all atoms in the molecule.

has_pains `class-attribute` `instance-attribute` ¶

has_pains: bool | None = None

hbond_acceptor_count `property` ¶

hbond_acceptor_count: int

Compute the number of hydrogen bond acceptors in the ligand molecule.

Returns:

Name	Type	Description
`int`	`int`	The number of hydrogen bond acceptors.

hbond_donor_count `property` ¶

hbond_donor_count: int

Compute the number of hydrogen bond donors in the ligand molecule.

Returns:

Name	Type	Description
`int`	`int`	The number of hydrogen bond donors.

herg `class-attribute` `instance-attribute` ¶

herg: dict[str, Any] | None = None

id `class-attribute` `instance-attribute` ¶

id: str | None = field(default=None, kw_only=True)

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

identifier: str | None = None

local_path `class-attribute` `instance-attribute` ¶

local_path: str | None = field(default=None, kw_only=True)

log_d `class-attribute` `instance-attribute` ¶

log_d: float | None = None

log_p `class-attribute` `instance-attribute` ¶

log_p: float | None = None

log_s `class-attribute` `instance-attribute` ¶

log_s: float | None = None

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

mol: Mol = field(kw_only=True)

molecular_weight `property` ¶

molecular_weight: float

Compute the exact molecular weight of the ligand molecule.

Returns:

Name	Type	Description
`float`	`float`	The exact molecular weight in atomic mass units.

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

name: str | None = None

pains_fragments `class-attribute` `instance-attribute` ¶

pains_fragments: list[Any] | None = None

prepared `class-attribute` `instance-attribute` ¶

prepared: bool = field(init=False, default=False)

project_id `class-attribute` `instance-attribute` ¶

project_id: str | None = field(default=None, kw_only=True)

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

properties: dict = field(default_factory=dict)

protonated_at_ph `class-attribute` `instance-attribute` ¶

protonated_at_ph: float | None = None

remote_path `class-attribute` `instance-attribute` ¶

remote_path: str | None = field(default=None, kw_only=True)

rotatable_bond_count `property` ¶

rotatable_bond_count: int

Compute the number of rotatable bonds in the ligand molecule.

Returns:

Name	Type	Description
`int`	`int`	The number of rotatable bonds.

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

seed: int | None = None

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

smiles: str | None = None

tpsa `property` ¶

tpsa: float

Compute the Topological Polar Surface Area (TPSA) of the ligand molecule.

Returns:

Name	Type	Description
`float`	`float`	The TPSA value in square Angstroms.

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¶

add_hydrogens ¶

add_hydrogens(add_coordinates: bool = True)

Add hydrogens to the molecule.

Parameters:

Name	Type	Description	Default
`add_coordinates`	`bool`	Whether to generate coordinates for added hydrogens	`True`

download ¶

download(
    *,
    lazy: bool = True,
    client: DeepOriginClient | None = None
) -> str

Download the entity file from remote storage.

No-ops if local_path is already set.

Parameters:

Name	Type	Description	Default
`client`	`DeepOriginClient \| None`	DeepOriginClient instance. If None, uses DeepOriginClient().	`None`

Returns:

Type	Description
`str`	The local file path.

Raises:

Type	Description
`ValueError`	If neither local_path nor remote_path is available.

draw ¶

draw()

Draw the contained rdkit molecule using rdkit methods

embed ¶

embed(add_hydrogens: bool = True, seed: int = -1)

Generate 3D coordinates for the molecule.

Parameters:

Name	Type	Description	Default
`add_hydrogens`	`bool`	Whether to add hydrogens	`True`
`seed`	`int`	Random seed for coordinate generation	`-1`

ensure_remote_path ¶

ensure_remote_path(
    *, client: DeepOriginClient, label: str
) -> None

Ensure :attr:remote_path is set after a lazy :meth:sync may have no-oped.

If the entity already has a platform id but remote_path was never populated (e.g. rehydrated metadata only), sync(lazy=True) returns early. This performs a full sync when needed, then raises if the path is still missing.

Parameters:

Name	Type	Description	Default
`client`	`DeepOriginClient`	Authenticated client for sync/upload.	required
`label`	`str`	Human-readable name for error messages (e.g. `"Protein"`).	required

Raises:

Type	Description
`ValueError`	If `remote_path` cannot be determined after sync.

from_base64 `classmethod` ¶

from_base64(
    base64_string: str, name: str = "", **kwargs: Any
) -> Self

Create a Ligand instance from a base64 encoded SDF string.

Parameters:

Name	Type	Description	Default
`base64_string`	`str`	Base64 encoded SDF content	required
`name`	`str`	Name of the ligand. Defaults to "".	`''`
`**kwargs`	`Any`	Additional arguments to pass to the constructor	`{}`

Returns:

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

Raises:

Type	Description
`DeepOriginException`	If the base64 string cannot be decoded or parsed

from_file `classmethod` ¶

from_file(
    file_path: str | Path,
    *,
    sanitize: bool = True,
    remove_hydrogens: bool = False
) -> Self

Create a Ligand from a file after verifying it is an SDF (extension and content).

This delegates to :meth:from_sdf after validation.

Parameters:

Name	Type	Description	Default
`file_path`	`str \| Path`	Path to the SDF file.	required
`sanitize`	`bool`	Whether to sanitize molecules. Defaults to True.	`True`
`remove_hydrogens`	`bool`	Whether to remove hydrogens. Defaults to False.	`False`

Returns:

Name	Type	Description
`Ligand`	`Self`	The Ligand instance created from the SDF file.

Raises:

Type	Description
`FileNotFoundError`	If the file does not exist.
`DeepOriginException`	If the path is not an SDF file or loading fails.

from_id `classmethod` ¶

from_id(
    id: str,
    *,
    client: Optional[DeepOriginClient] = None,
    download: bool = True
) -> Self

Create a Ligand instance from a Deep Origin Data Platform ID.

Fetches the ligand record from the platform. If the record has an associated mol file it is downloaded and used to construct the ligand; otherwise the SMILES string is used.

Parameters:

Name	Type	Description	Default
`id`	`str`	The Deep Origin Data Platform ID of the ligand.	required
`client`	`Optional[DeepOriginClient]`	Optional DeepOriginClient instance. If not provided, uses the default client.	`None`
`download`	`bool`	If False, skip mol file download and hydrate from SMILES with `remote_path` set to the platform mol file path.	`True`

Returns:

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

Raises:

Type	Description
`ValueError`	If the ligand data contains neither a mol file nor a SMILES string.

from_identifier `classmethod` ¶

from_identifier(identifier: str) -> Self

Create a Ligand instance from a compound name.

Parameters:

Name	Type	Description	Default
`identifier`	`str`	The identifier to resolve to a SMILES string.	required

Raises:

Type	Description
`DeepOriginException`	If no compound is found for the given name
`AssertionError`	If neither smiles nor name is provided

from_rdkit_mol `classmethod` ¶

from_rdkit_mol(
    mol: Mol, name: Optional[str] = None, **kwargs: Any
) -> Self

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 "".	`None`
`**kwargs`	`Any`	Additional arguments to pass to the constructor	`{}`

from_remote_file `classmethod` ¶

from_remote_file(
    remote_path: str,
    *,
    client: DeepOriginClient | None = None,
    lazy: bool = True,
    sanitize: bool = True,
    remove_hydrogens: bool = False
) -> Self

Create a Ligand from an SDF file stored on the platform.

Downloads the file via :meth:deeporigin.platform.files.FilesClient.download, then loads it with :meth:from_sdf. The SDF must contain exactly one molecule.

Parameters:

Name	Type	Description	Default
`remote_path`	`str`	Platform file path (e.g. org storage path) to the SDF file.	required
`client`	`DeepOriginClient \| None`	DeepOrigin client used for download. If `None`, uses `DeepOriginClient()`.	`None`
`lazy`	`bool`	Passed to `files.download`; if `True`, skip download when the file already exists locally at the default cache location.	`True`
`sanitize`	`bool`	Whether to sanitize molecules when reading the SDF (see :meth:`from_sdf`).	`True`
`remove_hydrogens`	`bool`	Whether to strip hydrogens when reading the SDF (see :meth:`from_sdf`).	`False`

Returns:

Name	Type	Description
`Ligand`	`Self`	A ligand with :attr:`~deeporigin.drug_discovery.structures.entity.Entity.remote_path`
	`Self`	set to `remote_path` and :attr:`~deeporigin.drug_discovery.structures.entity.Entity.local_path`
	`Self`	set to the downloaded file path.

from_sdf `classmethod` ¶

from_sdf(
    file_path: str | Path,
    *,
    sanitize: bool = True,
    remove_hydrogens: bool = False
) -> Self

Create a single Ligand instance from an SDF file containing exactly one molecule.

Parameters:

Name	Type	Description	Default
`file_path`	`str`	The path to the SDF file.	required
`sanitize`	`bool`	Whether to sanitize molecules. Defaults to True.	`True`
`remove_hydrogens`	`bool`	Whether to remove hydrogens. Defaults to False.	`False`

Returns:

Name	Type	Description
`Ligand`	`Self`	The Ligand instance created from the SDF file.

Raises:

Type	Description
`FileNotFoundError`	If the file does not exist.
`DeepOriginException`	If the file cannot be parsed correctly or contains more than one molecule.

from_smiles `classmethod` ¶

from_smiles(
    smiles: str, name: str = "", **kwargs: Any
) -> Self

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 "".	`''`
`**kwargs`	`Any`	Additional arguments to pass to the constructor	`{}`

Returns:

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

get_center ¶

get_center() -> list[number]

Get the center of the ligand based on its coordinates.

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

get_conformer ¶

get_conformer(conformer_id: int = 0)

Get a specific conformer of the molecule.

Parameters:

Name	Type	Description	Default
`conformer_id`	`int`	Conformer index	`0`

get_conformer_id ¶

get_conformer_id() -> int

Get the ID of the current conformer.

Returns:

Name	Type	Description
`int`	`int`	Conformer ID

get_coordinates ¶

get_coordinates(i: int = 0)

Get the coordinates of atoms in a specific conformer.

Parameters:

Name	Type	Description	Default
`i`	`int`	Conformer index	`0`

get_formula ¶

get_formula() -> str

Get the chemical formula of the molecule.

get_heavy_atom_count ¶

get_heavy_atom_count() -> int

Get the number of heavy atoms in the molecule.

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.

get_species ¶

get_species() -> list[str]

Get the atomic symbols of all atoms in the molecule.

Returns:

Name	Type	Description
`list`	`list[str]`	List of atomic symbols

has_3d_structure ¶

has_3d_structure() -> bool

Check if the ligand has 3D coordinates (not just 2D).

This method checks if the molecule has conformers with 3D coordinates. Ligands created from SMILES typically have 2D coordinates (z=0 for all atoms), while ligands with actual 3D structure have non-zero z coordinates.

Returns:

Name	Type	Description
`bool`	`bool`	True if the ligand has 3D coordinates (non-zero z values), False if it only has 2D coordinates or no conformers.

has_hydrogens ¶

has_hydrogens() -> bool

Check if the molecule contains hydrogen atoms.

This method determines if hydrogens are present by comparing the canonical SMILES string of the molecule with and without explicit hydrogens added. If the SMILES strings differ, the molecule contains hydrogens.

Returns:

Name	Type	Description
`bool`	`bool`	True if the molecule contains hydrogen atoms, False otherwise

has_unsupported_atoms ¶

has_unsupported_atoms() -> bool

Whether :attr:mol contains any atom type not supported for docking workflows.

is_charged ¶

is_charged() -> bool

Check if the molecule is charged.

mol_from_block `classmethod` ¶

mol_from_block(
    block_type: str,
    block: str,
    sanitize: bool = True,
    remove_hs: bool = False,
) -> Mol

Create a molecule from a block of text.

Parameters:

Name	Type	Description	Default
`block_type`	`str`	Type of the input block	required
`block`	`str`	Text block containing molecular data	required
`sanitize`	`bool`	Whether to sanitize the molecule	`True`
`remove_hs`	`bool`	Whether to remove hydrogens	`False`

Returns:

Type	Description
`Mol`	Chem.Mol: RDKit molecule object

mol_from_file `classmethod` ¶

mol_from_file(
    *,
    file_type: FILE_FORMATS,
    file_path: str,
    sanitize: bool = True,
    remove_hs: bool = False
) -> Mol

Create a molecule from a file.

Parameters:

Name	Type	Description	Default
`file_type`	`str`	Type of the input file (must be in FILE_FORMATS)	required
`file_path`	`str`	Path to the input file	required
`sanitize`	`bool`	Whether to sanitize the molecule	`True`
`remove_hs`	`bool`	Whether to remove hydrogens	`False`

Returns:

Type	Description
`Mol`	Chem.Mol: RDKit molecule object

Raises:

Type	Description
`DeepOriginException`	If the file format is invalid or parsing fails
`NotImplementedError`	If the file type is not supported

prepare ¶

prepare(*, remove_hydrogens: bool = False) -> Self

Prepare the ligand for downstream workflows.

The routine performs the following using RDKit and internal utilities: - Salt removal - Kekulization - Fragment validation (rejects multiple non-identical fragments) - Wildcard atom validation (rejects '*' atoms) - Validation of atom types against supported symbols

Parameters:

Name	Type	Description	Default
`remove_hydrogens`	`bool`	Whether to remove hydrogens from the SMILES representation. Defaults to False (preserve hydrogens).	`False`

Returns:

Name	Type	Description
`Ligand`	`Self`	The prepared ligand (self), for chaining.

Raises:

Type	Description
`DeepOriginException`	If preparation fails, unsupported atom types are present, or multiple non-identical fragments are detected.

process_mol ¶

process_mol() -> None

Clean the ligand molecule by removing hydrogens and sanitizing the structure.

Raises:

Type	Description
`DeepOriginException`	If salt removal or kekulization fails

protonate ¶

protonate(
    *,
    ph: number = 7.4,
    filter_percentage: number = 1.0,
    client: Optional[DeepOriginClient] = None,
    use_cache: bool = True,
    quote: bool = False
) -> FunctionResult

Protonate the ligand at a given pH using the DeepOrigin API.

Returns a FunctionResult whose .ligands attribute contains the protonated ligand. When quote=True, .ligands is empty and .estimate gives the cost in dollars.

The ligand is mutated in place: self.mol, self.smiles, and self.protonated_at_ph are updated with the most abundant protonation state.

Parameters:

Name	Type	Description	Default
`ph`	`number`	pH value at which to protonate the ligand. Defaults to 7.4 (physiological pH).	`7.4`
`filter_percentage`	`number`	Percentage threshold for filtering protonation states. Only species with abundance above this threshold are considered. Defaults to 1.0.	`1.0`
`client`	`Optional[DeepOriginClient]`	DeepOrigin client instance. If None, uses `DeepOriginClient()`.	`None`
`use_cache`	`bool`	Whether to use cached protonation results.	`True`
`quote`	`bool`	If True, request a cost estimate without executing.	`False`

Returns:

Name	Type	Description
`FunctionResult`	`FunctionResult`	A FunctionResult with a `.ligands` attribute (list of Ligand).

register ¶

register(
    *,
    client: Optional[DeepOriginClient] = None,
    remote_path: Optional[str] = None
) -> None

Register the ligand as a new record in the data platform.

Uploads the ligand file to remote storage (if available) and creates a new ligand record, regardless of whether one already exists for this canonical SMILES.

Parameters:

Name	Type	Description	Default
`client`	`Optional[DeepOriginClient]`	DeepOriginClient instance. If None, uses DeepOriginClient().	`None`
`remote_path`	`Optional[str]`	Custom remote path to upload to. Overrides the default hash-based path.	`None`

Returns:

Type	Description
`None`	None. As a side effect, uploads the ligand and sets `self.id`
`None`	to the newly created record's ID.

Note

If the ligand was created from a SMILES string without an SDF file, only the SMILES will be used (no file upload will occur).

resolved_project_id ¶

resolved_project_id(
    client: DeepOriginClient | None = None,
) -> str | None

Data platform project id for API calls.

Returns :attr:project_id when set; otherwise client.project_id when client is given; otherwise None. Does not read the filesystem.

Parameters:

Name	Type	Description	Default
`client`	`DeepOriginClient \| None`	Optional platform client (e.g. the one passed to :meth:`sync`).	`None`

Returns:

Type	Description
`str \| None`	Project id string, or None if neither the entity nor the client
`str \| None`	provides one.

set_conformer_id ¶

set_conformer_id(i=0)

Set the ID of the current conformer.

Parameters:

Name	Type	Description	Default
`i`	`int`	New conformer ID	`0`

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.

show ¶

show() -> str | None

Visualize the current state of the ligand molecule.

Returns: - str: HTML representation of the visualization.

Raises: - Exception: If visualization fails.

sync ¶

sync(
    *,
    lazy: bool = False,
    client: Optional[DeepOriginClient] = None,
    remote_path: Optional[str] = None
) -> None

Sync the ligand to the data platform.

Uploads the ligand file and links to an existing record if one with the same canonical SMILES already exists (setting id and remote_path from the record's mol_file when present), otherwise creates a new record via :meth:register.

Parameters:

Name	Type	Description	Default
`lazy`	`bool`	If True, skip syncing when the ligand already has an ID. Defaults to False.	`False`
`client`	`Optional[DeepOriginClient]`	DeepOriginClient instance. If None, uses DeepOriginClient().	`None`
`remote_path`	`Optional[str]`	Custom remote path to upload to. Overrides the default hash-based path.	`None`

Note

If the ligand was created from a SMILES string without an SDF file, only the SMILES will be used for syncing (no file upload will occur).

to_base64 ¶

to_base64() -> str

Convert the ligand to base64 encoded SDF format.

Returns:

Name	Type	Description
`str`	`str`	Base64 encoded string of the SDF file content

to_file ¶

to_file(file_path: Optional[str | Path] = None) -> str

Dump state to a file.

Parameters:

Name	Type	Description	Default
`file_path`	`Optional[str \| Path]`	Path where the file will be written. If None, uses default path.	`None`

Returns:

Name	Type	Description
`str`	`str`	Path to the written file.

to_hash ¶

to_hash() -> str

Convert the ligand to SHA256 hash of the SDF file content.

Returns:

Name	Type	Description
`str`	`str`	SHA256 hash string of the SDF file content

to_mol ¶

to_mol(output_path: Optional[str] = None) -> str | Path

Write the ligand to a MOL file.

to_molblock ¶

to_molblock() -> str

Generate a MOL block representation of the molecule.

Returns:

Name	Type	Description
`str`	`str`	MOL block string

to_pdb ¶

to_pdb(output_path: Optional[str] = None) -> str | Path

Write the ligand to a PDB file.

to_sdf ¶

to_sdf(output_path: Optional[str] = None) -> str

Write the ligand to an SDF file.

This is a local operation: it serializes the current :attr:mol. If the ligand has :attr:remote_path but no local file yet, raise; rehydrate with :meth:download first.

Parameters:

Name	Type	Description	Default
`output_path`	`Optional[str]`	Path for the SDF file, or default under `LIGANDS_DIR`.	`None`

unsupported_atom_symbols ¶

unsupported_atom_symbols() -> list[str]

Sorted unique atom symbols in :attr:mol not in SUPPORTED_ATOM_SYMBOLS.

update_coordinates ¶

update_coordinates(coordinates: ndarray)

update coordinates of the ligand structure

upload ¶

upload(
    *,
    client: DeepOriginClient | None = None,
    remote_path: str | None = None
) -> None

Upload the entity to the remote server.

Serializes via :meth:to_file with :attr:remote_path temporarily cleared so subclasses that guard exports when only remote metadata is present (e.g. :meth:Ligand.to_sdf) still write from in-memory state on repeat uploads.

Parameters:

Name	Type	Description	Default
`client`	`DeepOriginClient \| None`	DeepOriginClient instance. If None, uses DeepOriginClient().	`None`
`remote_path`	`str \| None`	Custom remote path to upload to. When provided, sets :attr:`remote_path` before uploading. If :attr:`remote_path` is still unset, it is set to the default hash-based path.	`None`

write_to_file ¶

write_to_file(
    output_path: Optional[str] = None,
    output_format: Literal["mol", "sdf", "pdb"] = "sdf",
) -> str | Path

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

Parameters: - output_path (str): Path where the ligand will be written. - output_format (Literal[".mol", ".sdf", ".pdb", "mol", "sdf", "pdb"]): Format to write the ligand in.

Raises:

Type	Description
`-DeepOriginException`	If the file extension is unsupported.
`-Exception`	If writing to the file fails.

ADMET (molprops) attributes¶

After you run Molprops on the ligand, scalar and structured predictions from the Deep Origin molprops tools are stored on the ligand as well as in properties and RDKit properties:

log_s, log_d, log_p — map to API keys logS, logD, logP
herg, cyp, ames — nested structures keyed as hERG, cyp, ames in the API response
has_pains, pains_fragments — PAINS screening results

Until molprops has been run successfully (via Molprops), these fields remain None.

Preparation¶

Use Ligand.prepare() to perform common preparation steps before docking:

salt removal, kekulization
fragment validation (rejects multiple non-identical fragments)
validation of atom symbols against supported types

Example:

from deeporigin.drug_discovery.structures import Ligand

lig = Ligand.from_smiles("CCO", name="Ethanol")
lig.prepare()  # Preserves hydrogens by default
lig.prepare(remove_hydrogens=True)  # Remove hydrogens from SMILES

deeporigin.drug_discovery.Ligand¶

Attributes¶

ames class-attribute instance-attribute ¶

atom_types property ¶

available_for_docking class-attribute instance-attribute ¶

block_content class-attribute instance-attribute ¶

block_type class-attribute instance-attribute ¶

canonical_smiles property ¶

contains_boron property ¶

coordinates property ¶

cyp class-attribute instance-attribute ¶

formal_charge property ¶

has_pains class-attribute instance-attribute ¶

hbond_acceptor_count property ¶

hbond_donor_count property ¶

herg class-attribute instance-attribute ¶

id class-attribute instance-attribute ¶

identifier class-attribute instance-attribute ¶

local_path class-attribute instance-attribute ¶

log_d class-attribute instance-attribute ¶

log_p class-attribute instance-attribute ¶

log_s class-attribute instance-attribute ¶

mol class-attribute instance-attribute ¶

molecular_weight property ¶

name class-attribute instance-attribute ¶

pains_fragments class-attribute instance-attribute ¶

prepared class-attribute instance-attribute ¶

project_id class-attribute instance-attribute ¶

properties class-attribute instance-attribute ¶

protonated_at_ph class-attribute instance-attribute ¶

remote_path class-attribute instance-attribute ¶

rotatable_bond_count property ¶

seed class-attribute instance-attribute ¶

smiles class-attribute instance-attribute ¶

tpsa property ¶

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¶

add_hydrogens ¶

download ¶

draw ¶

embed ¶

ensure_remote_path ¶

from_base64 classmethod ¶

from_file classmethod ¶

from_id classmethod ¶

from_identifier classmethod ¶

from_rdkit_mol classmethod ¶

from_remote_file classmethod ¶

from_sdf classmethod ¶

from_smiles classmethod ¶

get_center ¶

get_conformer ¶

get_conformer_id ¶

get_coordinates ¶

get_formula ¶

get_heavy_atom_count ¶

get_property ¶

get_species ¶

has_3d_structure ¶

has_hydrogens ¶

has_unsupported_atoms ¶

is_charged ¶

mol_from_block classmethod ¶

mol_from_file classmethod ¶

prepare ¶

process_mol ¶

protonate ¶

register ¶

resolved_project_id ¶

set_conformer_id ¶

set_property ¶

show ¶

sync ¶

to_base64 ¶

to_file ¶

to_hash ¶

to_mol ¶

`deeporigin.drug_discovery.Ligand`¶

ames `class-attribute` `instance-attribute` ¶

atom_types `property` ¶

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

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

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

canonical_smiles `property` ¶

contains_boron `property` ¶

coordinates `property` ¶

cyp `class-attribute` `instance-attribute` ¶

formal_charge `property` ¶

has_pains `class-attribute` `instance-attribute` ¶

hbond_acceptor_count `property` ¶

hbond_donor_count `property` ¶

herg `class-attribute` `instance-attribute` ¶

id `class-attribute` `instance-attribute` ¶

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

local_path `class-attribute` `instance-attribute` ¶

log_d `class-attribute` `instance-attribute` ¶

log_p `class-attribute` `instance-attribute` ¶

log_s `class-attribute` `instance-attribute` ¶

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

molecular_weight `property` ¶

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

pains_fragments `class-attribute` `instance-attribute` ¶

prepared `class-attribute` `instance-attribute` ¶

project_id `class-attribute` `instance-attribute` ¶

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

protonated_at_ph `class-attribute` `instance-attribute` ¶

remote_path `class-attribute` `instance-attribute` ¶

rotatable_bond_count `property` ¶

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

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

tpsa `property` ¶

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` ¶

from_base64 `classmethod` ¶

from_file `classmethod` ¶

from_id `classmethod` ¶

from_identifier `classmethod` ¶

from_rdkit_mol `classmethod` ¶

from_remote_file `classmethod` ¶

from_sdf `classmethod` ¶

from_smiles `classmethod` ¶

mol_from_block `classmethod` ¶

mol_from_file `classmethod` ¶