Merge pull request #99 from volkamerlab/theseus-mmligner

Check availability of theseus/mmligner executables

opencadd/structure/superposition/engines/base.py

@@ -27,8 +27,15 @@ def calculate(self, structures, *args, **kwargs):
             - ``metadata``: Contextual information provided by the method
 
         """
-        assert len(structures) == 2
+        self._safety_checks()
+        assert (
+            len(structures) == 2,
+            "This method can only be used for two structures at the same time, for now",
+        )
         return self._calculate(structures, *args, **kwargs)
 
     def _calculate(self, structures, *args, **kwargs):
         raise NotImplementedError("Reimplement in your subclass")
+
+    def _safety_checks(self):
+        raise NotImplementedError("Reimplement in your subclass")

opencadd/structure/superposition/engines/mda.py

@@ -94,6 +94,13 @@ def __init__(
         self.superposition_weights = superposition_weights
         self.superposition_delta_mass_tolerance = superposition_delta_mass_tolerance
 
+    def _safety_checks(self):
+        """
+        Check for `mda` installation passes; added here only for consistency across the engines.
+        """
+
+        pass
+
     def _calculate(self, structures, *args, **kwargs):
         """
 
@@ -109,10 +116,7 @@ def _calculate(self, structures, *args, **kwargs):
             rmsd
             metadata
         """
-        if len(structures) > 2:
-            raise NotImplementedError(
-                "This method can only be used for two structures at the same time, for now"
-            )
+
         ref_universe, mob_universe = structures
 
         # Get matching atoms

opencadd/structure/superposition/engines/mmligner.py

@@ -25,6 +25,7 @@
 import sys
 import subprocess
 import logging
+from distutils.spawn import find_executable
 
 import numpy as np
 import biotite.sequence.io.fasta as fasta
@@ -57,6 +58,21 @@ def __init__(self, executable=None, protein_selector="protein"):
             "Current MMLigner wrappers produces accurate RMSD values but slightly shifted structures!"
         )
 
+    def _safety_checks(self):
+        """
+        Check if `mmligner` is installed (executable found?).
+
+        Raises
+        ------
+        OSError
+            Raises error if executable `mmligner` cannot be found.
+        """
+
+        mmligner = find_executable("mmligner")
+        if mmligner is None:
+            raise OSError("mmligner cannot be located. Is it installed?")
+        # proceed normally
+
     def _calculate(self, structures, *args, **kwargs):
         """
         Calculates the superposition of two protein structures.

opencadd/structure/superposition/engines/theseus.py

@@ -21,6 +21,7 @@
 import os
 import subprocess
 import logging
+from distutils.spawn import find_executable
 
 import numpy as np
 
@@ -56,6 +57,21 @@ def __init__(self, alignment_max_iterations: int = 32, statistics_only: bool = F
         self._alignment_executable = "muscle"
         self._theseus_transformation_file = "theseus_transf.txt"
 
+    def _safety_checks(self):
+        """
+        Check if `theseus` is installed (executable found?).
+
+        Raises
+        ------
+        OSError
+            Raises error if executable `theseus` cannot be found.
+        """
+
+        theseus = find_executable("theseus")
+        if theseus is None:
+            raise OSError("theseus cannot be located. Is it installed?")
+        # proceed normally
+
     def _calculate(self, structures, *args, **kwargs) -> dict:
         """
         Align the sequences with an alignment tool (``muscle``)