Plotting

Plot residues — prolif.plotting.residues

New in version 2.0.0.

prolif.plotting.residues.display_residues(mol: Molecule, residues_slice: slice | None = None, *, size: tuple[int, int] = (200, 140), mols_per_row: int = 4, use_svg: bool = True, sanitize: bool = True) → Any

Display a grid image of the residues in the molecule. The hydrogens are stripped and the 3D coordinates removed for a clearer visualisation.

Parameters:

• mol (prolif.Molecule) – The molecule to show residues from.

• residues_slice (slice | None = None) – Optionally, a slice of residues to display, e.g. slice(20) for the first 20 residues, or slice(<start>, <stop>, <step>) for a more complex selection.

• size (tuple[int, int] = (200, 140)) – Size of each residue image.

• mols_per_row (int = 4) – Number of residues displayed per row.

• use_svg (bool = True) – Generate an SVG or PNG image.

• sanitize (bool = True) – Sanitize the residues before displaying.

• versionchanged: (..) – 2.1.0: Added sanitize parameter that defaults to False for easier debugging.

Plot interactions as a barcode — prolif.plotting.barcode

New in version 2.0.0.

class prolif.plotting.barcode.Barcode(df: DataFrame)

Creates a barcode plot of interactions.

Parameters:

df (pandas.DataFrame) – The DataFrame as obtained from Fingerprint.to_dataframe()

COLORS

Dictionnary of colors used in the plot for interactions.

Type:

dict

display(figsize: tuple[int, int] = (8, 10), dpi: int = 100, interactive: bool = False, n_frame_ticks: int = 10, residues_tick_location: Literal['top', 'bottom'] = 'top', xlabel: str = 'Frame', subplots_kwargs: dict | None = None, tight_layout_kwargs: dict | None = None) → Axes

Generate and display the barcode plot.

Parameters:

• figsize (tuple[int, int] = (8, 10)) – Size of the matplotlib figure.

• dpi (int = 100) – DPI used for the matplotlib figure.

• interactive (bool) – Add hover interactivity to the plot (only relevant for notebooks). You may need to add %matplotlib notebook or %matplotlib ipympl for it to work as expected.

• n_frame_ticks (int = 10) – Number of ticks on the X axis. May use ±1 tick to have them evenly spaced.

• residues_tick_location (Literal["top", "bottom"] = "top") – Whether the Y ticks appear at the top or at the bottom of the series of interactions of each residue.

• xlabel (str = "Frame") – Label displayed for the X axis.

• subplots_kwargs (dict | None = None) – Other parameters passed to matplotlib.pyplot.subplots().

• tight_layout_kwargs (dict | None = None) – Other parameters passed to matplotlib.figure.Figure.tight_layout().

classmethod from_fingerprint(fp: Fingerprint) → Barcode

Creates a barcode object from a fingerprint.

Plot interactions in 3D — prolif.plotting.complex3d

New in version 2.0.0.

class prolif.plotting.complex3d.Complex3D(ifp: IFP, lig_mol: Molecule, prot_mol: Molecule, water_mol: Molecule | None = None)

Creates a py3Dmol plot of interactions.

Parameters:

• ifp (IFP) – The interaction dictionary for a single frame.

• lig_mol (Molecule) – The ligand molecule to display.

• prot_mol (Molecule) – The protein molecule to display.

• water_mol (Optional[Molecule]) – Additional molecule (e.g. waters) to display.

COLORS

Dictionnary of colors used in the plot for interactions.

Type:

dict

LIGAND_STYLE

Style object passed to 3Dmol.js for the ligand.

Type:

dict[str, dict] = {“stick”: {“colorscheme”: “cyanCarbon”}}

RESIDUES_STYLE

Style object passed to 3Dmol.js for the protein residues involved in interactions.

Type:

dict[str, dict] = {“stick”: {}}

PROTEIN_STYLE

Style object passed to 3Dmol.js for the entire protein.

Type:

dict[str, dict] = {“cartoon”: {“style”: “edged”}}

PEPTIDE_STYLE

Style object passed to 3Dmol.js for the ligand as a peptide if appropriate.

Type:

dict[str, dict] = “cartoon”: {“style”: “edged”, “colorscheme”: “cyanCarbon”}

PEPTIDE_THRESHOLD

Ligands with this number of residues or more will be displayed using PEPTIDE_STYLE in addition to the LIGAND_STYLE.

Type:

int = 2

LIGAND_DISPLAYED_ATOM

Which atom should be used to display an atom-to-atom interaction for the ligand. Refers to the order defined in the SMARTS pattern used in interaction definition. Interactions not specified here use 0 by default.

Type:

dict[str, int]

PROTEIN_DISPLAYED_ATOM

Same as LIGAND_DISPLAYED_ATOM for the protein.

Type:

dict[str, int]

LIGAND_RING_INTERACTIONS

Which interactions should be displayed using the centroid instead of using LIGAND_DISPLAYED_ATOM for the ligand.

Type:

set[str]

PROTEIN_RING_INTERACTIONS

Which interactions should be displayed using the centroid instead of using PROTEIN_DISPLAYED_ATOM for the protein.

Type:

set[str]

BRIDGED_INTERACTIONS

For bridged-interactions such as WaterBridge. The key is the interaction name, and the value is the name of the molecule in the metadata indices dictionary.

Type:

dict[str, str]

RESIDUE_HOVER_CALLBACK

JavaScript callback executed when hovering a residue involved in an interaction.

Type:

str

INTERACTION_HOVER_CALLBACK

JavaScript callback executed when hovering an interaction line.

Type:

str

DISABLE_HOVER_CALLBACK

JavaScript callback executed when the hovering event is finished.

Type:

str

.. versionchanged:: 2.1.0

Added water_mol parameter to the constructor to display waters involved in WaterBridge interactions. Added save_png method to save the current state of the 3D viewer to a PNG. Added remove_hydrogens parameter to the display and compare methods to remove non-polar hydrogens that aren’t involved in an interaction. Added only_interacting parameter to the display and compare methods to show all protein residues in the vicinity of the ligand, or only the ones participating in an interaction.

compare(other: Complex3D, *, size: tuple[int, int] = (900, 600), display_all: bool = False, linked: bool = True, color_unique: str | None = 'magentaCarbon', only_interacting: bool = True, remove_hydrogens: Union[bool, Literal['ligand', 'protein', 'water']] = True) → Complex3D

Displays the initial complex side-by-side with a second one for easier comparison.

Parameters:

• other (Complex3D) – Other Complex3D object to compare to.

• size (tuple[int, int] = (900, 600)) – The size of the py3Dmol widget view.

• display_all (bool = False) – Display all occurences for a given pair of residues and interaction, or only the shortest one. Not relevant if count=False in the Fingerprint object.

• linked (bool = True) – Link mouse interactions (pan, zoom, translate) on both views.

• color_unique (str | None = "magentaCarbon",) – Which color to use for residues that have interactions that are found in one complex but not the other. Use None to disable the color override.

• only_interacting (bool = True) – Whether to show all protein residues in the vicinity of the ligand, or only the ones participating in an interaction.

• remove_hydrogens (bool | Literal["ligand", "protein", "water"] = True) – Whether to remove non-polar hydrogens (unless they are involved in an interaction).

• versionadded: (..) – 2.0.1:

• versionchanged: (..) – 2.1.0: Added only_interacting=True and remove_hydrogens=True parameters. Non-polar hydrogen atoms that aren’t involved in interactions are now hidden. Added support for waters involved in WaterBridge interactions.

display(size: tuple[int, int] = (650, 600), display_all: bool = False, only_interacting: bool = True, remove_hydrogens: Union[bool, Literal['ligand', 'protein', 'water']] = True) → Complex3D

Display as a py3Dmol widget view.

Parameters:

• size (tuple[int, int] = (650, 600)) – The size of the py3Dmol widget view.

• display_all (bool = False) – Display all occurences for a given pair of residues and interaction, or only the shortest one. Not relevant if count=False in the Fingerprint object.

• only_interacting (bool = True) – Whether to show all protein residues in the vicinity of the ligand, or only the ones participating in an interaction.

• remove_hydrogens (bool | Literal["ligand", "protein", "water"] = True) – Whether to remove non-polar hydrogens (unless they are involved in an interaction).

• versionchanged: (..) – 2.1.0: Added only_interacting=True and remove_hydrogens=True parameters. Non-polar hydrogen atoms that aren’t involved in interactions are now hidden. Added support for waters involved in WaterBridge interactions.

classmethod from_fingerprint(fp: Fingerprint, lig_mol: Molecule, prot_mol: Molecule, water_mol: Molecule | None = None, *, frame: int) → Complex3D

Creates a py3Dmol plot of interactions.

Parameters:

• fp (prolif.fingerprint.Fingerprint) – The fingerprint object already executed using one of the run or run_from_iterable methods.

• frame (int) – The frame number chosen to select which interactions are going to be displayed.

• lig_mol (Molecule) – The ligand molecule to display.

• prot_mol (Molecule) – The protein molecule to display.

• water_mol (Optional[Molecule]) – Additional molecule (e.g. waters) to display.

static get_ring_centroid(mol: Molecule, indices: tuple[int, ...]) → Point3D

Get the centroid of a ring system.

save_png() → None

Saves the current state of the 3D viewer to a PNG. Not available outside of a notebook.

New in version 2.1.0.