Hotspot Utilities API¶

The hotspots.utilities module contains classes to for general functionality.

The main classes of the hotspots.extraction module are:

hotspots.hs_utilities.Helper
hotspots.hs_utilities.Figures

class hotspots.hs_utilities.Coordinates(x, y, z)¶

property x¶: Alias for field number 0

property y¶: Alias for field number 1

property z¶: Alias for field number 2

class hotspots.hs_utilities.Figures[source]¶

Class to handle the generation of hotspot related figures

TO DO: is there a better place for this to live?

static histogram(hr)[source]¶

creates a histogram from the hotspot scores

Parameters: hr (hotspots.result.Results) – a Fragment Hotspot Map result
Returns: data, plot

class hotspots.hs_utilities.Helper[source]¶

A class to handle miscellaneous functionality

static cavity_centroid(obj)[source]¶

returns the centre of a cavity

Parameters: obj – can be a ccdc.cavity.Cavity or
Returns: Coordinate

static cavity_from_protein(prot)[source]¶

currently the Protein API doesn’t support the generation of cavities directly from the Protein instance this method handles the tedious writing / reading

Parameters: prot (ccdc.protein.Protein) – protein
Returns: ccdc.cavity.Cavity

static get_atom_type(atom)[source]¶

return the atom classification

Parameters: atom –
Returns

static get_distance(coords1, coords2)[source]¶

given two coordinates, calculates the distance

Parameters

coords1 (tup) – float(x), float(y), float(z), coordinates of point 1
coords2 (tup) – float(x), float(y), float(z), coordinates of point 2

Returns

float, distance

static get_label(input, threshold=None)[source]¶

creates a value labels from an input grid dictionary

Parameters: input (dic) – key = “probe identifier” and value = ccdc.utilities.Grid
Return ccdc.molecule.Moleculeccdc.molecule.Molecule: pseduomolecule which contains score labels

static get_lines_from_file(fname)[source]¶

gets lines from text file, used in Ghecom calculation

Returns: list, list of str

static get_out_dir(path)[source]¶

checks if directory exists, if not, it create the directory

Parameters: path (str) – path to directory
Return str: path to output directory