import numpy as np
import pyunitwizard as puw
[docs]class Pharmacophore:
""" A PharmacophoricPoint container.
Parameters
----------
points : list[PharmacophoricPoint], optional
List of pharmacophoric points.
score : float, optional
A score assigned to the pharmacophore.
ref_mol : int, optional
The index of the reference molecule from which the pharmacophore
was extracted.
ref_struct : int, optional
The index of the reference structure or conformer from which the pharmacophore
was extracted.
"""
def __init__(self, points=None, score=None,
ref_mol=None, ref_struct=None
):
if points is None:
self._points = []
else:
self._points = points
self.score = score
self.ref_mol = ref_mol
self.ref_struct = ref_struct
self.props = {}
[docs] def add(self, point):
""" Add a pharmacophoric point.
Parameters
----------
point : PharmacophoricPoint
"""
self._points.append(point)
[docs] def remove(self, index):
""" Remove a pharmacophoric point.
Parameters
----------
index : int
Index of the pharmacophoric point
"""
self._points.pop(index)
[docs] def to_matrix(self):
""" Returns a matrix with the coordinates of the
pharmacophoric points.
"""
matrix = np.zeros((len(self), 3))
for ii in range(len(self)):
center = puw.get_value(self[ii].center, "angstroms")
for jj in range(center.shape[0]):
matrix[ii][jj] = center[jj]
return puw.quantity(matrix, "angstroms")
def __eq__(self, other):
if isinstance(other, Pharmacophore):
if not self.score == other.score:
return False
if not self.ref_mol == other.ref_mol:
return False
if not self.ref_struct == other.ref_struct:
return False
if len(self) == len(other):
for ii in range(len(self)):
if self[ii] != other[ii]:
return False
else:
return False
return True
return False
def __len__(self):
return len(self._points)
def __getitem__(self, item):
return self._points[item]
def __repr__(self):
return f"{self.__class__.__name__}(points={self._points}, " \
f"score={self.score}, ref_mol={self.ref_mol}, ref_struct={self.ref_struct})"
