fix mapping (issue deepchem#3057)

deepchem/models/tests/test_mapper_dmpnn.py

@@ -13,7 +13,7 @@
   has_torch = False
 
 # Set up tests.
-smiles_list = ["C", "CC", "CCC", "C1=CC=CC=C1"]
+smiles_list = ["C", "CC", "CCC", "C1=CC=CC=C1", "[I-].[K+]"]
 featurizer = DMPNNFeaturizer(use_original_atom_ranks=True,
                              features_generators=['morgan'])
 graphs = featurizer.featurize(smiles_list)
@@ -97,3 +97,14 @@ def test_mapper_ring():
   assert (
       mapper.atom_to_incoming_bonds == benezene_atom_to_incoming_bonds).all()
   assert (mapper.mapping == benezene_mapping).all()
+
+
+@pytest.mark.torch
+def test_mapper_disconnected_compounds():
+  """
+  Test '[I-].[K+]' in _MapperDMPNN (disconnected compounds)
+  """
+  mapper = _MapperDMPNN(graphs[0])
+  assert (mapper.bond_to_ini_atom == np.empty(0)).all()
+  assert (mapper.atom_to_incoming_bonds == np.asarray([[-1], [-1]])).all()
+  assert (mapper.mapping == np.asarray([[-1]])).all()

deepchem/models/torch_models/dmpnn.py

@@ -132,7 +132,8 @@ def __init__(self, graph: GraphData):
       self.f_ini_atoms_bonds = np.zeros(
           (1, self.num_atom_features + self.num_bond_features))
 
-      self.atom_to_incoming_bonds = np.asarray([[-1]], dtype=int)
+      self.atom_to_incoming_bonds = np.asarray([[-1]] * self.num_atoms,
+                                               dtype=int)
       self.mapping = np.asarray([[-1]], dtype=int)
 
     else:
@@ -435,14 +436,14 @@ class DMPNNModel(TorchModel):
 
   .. note::
      Current implementation of the DMPNNModel class only supports features of 1 molecule per batch.
-  
+
   The DMPNN model has 2 phases, message-passing phase and read-out phase.
 
   - The goal of the message-passing phase is to generate 'hidden states of all the atoms in the molecule' using encoders.
   - Next in read-out phase, the features are passed into feed-forward neural network to get the task-based prediction.
 
   For additional information:
-  
+
   - `Mapper class <https://github.com/deepchem/deepchem/blob/31676cc2497d5f2de65d648c09fc86191b594501/deepchem/models/torch_models/dmpnn.py#L10-L92>`_
   - `Encoder layer class <https://github.com/deepchem/deepchem/blob/31676cc2497d5f2de65d648c09fc86191b594501/deepchem/models/torch_models/layers.py#L1223-L1374>`_
   - `Feed-Forward class <https://github.com/deepchem/deepchem/blob/31676cc2497d5f2de65d648c09fc86191b594501/deepchem/models/torch_models/layers.py#L689-L700>`_