MetricDistance(sel1, sel2, periodic, groupsel1=None, groupsel2=None, metric='distances', threshold=8, pbc=None, truncate=None)¶
Creates a MetricDistance object
periodic (str) – If periodic distances should be calculated and between which elements. If set to “chains” it will only calculate periodic distances between different chains. If set to “selections” it will calculate periodic distances between the two selections. If set to None it will not calculate any periodic distances.
groupsel1 (['all','residue'], optional) – Group all atoms in sel1 to the single minimum distance. Alternatively can calculate the minimum distance of a residue containing the atoms in sel1.
groupsel2 (['all','residue'], optional) – Same as groupsel1 but for sel2
metric (['distances','contacts'], optional) – Set to ‘contacts’ to calculate contacts instead of distances
threshold (float, optional) – The threshold under which a distance is considered in contact. Units in Angstrom.
truncate (float, optional) – Set all distances larger than truncate to truncate. Units in Angstrom.
update – Not functional yet
Returns the description of each projected dimension.
Molecule object) – A Molecule object which will be used to calculate the descriptions of the projected dimensions.
map – A DataFrame containing the descriptions of each dimension
MetricSelfDistance(sel, groupsel=None, metric='distances', threshold=8, periodic=None, pbc=None, truncate=None)¶
reconstructContactMap(vector, mapping, truecontacts=None, plot=True, figsize=7, 7, dpi=80, title=None, outfile=None, colors=None)¶
Plots a given vector as a contact map
vector (np.ndarray or list) – A 1D vector of contacts
mapping (pd.DataFrame) – A pandas DataFrame which describes the dimensions of the projection
truecontacts (np.ndarray or list) – A 1D vector of true contacts
plot (bool) – To plot or not to plot
figsize (tuple) – The size of the final plot in inches
dpi (int) – Dots per inch
outfile (str) – Path of file in which to save the plot
cm – The input vector converted into a 2D numpy array
>>> reconstructContactMap(contacts, mapping) To use it with distances instead of contacts pass ones as the concat vector >>> reconstructContactMap(np.ones(dists.shape, dtype=bool), mapping, colors=dists)