Merge pull request #1 from steineggerlab/main

Update OpenMM imports to work with new OpenMM API
lbl-cbg · May 10, 2023 · ba597e0 · ba597e0
2 parents 3d3fdde + 7386194
commit ba597e0
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Showing 3 changed files with 7 additions and 7 deletions.
diff --git a/alphafold/relax/amber_minimize.py b/alphafold/relax/amber_minimize.py
@@ -27,10 +27,10 @@
 import ml_collections
 import numpy as np
 import jax
-from simtk import openmm
-from simtk import unit
-from simtk.openmm import app as openmm_app
-from simtk.openmm.app.internal.pdbstructure import PdbStructure
+import openmm
+from openmm import unit
+from openmm import app as openmm_app
+from openmm.app.internal.pdbstructure import PdbStructure
 
 
 ENERGY = unit.kilocalories_per_mole

diff --git a/alphafold/relax/cleanup.py b/alphafold/relax/cleanup.py
@@ -20,8 +20,8 @@
 import io
 
 import pdbfixer
-from simtk.openmm import app
-from simtk.openmm.app import element
+from openmm import app
+from openmm.app import element
 
 
 def fix_pdb(pdbfile, alterations_info):

diff --git a/alphafold/relax/cleanup_test.py b/alphafold/relax/cleanup_test.py
@@ -17,7 +17,7 @@
 
 from absl.testing import absltest
 from alphafold.relax import cleanup
-from simtk.openmm.app.internal import pdbstructure
+from openmm.app.internal import pdbstructure
 
 
 def _pdb_to_structure(pdb_str):