remove double mapping validation, fix toluene to toluene test

OpenFreeEnergy · Sep 24, 2024 · 55b8765 · 55b8765
1 parent 82447f0
commit 55b8765
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Showing 3 changed files with 19 additions and 9 deletions.
diff --git a/feflow/protocols/nonequilibrium_cycling.py b/feflow/protocols/nonequilibrium_cycling.py
@@ -996,12 +996,10 @@ def _create(
  )
  from openfe.protocols.openmm_utils import system_validation
 
- # Handle parameters
- if mapping is None:
- raise ValueError("`mapping` is required for this Protocol")
  if extends:
  raise NotImplementedError("Can't extend simulations yet")
 
+ # Do manual validation until it is part of the protocol
  # Get alchemical components & validate them + mapping
  alchem_comps = system_validation.get_alchemical_components(stateA, stateB)
  # raise an error if we have more than one mapping

diff --git a/feflow/tests/conftest.py b/feflow/tests/conftest.py
@@ -221,8 +221,8 @@ def mapping_toluene_toluene(toluene):
  i: i for i in range(len(toluene.to_rdkit().GetAtoms()))
  }
  mapping_obj = LigandAtomMapping(
- componentA=toluene,
- componentB=toluene,
+ componentA=toluene.copy_with_replacements(name="toluene_a"),
+ componentB=toluene.copy_with_replacements(name="toluene_b"),
  componentA_to_componentB=mapping_toluene_to_toluene,
  )
  return mapping_obj

diff --git a/feflow/tests/test_nonequilibrium_cycling.py b/feflow/tests/test_nonequilibrium_cycling.py
@@ -303,7 +303,13 @@ def test_create_execute_gather(
  ],
  )
  def test_create_execute_gather_toluene_to_toluene(
- self, protocol, toluene_vacuum_system, mapping_toluene_toluene, tmpdir, request
+ self,
+ protocol,
+ toluene_vacuum_system,
+ mapping_toluene_toluene,
+ tmpdir,
+ request,
+ toluene,
  ):
  """
  Perform 20 independent simulations of the NEQ cycling protocol for the toluene to toluene
@@ -324,10 +330,16 @@ def test_create_execute_gather_toluene_to_toluene(
  import numpy as np
 
  protocol = request.getfixturevalue(protocol)
-
+ # rename the components
+ toluene_state_a = toluene_vacuum_system.copy_with_replacements(
+ components={"ligand": toluene.copy_with_replacements(name="toluene_a")}
+ )
+ toluene_state_b = toluene_vacuum_system.copy_with_replacements(
+ components={"ligand": toluene.copy_with_replacements(name="toluene_b")}
+ )
  dag = protocol.create(
- stateA=toluene_vacuum_system,
- stateB=toluene_vacuum_system,
+ stateA=toluene_state_a,
+ stateB=toluene_state_b,
  name="Toluene vacuum transformation",
  mapping=mapping_toluene_toluene,
  )