Merge pull request #428 from OpenBioSim/fix_426_427

Fix issues #426 and #427

Author: lohedges

python/BioSimSpace/Align/_squash.py

@@ -1,7 +1,6 @@
 import itertools as _it
 import numpy as _np
 import os as _os
-import parmed as _pmd
 import shutil as _shutil
 import tempfile
 
@@ -164,6 +163,8 @@ def _squash_molecule(molecule, explicit_dummies=False):
 
     # Perform the multi-residue squashing with ParmEd as it is much easier and faster.
     with tempfile.TemporaryDirectory() as tempdir:
+        import parmed as _pmd
+
         # Load in ParmEd.
         _saveMolecules(f"{tempdir}/temp", mol0 + mol1, "prm7,rst7")
         _shutil.move(f"{tempdir}/temp.prm7", f"{tempdir}/temp.parm7")

python/BioSimSpace/Parameters/_Protocol/_openforcefield.py

@@ -33,6 +33,7 @@
 # To override any protocols, just implement a custom "run" method in any
 # of the classes.
 
+from ..._Exceptions import MissingSoftwareError as _MissingSoftwareError
 from ..._Utils import _try_import, _have_imported
 
 import os as _os
@@ -106,6 +107,15 @@
     _OpenFFMolecule = _openff
     _Forcefield = _openff
 
+
+try:
+    from sire.legacy.Base import findExe as _findExe
+
+    _findExe("antechamber")
+    _has_antechamber = True
+except:
+    _has_antechamber = False
+
 # Reset stderr.
 _sys.stderr = _orig_stderr
 del _sys, _orig_stderr
@@ -269,6 +279,12 @@ def run(self, molecule, work_dir=None, queue=None):
                     raise _ThirdPartyError(msg) from None
             charge_from_molecules = [off_molecule]
         else:
+            if not _has_antechamber:
+                raise _MissingSoftwareError(
+                    f"{self._forcefield} is not supported. AnteChamber "
+                    "(http://ambermd.org) or OpenFF-NAGL are needed for "
+                    "charge calculation."
+                ) from None
             charge_from_molecules = None
 
         # Extract the molecular topology.

python/BioSimSpace/Parameters/_parameters.py

@@ -520,18 +520,6 @@ def _parameterise_openff(
         parameterisation is complete and get the parameterised molecule.
     """
 
-    from sire.legacy.Base import findExe as _findExe
-
-    try:
-        _findExe("antechamber")
-    except:
-        raise _MissingSoftwareError(
-            f"'{forcefield}' is not supported. AmberTools "
-            "(http://ambermd.org) is needed for charge "
-            "calculation and 'antechamber' executable "
-            "must be in your PATH."
-        ) from None
-
     # Validate arguments.
 
     if not isinstance(molecule, (_Molecule, str)):

python/BioSimSpace/Sandpit/Exscientia/Align/_squash.py

@@ -4,7 +4,6 @@
 import tempfile
 
 import numpy as _np
-import parmed as _pmd
 from sire.legacy import IO as _SireIO
 from sire.legacy import Mol as _SireMol
 
@@ -158,6 +157,8 @@ def _squash_molecule(molecule, explicit_dummies=False):
 
     # Perform the multi-residue squashing with ParmEd as it is much easier and faster.
     with tempfile.TemporaryDirectory() as tempdir:
+        import parmed as _pmd
+
         # Load in ParmEd.
         _saveMolecules(f"{tempdir}/temp", mol0 + mol1, "prm7,rst7")
         _shutil.move(f"{tempdir}/temp.prm7", f"{tempdir}/temp.parm7")

python/BioSimSpace/Sandpit/Exscientia/Parameters/_Protocol/_openforcefield.py

@@ -33,6 +33,7 @@
 # To override any protocols, just implement a custom "run" method in any
 # of the classes.
 
+from ..._Exceptions import MissingSoftwareError as _MissingSoftwareError
 from ..._Utils import _try_import, _have_imported
 
 import os as _os
@@ -106,6 +107,15 @@
     _OpenFFMolecule = _openff
     _Forcefield = _openff
 
+
+try:
+    from sire.legacy.Base import findExe as _findExe
+
+    _findExe("antechamber")
+    _has_antechamber = True
+except:
+    _has_antechamber = False
+
 # Reset stderr.
 _sys.stderr = _orig_stderr
 del _sys, _orig_stderr
@@ -269,6 +279,12 @@ def run(self, molecule, work_dir=None, queue=None):
                     raise _ThirdPartyError(msg) from None
             charge_from_molecules = [off_molecule]
         else:
+            if not _has_antechamber:
+                raise _MissingSoftwareError(
+                    f"{self._forcefield} is not supported. AnteChamber "
+                    "(http://ambermd.org) or OpenFF-NAGL are needed for "
+                    "charge calculation."
+                ) from None
             charge_from_molecules = None
 
         # Extract the molecular topology.

python/BioSimSpace/Sandpit/Exscientia/Parameters/_parameters.py

@@ -520,18 +520,6 @@ def _parameterise_openff(
         parameterisation is complete and get the parameterised molecule.
     """
 
-    from sire.legacy.Base import findExe as _findExe
-
-    try:
-        _findExe("antechamber")
-    except:
-        raise _MissingSoftwareError(
-            f"'{forcefield}' is not supported. AmberTools "
-            "(http://ambermd.org) is needed for charge "
-            "calculation and 'antechamber' executable "
-            "must be in your PATH."
-        ) from None
-
     # Validate arguments.
 
     if not isinstance(molecule, (_Molecule, str)):