def project(self, mol):
""" Project molecule.
Parameters
----------
mol : :class:`Molecule <moleculekit.molecule.Molecule>`
A :class:`Molecule <moleculekit.molecule.Molecule>` object to project.
Returns
-------
data : np.ndarray
An array containing the projected data.
"""
getMolProp = lambda prop: self._getMolProp(mol, prop)
sel1 = getMolProp('sel1')
sel2 = getMolProp('sel2')
if np.ndim(sel1) == 1 and np.ndim(sel2) == 1: # normal distances
metric = pp_calcDistances(mol,
sel1,
sel2,
self.metric,
self.threshold,
self.pbc,
truncate=self.truncate)
else: # minimum distances by groups
metric = pp_calcMinDistances(mol,
sel1,
sel2,
self.metric,
self.threshold,
pbc=self.pbc,
truncate=self.truncate)
return metric
def closestDistance(mol1, mol2):
from moleculekit.projections.util import pp_calcMinDistances
mol1 = mol1.copy()
mol1.segid[:] = "X"
mol2 = mol2.copy()
mol2.segid[:] = "Y"
mol1.append(mol2)
sel1 = mol1.atomselect("segid X")[None, :]
sel2 = mol1.atomselect("segid Y")[None, :]
return pp_calcMinDistances(mol1, sel1, sel2, periodic=None).squeeze()