def __init__(self, path, num_neighbours=20, n_jobs=1, cache=True):
     ProteinNetKNN.__init__(self,
                            path,
                            num_neighbours=num_neighbours,
                            n_jobs=n_jobs,
                            cache=cache)
     self.ors = torch.tensor(orientation(self.ters[1].numpy() /
                                         100).transpose(2, 0, 1),
                             dtype=torch.float)
 def __init__(self, path, num_neighbours=20, n_jobs=1, N=64, cache=True):
     ProteinNetKNN.__init__(self,
                            path,
                            num_neighbours=num_neighbours,
                            n_jobs=n_jobs,
                            cache=cache)
     self.backrub = Backrub(n_moves=0)
     self.ors = torch.tensor(orientation(self.ters[1].numpy() /
                                         100).transpose(2, 0, 1),
                             dtype=torch.float)
     self.N = N
     self.valid_indices = [
         index for index in range(len(self.index) - 1)
         if self.index[index + 1] - self.index[index] >= N
     ]
Example #3
0
 def __init__(self,
              path,
              radius=8,
              num_neighbours=15,
              n_jobs=1,
              cache=True):
     ProteinNetKNN.__init__(self,
                            path,
                            num_neighbours=num_neighbours,
                            n_jobs=n_jobs,
                            cache=cache)
     self.radius = radius
     self.backrub = Backrub(n_moves=0)  #10, phi=0.3, psi=0.3, tau=0.3)
     self.ors = torch.tensor(orientation(self.ters[1].numpy() /
                                         100).transpose(2, 0, 1),
                             dtype=torch.float)