Plotting

Plot residues — prolif.plotting.residues

New in version 2.0.0.

prolif.plotting.residues.display_residues(mol: Molecule, residues_slice: Optional[slice] = None, *, size: Tuple[int, int] = (200, 140), mols_per_row: int = 4, use_svg: 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 (Optional[slice] = 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.

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: Optional[dict] = None, tight_layout_kwargs: Optional[dict] = None)

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 (Optional[dict] = None) – Other parameters passed to matplotlib.pyplot.subplots().

• tight_layout_kwargs (Optional[dict] = 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)

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.

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]

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

compare(other: Complex3D, *, size: Tuple[int, int] = (900, 600), display_all: bool = False, linked: bool = True, color_unique: Optional[str] = 'magentaCarbon') → view

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 (Optional[str] = "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.

• versionadded: (..) – 2.0.1:

display(size: Tuple[int, int] = (650, 600), display_all: bool = False) → view

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.

classmethod from_fingerprint(fp: Fingerprint, lig_mol: Molecule, prot_mol: Molecule, *, 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.

Plot a Ligand Interaction Network — prolif.plotting.network

New in version 0.3.2.

Changed in version 2.0.0: Replaced LigNetwork.from_ifp with LigNetwork.from_fingerprint which works without requiring a dataframe with atom indices.

class prolif.plotting.network.LigNetwork(df, lig_mol, use_coordinates=False, flatten_coordinates=True, kekulize=False, molsize=35, rotation=0, carbon=0.16)

Creates a ligand interaction diagram

Parameters:

• df (pandas.DataFrame) – Dataframe with a 4-level index (ligand, protein, interaction, atoms) and weight and distance columns for values

• lig_mol (rdkit.Chem.rdChem.Mol) – Ligand molecule

• use_coordinates (bool) – If True, uses the coordinates of the molecule directly, otherwise generates 2D coordinates from scratch. See also flatten_coordinates.

• flatten_coordinates (bool) – If this is True and use_coordinates=True, generates 2D coordinates that are constrained to fit the 3D conformation of the ligand as best as possible.

• kekulize (bool) – Kekulize the ligand

• molsize (int) – Multiply the coordinates by this number to create a bigger and more readable depiction

• rotation (int) – Rotate the structure on the XY plane

• carbon (float) – Size of the carbon atom dots on the depiction. Use 0 to hide the carbon dots

COLORS

Dictionnary of colors used in the diagram. Subdivided in several dictionaries:

• “interactions”: mapping between interactions types and colors

• “atoms”: mapping between atom symbol and colors

• “residues”: mapping between residues types and colors

Type:

dict

RESIDUE_TYPES

Mapping between residue names (3 letter code) and types. The types are then used to define how each residue should be colored.

Type:

dict

Notes

You can customize the diagram by tweaking LigNetwork.COLORS and LigNetwork.RESIDUE_TYPES by adding or modifying the dictionaries inplace.

Changed in version 2.0.0: Replaced LigNetwork.from_ifp with LigNetwork.from_fingerprint which works without requiring a dataframe with atom indices. Replaced match3D parameter with use_coordinates and flatten_coordinates to give users more control and allow them to provide their own 2D coordinates. Added support for displaying peptides as the “ligand”. Changed the default color for VanDerWaals.

display(**kwargs)

Prepare and display the network

classmethod from_fingerprint(fp, ligand_mol, kind='aggregate', frame=0, display_all=False, threshold=0.3, **kwargs)

Helper method to create a ligand interaction diagram from a Fingerprint object.

Notes

Two kinds of diagrams can be rendered: either for a designated frame or by aggregating the results on the whole IFP and optionnally discarding interactions that occur less frequently than a threshold. In the latter case (aggregate), only the group of atoms most frequently involved in each interaction is used to draw the edge.

Parameters:

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

• lig (rdkit.Chem.rdChem.Mol) – Ligand molecule

• kind (str) – One of "aggregate" or "frame"

• frame (int) – Frame number (see ifp). Only applicable for kind="frame"

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

• threshold (float) – Frequency threshold, between 0 and 1. Only applicable for kind="aggregate"

• kwargs (object) – Other arguments passed to the LigNetwork class

Changed in version 2.0.0: Added the display_all parameter.

save(fp, **kwargs)

Save the network to an HTML file

Parameters:

fp (str or file-like object) – Name of the output file, or file-like object

show(filename, **kwargs)

Save the network as HTML and display the resulting file