`deeporigin.drug_discovery.Protein`¶

Pocket finding (find_pockets removed)

Protein.find_pockets() was deprecated and has been removed. Use the PocketFinder class instead (see PocketFinder).

Bases: Entity

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

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

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

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

info: Optional[dict] = None

length `property` ¶

length: int

get the length of the protein structure

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

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

name `instance-attribute` ¶

name: str

num_atoms `property` ¶

num_atoms: int

Count the number of atoms in PDB file for this protein

Returns:

Name	Type	Description
`int`	`int`	The number of atoms in the PDB file.

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

pdb_id: Optional[str] = None

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

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

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

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

sequence `property` ¶

sequence: list[Seq]

Retrieve the amino acid sequences of all polypeptide chains in the protein structure.

This property parses the protein structure file using Bio.PDB and extracts the sequences of all peptide chains present. Each sequence is returned as a Bio.Seq object, which can be converted to a string if needed. The method is useful for analyzing the primary structure of the protein or for downstream sequence-based analyses.

Returns:

Type	Description
`list[Seq]`	list[str]: A list of amino acid sequences (as Bio.Seq objects) for each polypeptide chain found in the protein structure. If the structure contains multiple chains, each chain's sequence is included as a separate entry in the list.

Example

protein = Protein.from_file("example.pdb") sequences = protein.sequence for seq in sequences: ... print(seq)

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

structure: Any | None = field(default=None, repr=False)

tags `class-attribute` `instance-attribute` ¶

tags: dict[str, Any] | None = field(
    default=None, kw_only=True
)

uniprot_accession `class-attribute` `instance-attribute` ¶

uniprot_accession: Optional[str] = None

Methods:¶

bounding_box_volume ¶

bounding_box_volume() -> float

Compute the volume of the axis-aligned bounding box of the protein.

Uses atomic coordinates to estimate size as the product of the spans along each axis. Coordinates are in Angstroms, so the result is in cubic Angstroms (Å³).

Returns:

Name	Type	Description
`float`	`float`	Bounding box volume in Å³.

Raises:

Type	Description
`ValueError`	If the protein structure is not loaded.

download ¶

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

Download the remote structure file and load :attr:structure from it.

If :attr:structure is already loaded (e.g. from :meth:from_pdb_id or :meth:from_file), returns :attr:local_path when set without hitting the files API.

Otherwise delegates to :meth:Entity.download, then parses the returned path with :meth:from_file when :attr:structure is still None.

Parameters:

Name	Type	Description	Default
`client`	`DeepOriginClient \| None`	DeepOriginClient instance. If None, uses the default client.	`None`

Returns:

Type	Description
`str`	Local file path returned by the files client, or an existing on-disk
`str`	path when the structure was already loaded from a local file.

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.

extract_ligand ¶

extract_ligand(
    exclude_resnames: Optional[set[str]] = None,
) -> Ligand

Extracts ligand(s) from a Protein object and removes them from the protein structure. This method mutates the protein object by removing ligand records.

Parameters:

Name	Type	Description	Default
`exclude_resnames`	`set`	Residue names to exclude (e.g., water).	`None`

Returns:

Name	Type	Description
`Ligand`	`Ligand`	The extracted ligand molecule.

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_missing_residues ¶

find_missing_residues() -> dict[str, list[tuple[int, int]]]

find missing residues in the protein structure

from_base64 `classmethod` ¶

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

Create a Protein instance from a base64 encoded PDB string.

Parameters:

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

Returns:

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

Raises:

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

from_file `classmethod` ¶

from_file(
    file_path: str | Path,
    struct_ind: int = 0,
    *,
    validate: bool = True
) -> Self

Create a Protein instance from a file.

Parameters:

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

Returns:

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

Raises:

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

from_id `classmethod` ¶

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

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

Parameters:

Name	Type	Description	Default
`id`	`str`	The Deep Origin Data Platform ID of the protein.	required
`client`	`Optional[DeepOriginClient]`	Optional DeepOriginClient instance. If not provided, uses the default client.	`None`
`download`	`bool`	If True (default), download the structure file and load coordinates when the record has a `file_path`. If False, fetch metadata only and set :attr:`remote_path` to the platform file path (`remote_path_override` or the record's `file_path`) without downloading; :attr:`structure` stays `None` until :meth:`download` or :meth:`load_structure_from_local`. When the record has no `file_path`, returns metadata only regardless of `download`.	`True`
`remote_path_override`	`Optional[str]`	When `download` is False, use this as `remote_path` instead of the API record's `file_path` (e.g. the path stored on the execution `userInputs`).	`None`

Returns:

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

Raises:

Type	Description
`RuntimeError`	If the file cannot be downloaded or loaded.

from_name `classmethod` ¶

from_name(name: str) -> Self

Create a Protein instance from a name.

from_pdb_id `classmethod` ¶

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

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`	`Self`	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.

from_remote_file `classmethod` ¶

from_remote_file(
    remote_path: str,
    *,
    client: DeepOriginClient | None = None,
    lazy: bool = True,
    struct_ind: int = 0,
    validate: bool = True
) -> Self

Create a Protein from a structure file stored on the platform.

Downloads the file via :meth:deeporigin.platform.files.FilesClient.download, then loads it with :meth:from_file. Supported formats are PDB, PDBQT, and mmCIF.

Parameters:

Name	Type	Description	Default
`remote_path`	`str`	Platform file path (e.g. org storage path) to the structure 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`
`struct_ind`	`int`	Index of the structure to select if multiple are present (see :meth:`from_file`).	`0`
`validate`	`bool`	Whether to validate PDB files when reading (see :meth:`from_file`).	`True`

Returns:

Name	Type	Description
`Protein`	`Self`	A protein 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_uniprot `classmethod` ¶

from_uniprot(
    uniprot_accession: str,
    *,
    project_id: str | None = None,
    client: Optional[DeepOriginClient] = None
) -> Self

Import the recommended PDB for a UniProt accession into a project.

Thin sugar over :meth:~deeporigin.drug_discovery.uniprot_discovery.UniprotDiscovery.import_proteins for the single recommended candidate. For browsing all candidates or importing multiple PDB IDs, use :class:~deeporigin.drug_discovery.uniprot_discovery.UniprotDiscovery directly.

Parameters:

Name	Type	Description	Default
`uniprot_accession`	`str`	UniProtKB accession (6 or 10 characters).	required
`project_id`	`str \| None`	Project to sync into. Falls back to `client.project_id`.	`None`
`client`	`Optional[DeepOriginClient]`	Optional API client.	`None`

Returns:

Type	Description
`Self`	The synced recommended :class:`Protein`.

Raises:

Type	Description
`DeepOriginException`	If discovery or import fails (see :meth:`~deeporigin.drug_discovery.uniprot_discovery.UniprotDiscovery.import_proteins`).

has_ligand_clashes ¶

has_ligand_clashes(
    ligand: Ligand | str | Path,
    *,
    contact_distance: float = 2.5,
    protein_atoms_only: bool = True,
    exclude_waters: bool = True,
    heavy_atoms_only: bool = True
) -> bool

Check whether a ligand pose sterically clashes with this protein.

Compares ligand atom coordinates against protein atom coordinates and returns True when any pair is closer than contact_distance.

The ligand SDF must already be in the same coordinate frame as the protein structure (for example, a docked pose aligned to the receptor).

Parameters:

Name	Type	Description	Default
`ligand`	`Ligand \| str \| Path`	A :class:`Ligand` instance or path to a single-molecule SDF.	required
`contact_distance`	`float`	Distance threshold (Å) below which a pair is a clash.	`2.5`
`protein_atoms_only`	`bool`	When `True`, exclude HETATM records so the check compares the ligand against the receptor only.	`True`
`exclude_waters`	`bool`	When `True`, remove solvent before checking.	`True`
`heavy_atoms_only`	`bool`	When `True`, ignore hydrogen atoms on both sides.	`True`

Returns:

Type	Description
`bool`	`True` if at least one ligand atom clashes with a protein atom.

Raises:

Type	Description
`ValueError`	If the protein structure is not loaded or `contact_distance` is not positive.
`DeepOriginException`	If the ligand does not have 3D coordinates.

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
)

Load a protein structure from block content.

Parameters:

Name	Type	Description	Default
`block_content`	`str`	The content of the structure file.	required
`block_type`	`str`	The type of the structure file (pdb, pdbqt, or cif).	required

Raises:

Type	Description
`ValueError`	If the block type is unsupported.

load_structure_from_local ¶

load_structure_from_local(
    path: str | Path | None = None,
) -> None

Load :attr:structure from disk without using the remote API.

Parameters:

Name	Type	Description	Default
`path`	`str \| Path \| None`	Path to a PDB/mmCIF file. If None, uses :attr:`local_path` (see :class:`Entity`).	`None`

mark_as_prepared ¶

mark_as_prepared() -> Self

Stamp the on-disk protein file as a Prepared Protein.

Writes the canonical Prepared Protein token onto :attr:local_path in the file's native format (PDB REMARK 99 DO_PREPARED or mmCIF _deeporigin.prepared DO_PREPARED). Does not convert CIF to PDB or vice versa. Does not upload; call :meth:sync afterward to push the stamped bytes to UFA.

Idempotent when the file is already stamped. Requires a readable :attr:local_path (for example after :meth:from_file or :meth:download).

Returns:

Type	Description
`Self`	Self, for chaining.

Raises:

Type	Description
`DeepOriginException`	If :attr:`local_path` is unset or not a file.

register ¶

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

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

Uploads the protein file when needed, then creates a new protein record, regardless of whether one already exists for this file path. When :attr:local_path is a readable file, uploads those bytes (create or overwrite :attr:remote_path) without a biotite rewrite. When there is no local file and :attr:remote_path is already set, skips upload.

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 protein when needed and sets
`None`	`self.id` to the newly created record's ID.

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:

Name	Type	Description	Default
`keep_resnames`	`Optional[list[str]]`	A list of residue names (strings) to keep in the structure even if they are HETATM records.	`None`
`remove_metals`	`Optional[list[str]]`	A list of metal names (strings) to exclude from removal. These metals will be retained in the structure.	`None`

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.

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.

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.

select_chain ¶

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

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.

select_chains ¶

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

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, index: int)

Select a specific structure by index.

show ¶

show(
    *,
    pockets: Optional[list[Pocket]] = None,
    ligand: Optional[Ligand] = None,
    ligands: Optional[LigandSet | list[Ligand]] = None,
    poses: Optional[
        LigandSet | PoseSet | list[Ligand] | list[Pose]
    ] = None
)

Visualize the protein structure in a Jupyter notebook using Mol*.

Renders via the hosted molstarLib bundle. Protein-only and pockets-only views, docked poses, and pockets+poses are supported.

When more than one pose is supplied, all poses are loaded and overlaid, and a navigation bar is shown at the bottom of the viewer. Use its ◀ / ▶ buttons or the Left/Right arrow keys to cycle through an "all poses" view and each individual pose one at a time.

Parameters:

Name	Type	Description	Default
`pockets`	`Optional[list[Pocket]]`	Optional pocket overlays (gaussian surfaces).	`None`
`ligand`	`Optional[Ligand]`	Optional single ligand / docked pose to overlay.	`None`
`ligands`	`Optional[LigandSet \| list[Ligand]]`	Optional ligand set (or list) to overlay as docked poses.	`None`
`poses`	`Optional[LigandSet \| PoseSet \| list[Ligand] \| list[Pose]]`	Alias for `ligands`; also accepts :class:`PoseSet`.	`None`

Raises:

Type	Description
`DeepOriginException`	If both `ligand` and `ligands`/`poses` are set.
`ValueError`	If `ligands` or `poses` is provided but empty.

sync ¶

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

Sync the protein to the data platform.

Uploads the protein file when needed and links to an existing record if one with the same file path already exists, otherwise creates a new record via :meth:register.

When :attr:local_path is a readable file, always uploads those bytes to :attr:remote_path (creating or overwriting the UFA object) without converting CIF→PDB. When there is no local file and :attr:remote_path is already set, skips upload.

Parameters:

Name	Type	Description	Default
`lazy`	`bool`	If True, skip syncing when the protein 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`

Returns:

Type	Description
`None`	None. As a side effect, uploads the protein (if necessary) and updates
`None`	`self.id` with the ID of the existing or newly created protein record,
`None`	and sets :attr:`project_id` when a project scope applies or the platform
`None`	row includes `project_id`.

to_base64 ¶

to_base64() -> str

Convert the protein to base64 encoded PDB format.

Returns:

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

to_cif ¶

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

Write the protein structure to an mmCIF file.

Use this when the structure cannot be represented as classic PDB (for example residue names longer than 3 characters). This is a local operation on :attr:structure; rehydrate with :meth:download first if only :attr:remote_path is set.

When the source carries a Prepared Protein stamp (PDB or mmCIF), the mmCIF stamp is written after the biotite rewrite so the token is preserved (including PDB→CIF translation). External converters that do not go through this method may still drop the stamp.

Parameters:

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

Returns:

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

Raises:

Type	Description
`DeepOriginException`	If `remote_path` is set but no local file exists yet, or if :attr:`structure` is not loaded.
`RuntimeError`	If biotite fails to serialize the structure.

to_file ¶

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

Dump state to a PDB 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 protein to SHA256 hash of the PDB file content.

Returns:

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

to_pdb ¶

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

Write the protein structure to a PDB file.

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

When the source structure file (:attr:local_path or :attr:block_content) carries a Prepared Protein stamp (PDB REMARK or mmCIF _deeporigin.prepared), the PDB stamp is re-prepended after the biotite rewrite so the token is never dropped (including CIF→PDB translation).

Parameters:

Name	Type	Description	Default
`file_path`	`str`	Path where the PDB file will be written.	`None`

Raises:

Type	Description
`DeepOriginException`	If `remote_path` is set but no local file exists yet, or if :attr:`structure` is not loaded.

update ¶

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

Update the protein's file_path on an existing platform record.

Uploads the local structure file when present, then PATCHes file_path on the record identified by self.id. Use :meth:sync to link or create by identity; use update when you already have a platform ID.

Parameters:

Name	Type	Description	Default
`client`	`Optional[DeepOriginClient]`	DeepOriginClient instance. If None, uses DeepOriginClient().	`None`
`remote_path`	`Optional[str]`	Explicit remote path to set as `file_path`. When omitted, uploads `local_path` and uses the resulting path.	`None`

Returns:

Type	Description
`None`	None. Refreshes `self.remote_path` from the platform response.

Raises:

Type	Description
`ValueError`	If `self.id` is unset or no file path can be resolved.

update_coordinates ¶

update_coordinates(coords: ndarray)

update coordinates of the protein structure

upload ¶

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

Upload the protein file to remote storage.

When :attr:local_path points to an existing file, uploads those bytes as-is (preserving PDB vs CIF and any Prepared Protein stamp). Does not rewrite through :meth:to_file / :meth:to_pdb on that path. When no local file exists, falls back to :meth:Entity.upload (serialize via :meth:to_file).

Parameters:

Name	Type	Description	Default
`client`	`Optional[DeepOriginClient]`	DeepOriginClient instance. If None, uses DeepOriginClient().	`None`
`remote_path`	`Optional[str]`	Destination remote path. When provided, sets :attr:`remote_path` before uploading. If still unset, uses a hash-based path whose extension matches the local file when present.	`None`

deeporigin.drug_discovery.Protein¶

Attributes¶

atom_types class-attribute instance-attribute ¶

block_content class-attribute instance-attribute ¶

block_type class-attribute instance-attribute ¶

coordinates property ¶

id class-attribute instance-attribute ¶

info class-attribute instance-attribute ¶

length property ¶

local_path class-attribute instance-attribute ¶

name instance-attribute ¶

num_atoms property ¶

pdb_id class-attribute instance-attribute ¶

project_id class-attribute instance-attribute ¶

remote_path class-attribute instance-attribute ¶

sequence property ¶

structure class-attribute instance-attribute ¶

tags class-attribute instance-attribute ¶

uniprot_accession class-attribute instance-attribute ¶

Methods:¶

bounding_box_volume ¶

download ¶

ensure_remote_path ¶

extract_ligand ¶

extract_metals_and_cofactors ¶

find_missing_residues ¶

from_base64 classmethod ¶

from_file classmethod ¶

from_id classmethod ¶

from_name classmethod ¶

from_pdb_id classmethod ¶

from_remote_file classmethod ¶

from_uniprot classmethod ¶

has_ligand_clashes ¶

list_chain_names ¶

list_hetero_names ¶

load_structure_from_block staticmethod ¶

load_structure_from_local ¶

mark_as_prepared ¶

register ¶

remove_hetatm ¶

remove_resnames ¶

remove_water ¶

resolved_project_id ¶

select_chain ¶

select_chains ¶

select_structure staticmethod ¶

show ¶

sync ¶

to_base64 ¶

to_cif ¶

to_file ¶

to_hash ¶

to_pdb ¶

update ¶

update_coordinates ¶

upload ¶

`deeporigin.drug_discovery.Protein`¶

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

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

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

coordinates `property` ¶

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

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

length `property` ¶

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

name `instance-attribute` ¶

num_atoms `property` ¶

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

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

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

sequence `property` ¶

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

tags `class-attribute` `instance-attribute` ¶

uniprot_accession `class-attribute` `instance-attribute` ¶

from_base64 `classmethod` ¶

from_file `classmethod` ¶

from_id `classmethod` ¶

from_name `classmethod` ¶

from_pdb_id `classmethod` ¶

from_remote_file `classmethod` ¶

from_uniprot `classmethod` ¶

load_structure_from_block `staticmethod` ¶

select_structure `staticmethod` ¶