def obs_function(trajchunk):
r = md.compute_distances(trajchunk,pairs,periodic=periodic)
Econtact = np.zeros(trajchunk.n_frames,float)
for i in range(pairs.shape[0]):
pair_Vi = get_pair_potential(pair_type[i])
Econtact += eps[i]*pair_Vi(r[:,i],*contact_params[i])
return Econtact
def map(self,traj):
from model_builder.models.pairwise_potentials import get_pair_potential
r = mdtraj.compute_distances(traj, self.pairs, periodic=self.periodic)
Epair = np.zeros((traj.n_frames, self.dimension), float)
for i in range(self.pairs.shape[0]):
Vi = get_pair_potential(self.pair_type[i])
Epair[:,0] += self.eps[i]*Vi(r[:,i],*self.pair_params[i])
return Epair
