moleculekit.representations module#

class moleculekit.representations.Representations(mol)#

Bases: object

Class that stores representations for Molecule.

Parameters:

mol (Molecule) – The Molecule object for which the representations are stored.

Examples

>>> from moleculekit.molecule import Molecule
>>> mol = tryp.copy()
>>> mol.reps.add('protein', 'NewCartoon')
>>> print(mol.reps)
rep 0: sel='protein', style='NewCartoon', color='Name'
>>> mol.view()
>>> mol.reps.remove()
add(sel=None, style=None, color=None, frames=None, opacity=None)#

Adds a new representation for Molecule.

Parameters:

  • sel (str | ndarray | None) – Atom selection (string, boolean mask, or integer index array) for the representation. See more here

  • style (str | None) – Representation style. See more here.

  • color (str | int | None) – Coloring mode (str) or ColorID (int). See more here.

  • frames (list | None) – List of frames to visualize with this representation. If None it will visualize the current frame only.

  • opacity (float | None) – Opacity of the representation. 0 is fully transparent and 1 is fully opaque.

append(reps)#

Append the representations of another Representations object.

Parameters:

reps (Representations) – The Representations object whose representations will be appended to this one.

Raises:

RuntimeError – If reps is not a Representations object.

list()#

Print all currently stored representations.

Prints, for each representation, its index, atom selection, style and color. Equivalent to printing the Representations object directly.

remove(index=None)#

Removed one or all representations.

Parameters:

index (int | None) – The index of the representation to delete. If none is given it deletes all.