cgexplore.utilities.Pymol

class cgexplore.utilities.Pymol(output_dir, file_prefix, pymol_path, settings=None)

Bases: object

Pymol visualiser.

Methods

visualise	Run pymol to visualise a molecule.
visualise_host_guest	Run pymol to visualise a molecule.

Parameters:

• output_dir (Path)

• file_prefix (str)

• pymol_path (Path)

• settings (dict | None)

visualise(structure_files, structure_colours=None, orient_atoms=None)

Run pymol to visualise a molecule.

Parameters:

• structure_files (list)

• structure_colours (list | None)

• orient_atoms (str | None)

Return type:

None

visualise_host_guest(structure_file, host_atoms, host_transperancy, radii, epsilons, epsilon_min, epsilon_max, epsilon_palette, structure_colour=None, orient_atoms=None)

Run pymol to visualise a molecule.

Parameters:

• structure_file (Path)

• host_atoms (list[str])

• host_transperancy (float)

• radii (dict[str, float])

• epsilons (dict[str, float])

• epsilon_min (float)

• epsilon_max (float)

• epsilon_palette (str)

• structure_colour (str | None)

• orient_atoms (str | None)

Return type:

None