Plotting
flat.plotting
Module for plotting data within PyMOL.
Note
Module has optional dependency to mplcursors python package. Install package with pip install mplcursors.
- flat.plotting.plot(expression='b', selection='all', fmt=None, byres=True, filename=None, *, quiet=1, _self=cmd, **kwargs)
- DESCRIPTION
Plot selected property or expression with matplotlib
- USAGE
plot [ expression [, selection [, fmt, [, byres, [, filename ]]]]]
- ARGUMENTS
- expressionstr, default = ‘b’
Atom property or expression to plot.
- selectionstr, default = ‘all’
Atom selection.
- fmtstr, default = None
Plotting format (see matplotlib documentation). By default plot as bars.
- byresbool, default = True
Plot properties per-residue instead of per-atom.
- filenamestr, optional
Save figure to file.
- RETURNS
- : matplotlib.figure.Figure
Figure object.
- flat.plotting.plot_contacts(selection='guide', metric='euclidean', *, state=-1, filename=None, quiet=1, _self=cmd)
- DESCRIPTION
Plot a contact map.
- USAGE
plot_contacts [ selection [, metric [, state [, filename ]]]]
- ARGUMENTS
- selectionstr, default = ‘guide’
Atom selection.
- metricstr, default = ‘euclidean’
Metric for distance matrix.
- stateint, default = -1
State index or all states if state=0 {default: -1}
- filenamestr, optional
Save figure to file.
- RETURNS
- : matplotlib.figure.Figure
Figure object.
- SOURCE
From PSICO (c) 2011-2012 Thomas Holder, MPI for Developmental Biology
- flat.plotting.plot_ramachandran(selection='guide', fmt='.', state=-1, ref=1, filename=None, *, quiet=1, _self=cmd, **kwargs)
- DESCRIPTION
Plot a Ramachandra dihedral map.
- USAGE
plot_ramachandran [ selection [, fmt [, state [, ref [, filename ]]]]]
- ARGUMENTS
- selectionstr, default = ‘guide’
Atom selection.
- fmtstr, default = ‘.’
Plotting format (see matplotlib documentation).
- stateint, default = -1
State index or all states if state=0 {default: -1}
- refbool, default = True
Plot reference Ramachandra dihedrals.
- filenamestr, optional
Save figure to file.
- RETURNS
- : matplotlib.figure.Figure
Figure object.
- SOURCE
Reference Ramachandra plot was taken from MDAnalysis dihedral package: Michaud-Agrawal, J. Comput. Chem., 2011, doi:10.1002/jcc.21787
- SEE ALSO
phi_psi()