def get_rate_matrix(self, X):
self._check_params(X)
n = self.get_nstates()
M = Path_N_0(n).get_rate_matrix()
u = np.zeros(n)
v = self.get_energies(X)
return mrate.to_gtr_hb_known_energies(M, u, v)
def get_rate_matrix(self, X):
self._check_params(X)
M = np.array([
[-1, 1, 0, 0, 0],
[1, -2, 1, 0, 0],
[0, 1, -2, 1, 0],
[0, 0, 1, -2, 1],
[0, 0, 0, 1, -1]], dtype=float)
u = np.zeros(self.get_nstates())
v = self._get_energies(X)
return mrate.to_gtr_hb_known_energies(M, u, v)
def get_rate_matrix(self, X):
self._check_params(X)
M = Hypercube_d_0(self.d).get_rate_matrix()
u = np.zeros(self.get_nstates())
v = self.get_energies(X)
return mrate.to_gtr_hb_known_energies(M, u, v)