moleculekit.projections.metricdistance module#
- class moleculekit.projections.metricdistance.MetricDistance(sel1, sel2, periodic, groupsel1=None, groupsel2=None, metric='distances', threshold=8, pbc=None, truncate=None)#
Bases:
Projection
Creates a MetricDistance object
- Parameters
sel1 (str) – Atom selection string for the first set of atoms. See more here
sel2 (str) – Atom selection string for the second set of atoms. If sel1 != sel2, it will calculate inter-set distances. If sel1 == sel2, it will calculate intra-set distances. See more here
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
proj
- Return type
MetricDistance object
- getMapping(mol)#
Returns the description of each projected dimension.
- Parameters
mol (
Molecule
object) – A Molecule object which will be used to calculate the descriptions of the projected dimensions.- Returns
map – A DataFrame containing the descriptions of each dimension
- Return type
DataFrame
object
- class moleculekit.projections.metricdistance.MetricSelfDistance(sel, groupsel=None, metric='distances', threshold=8, periodic=None, pbc=None, truncate=None)#
Bases:
MetricDistance
- moleculekit.projections.metricdistance.contactVecToMatrix(vector, atomIndexes)#
- moleculekit.projections.metricdistance.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
- Parameters
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
- Returns
cm – The input vector converted into a 2D numpy array
- Return type
np.ndarray
Examples
>>> 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)