molgri.plotting.molecule_plots
Plots connected with (pseudo)trajectories and their energies.
Enables plotting COM of ParsedTrajectory and coloring them according to energies, convergence of energies with the length of the (pseudo)trajectory.
Classes
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In the __init__, defaults should be set that will generally be used for an entire class of figures - but it is still possible to not use defaults for some of the plots. |
- class molgri.plotting.molecule_plots.TrajectoryPlot(parsed_trajectory: ParsedTrajectory, N_used: int | None = None)
In the __init__, defaults should be set that will generally be used for an entire class of figures - but it is still possible to not use defaults for some of the plots.
- Args:
data_name: keyword that combines all figures of a specific sub-class fig_path: folder to save figures if created, should be set in subclasses ani_path: folder to save animations if created, should be set in subclasses default_context: forwarded to sns.set_context -> should be one of: paper, notebook, talk, poster default_color_style: describes the general color scheme of the plots (dark, white) default_complexity_level: select from full, half_empty, empty
- __init__(parsed_trajectory: ParsedTrajectory, N_used: int | None = None)
In the __init__, defaults should be set that will generally be used for an entire class of figures - but it is still possible to not use defaults for some of the plots.
- Args:
data_name: keyword that combines all figures of a specific sub-class fig_path: folder to save figures if created, should be set in subclasses ani_path: folder to save animations if created, should be set in subclasses default_context: forwarded to sns.set_context -> should be one of: paper, notebook, talk, poster default_color_style: describes the general color scheme of the plots (dark, white) default_complexity_level: select from full, half_empty, empty
- get_possible_title()
- make_COM_plot(ax=None, fig=None, save=True, atom_selection=None, projection='3d', animate_rot=False, fg=None)
- make_energy_COM_plot(ax=None, fig=None, save=True, atom_selection=None, projection='3d', animate_rot=False, energy_type='Potential', vmin=None, vmax=None, lowest_k=None, highest_j=None)
- make_molecule_plot()
- make_energy_violin_plot(ax=None, fig=None, save=True, energy_type: str = 'Potential', **kwargs)
- create_all_plots(and_animations=False)
- class molgri.plotting.molecule_plots.ConvergenceMultiCollection(parsed_trajectory: ParsedTrajectory, N_set: tuple | None = None)
- __init__(parsed_trajectory: ParsedTrajectory, N_set: tuple | None = None)
- make_all_COM_3d_plots(animate_rot=False, save=True)
- make_all_COM_hammer_plots(save=True)
- make_all_energy_plots(dim, animate_rot=False, save=True, energy_type: str = 'Potential')
- create_all_plots(and_animations=False)