Figures module

Plot configuration.

sdanalysis.figures.configuration.colour_orientation(orientations, light_colours=False)[source]
Return type


sdanalysis.figures.configuration.frame2data(frame, order_function=None, order_list=None, molecule=Trimer(radius=0.637556, distance=1.0, angle=120, moment_inertia_scale=1.0), categorical_colour=False)[source]

Convert a Frame to data for plotting in Bokeh.

This takes a frame and performs all the necessary calculations for plotting, in particular the colouring of the orientation and crystal classification.

  • frame (Frame) – The configuration which is to be plotted.

  • order_function (Optional[Callable[[Frame], ndarray]]) – A function which takes a frame as it’s input which can be used to classify the crystal.

  • order_list (Optional[ndarray]) – A pre-classified collection of values. This is an alternate approach to using the order_function

  • molecule (Molecule) – The molecule which is being plotted.

  • categorical_colour (bool) – Whether to classify as categories, or liquid/crystalline.

Return type

Dict[str, Any]


Dictionary containing x, y, colour, orientation and radius values for each


sdanalysis.figures.configuration.plot_circles(mol_plot, source, categorical_colour=False, factors=None, colormap=('#1f77b4', '#ff7f0e', '#2ca02c', '#d62728', '#9467bd', '#8c564b', '#e377c2', '#7f7f7f', '#bcbd22', '#17becf'))[source]

Add the points to a bokeh figure to render the trimer molecule.

This enables the trimer molecules to be drawn on the figure using only the position and the orientations of the central molecule.

Return type


sdanalysis.figures.configuration.plot_frame(frame, order_function=None, order_list=None, source=None, molecule=Trimer(radius=0.637556, distance=1.0, angle=120, moment_inertia_scale=1.0), categorical_colour=False, factors=None, colormap=None)[source]

Plot a snapshot using bokeh.

  • frame (Frame) – The frame determining the positions to plot

  • order_function (Optional[Callable[[Frame], ndarray]]) – A function which takes a frame and determines ordering

  • order_list (Optional[ndarray]) – A pre-computed list of ordering.

  • source (Optional[ColumnDataSource]) – An existing bokeh ColumnDataSource to use for plotting.

  • molecule (Molecule) – The molecule which is being plotted, used to calculate additional positions.

  • categorical_colour (bool) – Toggle which colours liquid/crystal, or each crystal

  • factors (Optional[List[Any]]) – The factors used for plotting. This is for continuity across a range of figures.

  • colourmap – The collection of colours to use when plotting.


Bokeh plot

Bokeh dashboard for interactive visualisation of thermodynamic properties.


Read a file into a pandas dataframe.

sdanalysis.figures.thermodynamics.update_datacolumns(attr, old, new)[source]

Update data as a callback.

sdanalysis.figures.thermodynamics.update_factors(attr, old, new)[source]

Update factors as a callback.

sdanalysis.figures.thermodynamics.update_file(attr, old, new)[source]

Update current file as a callback.

sdanalysis.figures.thermodynamics.update_file_list(attr, old, new)[source]

Update list of all files as a callback.