openpharmacophore.PharmacophoricPoint

class openpharmacophore.PharmacophoricPoint(feat_type, center, radius, direction=None, atom_indices=None)[source]

Bases: object

Class to store pharmacophoric points of any feature type.

Parameters:

  • feat_type (str) – The feature type of the point. This can be hb donor, hb acceptor, aromatic ring hydrophobic, positive charge, negative charge, excluded volume.

  • center (Quantity (dimensionality:{‘[L]’:1}; shape:(3,))) – Coordinates of the sphere center.

  • radius (Quantity (dimensionality:{‘[L]’:1})) – Radius of the pharmacophoric sphere.

  • direction (array-like; shape:(3,), optional) – Direction as a three-dimensional vector.

  • atom_indices (array-like of int, optional) – The indices of the atoms corresponding to the pharmacophoric point in the molecule from which they were extracted.

Variables:

  • feature_name (str) – The feature type of the point.

  • center (Quantity (dimensionality:{'[L]':1}; shape:(3,))) – Coordinates of the sphere center.

  • radius (Quantity (dimensionality:{'[L]':1}; value:float)) – Radius of the pharmacophoric sphere.

  • direction (ndarray; shape:(3,)) – Unit vector.

  • atom_indices (set of int) – A set of the indices of the atoms corresponding to the pharmacophoric point in the molecule from which they were extracted.

Methods

get_valid_features

Get a list of all valid chemical features for a PharmacophoricPoint object

Attributes

atom_indices

center

direction

feature_name

has_direction

radius

short_name

static get_valid_features()[source]

Get a list of all valid chemical features for a PharmacophoricPoint object