Merge branch 'installation-updates' of https://github.com/aqlaboratory/openfold into installation-updates

Merging changes from different systems

lib/openmm.patch

@@ -1,42 +0,0 @@
-Index: simtk/openmm/app/topology.py
-===================================================================
---- simtk.orig/openmm/app/topology.py
-+++ simtk/openmm/app/topology.py
-@@ -356,19 +356,35 @@
-         def isCyx(res):
-             names = [atom.name for atom in res._atoms]
-             return 'SG' in names and 'HG' not in names
-+        # This function is used to prevent multiple di-sulfide bonds from being
-+        # assigned to a given atom. This is a DeepMind modification.
-+        def isDisulfideBonded(atom):
-+            for b in self._bonds:
-+                if (atom in b and b[0].name == 'SG' and
-+                    b[1].name == 'SG'):
-+                    return True
-+
-+            return False
- 
-         cyx = [res for res in self.residues() if res.name == 'CYS' and isCyx(res)]
-         atomNames = [[atom.name for atom in res._atoms] for res in cyx]
-         for i in range(len(cyx)):
-             sg1 = cyx[i]._atoms[atomNames[i].index('SG')]
-             pos1 = positions[sg1.index]
-+            candidate_distance, candidate_atom = 0.3*nanometers, None
-             for j in range(i):
-                 sg2 = cyx[j]._atoms[atomNames[j].index('SG')]
-                 pos2 = positions[sg2.index]
-                 delta = [x-y for (x,y) in zip(pos1, pos2)]
-                 distance = sqrt(delta[0]*delta[0] + delta[1]*delta[1] + delta[2]*delta[2])
--                if distance < 0.3*nanometers:
--                    self.addBond(sg1, sg2)
-+                if distance < candidate_distance and not isDisulfideBonded(sg2):
-+                    candidate_distance = distance
-+                    candidate_atom = sg2
-+            # Assign bond to closest pair.
-+            if candidate_atom:
-+                self.addBond(sg1, candidate_atom)
-+
-+
- 
- class Chain(object):
-     """A Chain object represents a chain within a Topology."""

openfold/np/relax/amber_minimize.py

@@ -28,18 +28,10 @@ import openfold.utils.loss as loss
 from openfold.np.relax import cleanup, utils
 import ml_collections
 import numpy as np
-try:
-    # openmm >= 7.6
-    import openmm
-    from openmm import unit
-    from openmm import app as openmm_app
-    from openmm.app.internal.pdbstructure import PdbStructure
-except ImportError:
-    # openmm < 7.6 (requires DeepMind patch)
-    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
 LENGTH = unit.angstroms

openfold/np/relax/cleanup.py

@@ -20,14 +20,8 @@ cases like removing chains of length one (see clean_structure).
 import io
 
 import pdbfixer
-try:
-    # openmm >= 7.6
-    from openmm import app
-    from openmm.app import element
-except ImportError:
-    # openmm < 7.6 (requires DeepMind patch)
-    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):

openfold/np/relax/utils.py

@@ -18,14 +18,8 @@ import io
 from openfold.np import residue_constants
 from Bio import PDB
 import numpy as np
-try:
-    # openmm >= 7.6
-    from openmm import app as openmm_app
-    from openmm.app.internal.pdbstructure import PdbStructure
-except ImportError:
-    # openmm < 7.6 (requires DeepMind patch)
-    from simtk.openmm import app as openmm_app
-    from simtk.openmm.app.internal.pdbstructure import PdbStructure
+from openmm import app as openmm_app
+from openmm.app.internal.pdbstructure import PdbStructure
 
 
 def overwrite_pdb_coordinates(pdb_str: str, pos) -> str: