Unverified Commit 7ed0125d authored by Nathan Frey's avatar Nathan Frey Committed by GitHub
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Merge pull request #2431 from ncfrey/atomicconv-tutorial 

[WIP] Tutorial 14 - Modeling Protein-Ligand Interactions with Atomic Convolutions
parents 90f983d4 b730a792

deepchem/feat/complex_featurizers/complex_atomic_coordinates.py

+4 −1
Original line number Diff line number Diff line
@@ -19,7 +19,10 @@ def compute_neighbor_list(coords, neighbor_cutoff, max_num_neighbors, 
                          periodic_box_size):

  """Computes a neighbor list from atom coordinates."""

  N = coords.shape[0]

  try:

    import mdtraj

  except ModuleNotFoundError:

    raise ImportError("This function requires mdtraj to be installed.")

  traj = mdtraj.Trajectory(coords.reshape((1, N, 3)), None)

  box_size = None

  if periodic_box_size is not None:

examples/tutorials/14_Modeling_Protein_Ligand_Interactions_With_Atomic_Convolutions.ipynb

+1 −324

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