Update OpenMM imports to work with new OpenMM API

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

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):

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):

setup.py

@@ -18,7 +18,7 @@
 
 setup(
     name='alphafold-colabfold',
-    version='2.3.4',
+    version='2.3.5',
     long_description_content_type='text/markdown',
     description='An implementation of the inference pipeline of AlphaFold v2.3.1. '
     'This is a completely new model that was entered as AlphaFold2 in CASP14 '