MetricDistance(sel1, sel2, groupsel1=None, groupsel2=None, metric='distances', threshold=8, pbc=True, truncate=None)¶
Creates a MetricDistance object
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.
pbc (bool, optional) – Set to false to disable distance calculations using periodic distances
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, pbc=True, 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)