Figure Managers

MolDynPlot includes several figure managers that build on FigureManager with additions specific for molecular dynamics simulation data.

CorrFigureManager

Generates one or more correlation figures to specifications in a YAML file.

class moldynplot.CorrFigureManager.CorrFigureManager(*args, **kwargs)

Bases: moldynplot.myplotspec.FigureManager.FigureManager

Manages the generation of correlation figures.

Parameters:
  • defaults (string, dict, optional) – Default arguments; may be a yaml string, path to a yaml file, or a dictionary; if not provided pulled from self.defaults
  • args (tuple) – Additional positional arguments
  • kwargs (dict) – Additional keyword arguments
draw_dataset(*in_args, **in_kwargs)

Draws dataset

HSQCFigureManager

Generates one or more HSQC figures to specifications provided in a YAML file.

class moldynplot.HSQCFigureManager.HSQCFigureManager(*args, **kwargs)

Bases: moldynplot.myplotspec.FigureManager.FigureManager

Manages the generation of HSQC figures.

Sample Output:

_images/hsqc.png
Parameters:
  • defaults (string, dict, optional) – Default arguments; may be a yaml string, path to a yaml file, or a dictionary; if not provided pulled from self.defaults
  • args (tuple) – Additional positional arguments
  • kwargs (dict) – Additional keyword arguments
static get_slice(collection, lower_bound, upper_bound)

Extracts a slice from a collection; used to avoid plotting data outside the visible region of a figure

Parameters:
  • collection (ndarry) – Complete array sorted in increasing order
  • lower_bound (float) – Lower bound of region to slice out; slice will start 1 below this cutoff
  • upper_bound (float) – Upper bound of region to slice out; slice will start 1 above this cutoff
Returns:

slice – slice
static get_contour_levels(I, cutoff=0.9875, n_levels=10, min_level=None, max_level=None, **kwargs)

Generates contour levels.

Parameters:
  • I (ndarray) – Intensity
  • cutoff (float) – Proportion of Intensity below minimum level
  • n_levels (int) – Number of contour levels
  • min_level (float) – Intensity level of lowest contour level
  • max_level (float) – Intensity level of highest contour level; default = max(I)
Returns:

ndarray – levels
draw_dataset(*in_args, **in_kwargs)

Draws a dataset on a subplot.

Parameters:
  • subplot (Axes) – Axes on which to draw
  • dataset_kw (dict) – Keyword arguments used to passed to load_dataset()
  • plot_kw (dict) – Keyword arguments passed to methods of Axes
  • draw_contour (bool) – Draw contour
  • contour_kw (dict) – Keyword arguments passed to contour or contourf
  • contour_kw[levels] (ndarray, list) – Contour levels; if omitted; will be calculated using get_contour_levels()
  • contour_kw[cmap] (LinearSegmentedColormap) – Color map used for contours; if omitted, a uniform colormap will be generated from contour_kw[color] using moldynplot.myplotspec.get_cmap()
  • contour_kw[fill] (bool) – If true, draw filled contour levels using contourf; if false, draw contour lines using contour
  • handles (OrderedDict) – Nacsent collection of legend handles
  • label (str) – Name to be assigned to egend handle
  • handle_kw (dict) – Keyword arguments used to configure legend handle
  • verbose (int) – Level of verbose output
  • kwargs (dict) – Additional keyword arguments

MDGXFigureManager

Generates one or more MDGX figures to specifications provided in a YAML file.

class moldynplot.MDGXFigureManager.MDGXFigureManager(*args, **kwargs)

Bases: moldynplot.myplotspec.FigureManager.FigureManager

Manages the generation of MDGX figures.

Parameters:
  • defaults (string, dict, optional) – Default arguments; may be a yaml string, path to a yaml file, or a dictionary; if not provided pulled from self.defaults
  • args (tuple) – Additional positional arguments
  • kwargs (dict) – Additional keyword arguments
draw_dataset(*in_args, **in_kwargs)

PDistFigureManager

Generates one or more probability distribution figures to specifications in a YAML file.

class moldynplot.PDistFigureManager.PDistFigureManager(*args, **kwargs)

Bases: moldynplot.myplotspec.FigureManager.FigureManager

Manages the generation of probability distribution figures.

Parameters:
  • defaults (string, dict, optional) – Default arguments; may be a yaml string, path to a yaml file, or a dictionary; if not provided pulled from self.defaults
  • args (tuple) – Additional positional arguments
  • kwargs (dict) – Additional keyword arguments
draw_dataset(*in_args, **in_kwargs)

Loads a dataset and draws it on a subplot.

Loaded dataset should have attribute pdist_df.

Parameters:
  • subplot (Axes) – Axes on which to draw
  • dataset_kw (dict) – Keyword arguments passed to load_dataset
  • plot_kw (dict) – Keyword arguments passed to methods of Axes
  • column (str) – Column within pdist_df to use
  • draw_fill_between (bool) – Fill between specified region
  • fill_between_kw (dict) – Keyword arguments used to configure call to fill_between
  • fill_between_kw[x] (list, ndarray) – x values passed to fill_between
  • fill_between_kw[ylb] (list, ndarray) – y lower bound values passed to fill_between
  • fill_between_kw[yub] (list, ndarray) – y upper bound values passed to fill_between
  • draw_pdist (bool) – Draw probability distribution
  • pdist_kw (dict) – Keyword arguments using to configure call to plot
  • draw_mean (bool) – Draw point at mean value
  • mean_kw (dict) – Keyword arguments used to configure call to plot
  • verbose (int) – Level of verbose output
  • kwargs (dict) – Additional keyword arguments

SAXSFigureManager

Generates one or more time series figures to specifications in a YAML file.

class moldynplot.SAXSFigureManager.SAXSFigureManager(*args, **kwargs)

Bases: moldynplot.myplotspec.FigureManager.FigureManager

Manages the generation of time series figures

Parameters:
  • defaults (string, dict, optional) – Default arguments; may be a yaml string, path to a yaml file, or a dictionary; if not provided pulled from self.defaults
  • args (tuple) – Additional positional arguments
  • kwargs (dict) – Additional keyword arguments

SequenceFigureManager

Generates one or more sequence figures to specifications in a YAML file.

class moldynplot.SequenceFigureManager.SequenceFigureManager(*args, **kwargs)

Bases: moldynplot.myplotspec.FigureManager.FigureManager

Manages the generation of sequence figures.

Supported Presets:

Relaxation (relax_4_s2):

_images/relax.png
Parameters:
  • defaults (string, dict, optional) – Default arguments; may be a yaml string, path to a yaml file, or a dictionary; if not provided pulled from self.defaults
  • args (tuple) – Additional positional arguments
  • kwargs (dict) – Additional keyword arguments

StateProbFigureManager

Generates one or more state probability figures to specifications in a YAML file.

class moldynplot.StateProbFigureManager.StateProbFigureManager(*args, **kwargs)

Bases: moldynplot.myplotspec.FigureManager.FigureManager

Class to manage the generation of probability distribution figures

Parameters:
  • defaults (string, dict, optional) – Default arguments; may be a yaml string, path to a yaml file, or a dictionary; if not provided pulled from self.defaults
  • args (tuple) – Additional positional arguments
  • kwargs (dict) – Additional keyword arguments
draw_dataset(*in_args, **in_kwargs)

Draws a dataset.

Parameters:
  • subplot (Axes) – Axes on which to draw
  • x (float) – X coordinate of bar
  • label (str, optional) – Dataset label
  • color (str, list, ndarray, float, optional) – Dataset color
  • bar_kw (dict, optional) – Additional keyword arguments passed to subplot.plot()
  • handles (OrderedDict, optional) – Nascent OrderedDict of [labels]: handles on subplot
  • kwargs (dict) – Additional keyword arguments

TimeSeriesFigureManager

Generates one or more time series figures to specifications in a YAML file.

class moldynplot.TimeSeriesFigureManager.TimeSeriesFigureManager(*args, **kwargs)

Bases: moldynplot.myplotspec.FigureManager.FigureManager

Manages the generation of time series figures.

Supported Presets:

Root-mean standard deviation (rmsd):

_images/rmsd.png

Radius of gyration (radgyr):

_images/radgyr.png
Parameters:
  • defaults (string, dict, optional) – Default arguments; may be a yaml string, path to a yaml file, or a dictionary; if not provided pulled from self.defaults
  • args (tuple) – Additional positional arguments
  • kwargs (dict) – Additional keyword arguments
draw_dataset(*in_args, **in_kwargs)

Draws a dataset on a subplot.

Loaded dataset should have attribute timeseries_df

Parameters:
  • subplot (Axes) – Axes on which to draw
  • dataset_kw (dict) – Keyword arguments passed to load_dataset
  • plot_kw (dict) – Keyword arguments passed to methods of Axes
  • draw_plot (bool) – Draw plot
  • draw_pdist (bool) – Draw probability distribution
  • draw_fill_between (bool) – Fill between specified region for this dataset
  • draw_mean (bool) – Draw point at mean value value of probability distribution
  • verbose (int) – Level of verbose output
  • kwargs (dict) – Additional keyword arguments

TimeSeries2DFigureManager

Generates one or more 2D time series figures to specifications in a YAML file.

class moldynplot.TimeSeries2DFigureManager.TimeSeries2DFigureManager(*args, **kwargs)

Bases: moldynplot.myplotspec.FigureManager.FigureManager

Manages the generation of 2D time series figures.

Supported Presets:

Per-residue root-mean standard deviation (perresrmsd):

_images/perresrmsd.png

Dictionary of secondary structure prediction (dssp):

_images/dssp.png
Parameters:
  • defaults (string, dict, optional) – Default arguments; may be a yaml string, path to a yaml file, or a dictionary; if not provided pulled from self.defaults
  • args (tuple) – Additional positional arguments
  • kwargs (dict) – Additional keyword arguments