Post merge fixes.

Author: lohedges

nodes/playground/BSSSetup/FESetup_parser.py

@@ -7,7 +7,6 @@ def parse_fesetup_input(filename):
 
 
 def validate_fesetup_input(fe_dictionary):
-
     return False
 
 

python/BioSimSpace/Sandpit/Exscientia/Process/_amber.py

@@ -283,7 +283,7 @@ def __init__(
         self._config_file = "%s/%s.cfg" % (self._work_dir, name)
 
         # Set the reference system
-        self._ref_file = f"{self._work_dir}/{name}_ref.rst7"
+        self._ref_file = f"{self._work_dir}/{name}_ref"
         self._ref_system = reference_system
 
         # Create the list of input files.
@@ -302,8 +302,9 @@ def _setup(self):
 
         # Create the reference file
         if self._ref_system is not None and self._protocol.getRestraint() is not None:
-            self._write_system(self._ref_system, coord_file=self._ref_file)
+            self._write_system(self._ref_system, ref_file=self._ref_file)
         else:
+            self._ref_file += ".rst7"
             _shutil.copy(self._rst_file, self._ref_file)
 
         # Generate the AMBER configuration file.
@@ -320,7 +321,7 @@ def _setup(self):
         # Return the list of input files.
         return self._input_files
 
-    def _write_system(self, system, coord_file=None, topol_file=None):
+    def _write_system(self, system, coord_file=None, topol_file=None, ref_file=None):
         """Validates an input system and makes some internal modifications to it,
         if needed, before writing it out to a coordinate and/or a topology file.
 
@@ -336,6 +337,9 @@ def _write_system(self, system, coord_file=None, topol_file=None):
         topol_file : str or None
             The topology file to which to write out the system.
 
+        ref_file : str or None
+            The coordinate file for the reference system used for position restraints.
+
         Returns
         -------
 
@@ -377,6 +381,21 @@ def _write_system(self, system, coord_file=None, topol_file=None):
                 else:
                     raise IOError(msg) from None
 
+        # RST file (reference for position restraints).
+        if ref_file is not None:
+            try:
+                _IO.saveMolecules(
+                    self._ref_file, system, "rst7", property_map=self._property_map
+                )
+                self._ref_file += ".rst7"
+                self._input_files.append(self._ref_file)
+            except Exception as e:
+                msg = "Failed to write system to 'RST7' format."
+                if _isVerbose():
+                    raise IOError(msg) from e
+                else:
+                    raise IOError(msg) from None
+
         # PRM file (topology).
         if topol_file is not None:
             try:

python/BioSimSpace/Sandpit/Exscientia/Process/_gromacs.py

@@ -208,7 +208,7 @@ def __init__(
         self._config_file = "%s/%s.mdp" % (self._work_dir, name)
 
         # Set the reference system
-        self._ref_file = f"{self._work_dir}/{name}_ref.gro"
+        self._ref_file = f"{self._work_dir}/{name}_ref"
         self._ref_system = reference_system
 
         # Create the list of input files.
@@ -243,8 +243,9 @@ def _setup(self):
 
         # Create the reference file
         if self._ref_system is not None and self._protocol.getRestraint() is not None:
-            self._write_system(self._ref_system, coord_file=self._ref_file)
+            self._write_system(self._ref_system, ref_file=self._ref_file)
         else:
+            self._ref_file += ".gro"
             _shutil.copy(self._gro_file, self._ref_file)
 
         # Create the binary input file name.
@@ -265,7 +266,7 @@ def _setup(self):
         # Return the list of input files.
         return self._input_files
 
-    def _write_system(self, system, coord_file=None, topol_file=None):
+    def _write_system(self, system, coord_file=None, topol_file=None, ref_file=None):
         """Validates an input system and makes some internal modifications to it,
         if needed, before writing it out to a coordinate and/or a topology file.
 
@@ -280,6 +281,9 @@ def _write_system(self, system, coord_file=None, topol_file=None):
 
         topol_file : str or None
             The topology file to which to write out the system.
+
+        ref_file : str or None
+            The file to which to write out the reference system for position restraints.
         """
         # Create a copy of the system.
         system = system.copy()
@@ -328,17 +332,23 @@ def _write_system(self, system, coord_file=None, topol_file=None):
                 self._property_map.get("space", "space"), space
             )
 
-        # GRO87 file.
+        # GRO87 coordinate files.
         if coord_file is not None:
             _IO.saveMolecules(
                 coord_file, system, "gro87", property_map=self._property_map
             )
             self._gro_file += ".gro"
             self._input_files.append(self._gro_file)
 
+        # GRO87 reference files.
+        if ref_file is not None:
+            _IO.saveMolecules(
+                ref_file, system, "gro87", property_map=self._property_map
+            )
+            self._ref_file += ".gro"
+
         # TOP file.
         if topol_file is not None:
-            top.writeToFile(topol_file)
             _IO.saveMolecules(
                 topol_file, system, "grotop", property_map=self._property_map
             )
@@ -2260,7 +2270,6 @@ def _sanitise_energy_term(key):
         -------
         str
             The formatted name of the energy term.
-
         """
         # Convert to upper case.
         key = key.upper()

python/BioSimSpace/Sandpit/Exscientia/Protocol/_position_restraint.py

@@ -136,7 +136,7 @@ def getForceConstant(self):
         Returns
         -------
 
-        force_constant :class:`GeneralUnit <BioSimSpace.Types._GeneralUnit>`
+        force_constant : class:`GeneralUnit <BioSimSpace.Types._GeneralUnit>`
             The force constant for the restraint, in units of
             kcal_per_mol/angstrom**2.
         """

python/BioSimSpace/_Config/__init__.py

@@ -22,7 +22,6 @@
 """
 .. currentmodule:: BioSimSpace._Config
 
-
 Classes
 =======
 

python/BioSimSpace/_Config/_config.py

@@ -128,7 +128,7 @@ def reportInterval(self):
 
     def isRestart(self):
         """
-        Return whether this is a restart simulation
+        Return whether this is a restart simulation.
 
         Returns
         -------

test/Align/test_align.py

@@ -9,14 +9,24 @@
 url = BSS.tutorialUrl()
 
 
-def test_flex_align():
-    # Load the ligands.
-    s0 = BSS.IO.readMolecules([f"{url}/ligand01.prm7.bz2", f"{url}/ligand01.rst7.bz2"])
-    s1 = BSS.IO.readMolecules([f"{url}/ligand02.prm7.bz2", f"{url}/ligand02.rst7.bz2"])
+@pytest.fixture(scope="session")
+def system0():
+    return BSS.IO.readMolecules(
+        [f"{url}/ligand01.prm7.bz2", f"{url}/ligand01.rst7.bz2"]
+    )
+
+
+@pytest.fixture(scope="session")
+def system1():
+    return BSS.IO.readMolecules(
+        [f"{url}/ligand02.prm7.bz2", f"{url}/ligand02.rst7.bz2"]
+    )
+
 
+def test_flex_align(system0, system1):
     # Extract the molecules.
-    m0 = s0.getMolecules()[0]
-    m1 = s1.getMolecules()[0]
+    m0 = system0.getMolecules()[0]
+    m1 = system1.getMolecules()[0]
 
     # Get the best mapping between the molecules that contains the prematch.
     mapping = BSS.Align.matchAtoms(
@@ -49,14 +59,10 @@ def test_flex_align():
 
 # Parameterise the function with a set of valid atom pre-matches.
 @pytest.mark.parametrize("prematch", [{3: 1}, {5: 9}, {4: 5}, {1: 0}])
-def test_prematch(prematch):
-    # Load the ligands.
-    s0 = BSS.IO.readMolecules([f"{url}/ligand01.prm7.bz2", f"{url}/ligand01.rst7.bz2"])
-    s1 = BSS.IO.readMolecules([f"{url}/ligand02.prm7.bz2", f"{url}/ligand02.rst7.bz2"])
-
+def test_prematch(system0, system1, prematch):
     # Extract the molecules.
-    m0 = s0.getMolecules()[0]
-    m1 = s1.getMolecules()[0]
+    m0 = system0.getMolecules()[0]
+    m1 = system1.getMolecules()[0]
 
     # Get the best mapping between the molecules that contains the prematch.
     mapping = BSS.Align.matchAtoms(
@@ -70,14 +76,10 @@ def test_prematch(prematch):
 
 # Parameterise the function with a set of invalid atom pre-matches.
 @pytest.mark.parametrize("prematch", [{-1: 1}, {50: 9}, {4: 48}, {1: -1}])
-def test_invalid_prematch(prematch):
-    # Load the ligands.
-    s0 = BSS.IO.readMolecules([f"{url}/ligand01.prm7.bz2", f"{url}/ligand01.rst7.bz2"])
-    s1 = BSS.IO.readMolecules([f"{url}/ligand02.prm7.bz2", f"{url}/ligand02.rst7.bz2"])
-
+def test_invalid_prematch(system0, system1, prematch):
     # Extract the molecules.
-    m0 = s0.getMolecules()[0]
-    m1 = s1.getMolecules()[0]
+    m0 = system0.getMolecules()[0]
+    m1 = system1.getMolecules()[0]
 
     # Assert that the invalid prematch raises a ValueError.
     with pytest.raises(ValueError):

test/Sandpit/Exscientia/Align/test_align.py

@@ -10,14 +10,24 @@
 url = BSS.tutorialUrl()
 
 
-def test_flex_align():
-    # Load the ligands.
-    s0 = BSS.IO.readMolecules([f"{url}/ligand01.prm7.bz2", f"{url}/ligand01.rst7.bz2"])
-    s1 = BSS.IO.readMolecules([f"{url}/ligand02.prm7.bz2", f"{url}/ligand02.rst7.bz2"])
+@pytest.fixture(scope="session")
+def system0():
+    return BSS.IO.readMolecules(
+        [f"{url}/ligand01.prm7.bz2", f"{url}/ligand01.rst7.bz2"]
+    )
+
+
+@pytest.fixture(scope="session")
+def system1():
+    return BSS.IO.readMolecules(
+        [f"{url}/ligand02.prm7.bz2", f"{url}/ligand02.rst7.bz2"]
+    )
+
 
+def test_flex_align(system0, system1):
     # Extract the molecules.
-    m0 = s0.getMolecules()[0]
-    m1 = s1.getMolecules()[0]
+    m0 = system0.getMolecules()[0]
+    m1 = system1.getMolecules()[0]
 
     # Get the best mapping between the molecules that contains the prematch.
     mapping = BSS.Align.matchAtoms(
@@ -50,14 +60,10 @@ def test_flex_align():
 
 # Parameterise the function with a set of valid atom pre-matches.
 @pytest.mark.parametrize("prematch", [{3: 1}, {5: 9}, {4: 5}, {1: 0}])
-def test_prematch(prematch):
-    # Load the ligands.
-    s0 = BSS.IO.readMolecules([f"{url}/ligand01.prm7.bz2", f"{url}/ligand01.rst7.bz2"])
-    s1 = BSS.IO.readMolecules([f"{url}/ligand02.prm7.bz2", f"{url}/ligand02.rst7.bz2"])
-
+def test_prematch(system0, system1, prematch):
     # Extract the molecules.
-    m0 = s0.getMolecules()[0]
-    m1 = s1.getMolecules()[0]
+    m0 = system0.getMolecules()[0]
+    m1 = system1.getMolecules()[0]
 
     # Get the best mapping between the molecules that contains the prematch.
     mapping = BSS.Align.matchAtoms(
@@ -71,14 +77,10 @@ def test_prematch(prematch):
 
 # Parameterise the function with a set of invalid atom pre-matches.
 @pytest.mark.parametrize("prematch", [{-1: 1}, {50: 9}, {4: 48}, {1: -1}])
-def test_invalid_prematch(prematch):
-    # Load the ligands.
-    s0 = BSS.IO.readMolecules([f"{url}/ligand01.prm7.bz2", f"{url}/ligand01.rst7.bz2"])
-    s1 = BSS.IO.readMolecules([f"{url}/ligand02.prm7.bz2", f"{url}/ligand02.rst7.bz2"])
-
+def test_invalid_prematch(system0, system1, prematch):
     # Extract the molecules.
-    m0 = s0.getMolecules()[0]
-    m1 = s1.getMolecules()[0]
+    m0 = system0.getMolecules()[0]
+    m1 = system1.getMolecules()[0]
 
     # Assert that the invalid prematch raises a ValueError.
     with pytest.raises(ValueError):
@@ -264,16 +266,14 @@ def test_merge():
 
 @pytest.fixture(scope="module")
 def roi_mol0():
-    return BSS.IO.readMolecules(
-        BSS.IO.glob("test/Sandpit/Exscientia/input/ligands/wild*")
-    )[0]
+    files = BSS.IO.expand(url, ["wild.prmtop", "wild.inpcrd"], ".bz2")
+    return BSS.IO.readMolecules(files)[0]
 
 
 @pytest.fixture(scope="module")
 def roi_mol1():
-    return BSS.IO.readMolecules(
-        BSS.IO.glob("test/Sandpit/Exscientia/input/ligands/mutated*")
-    )[0]
+    files = BSS.IO.expand(url, ["mutated.prmtop", "mutated.inpcrd"], ".bz2")
+    return BSS.IO.readMolecules(files)[0]
 
 
 @pytest.fixture(scope="module")

test/Sandpit/Exscientia/IO/test_openff_gromacs.py

@@ -44,8 +44,8 @@ def test_molecule_combine():
     protocol = BSS.Protocol.Minimisation(steps=1)
 
     # Create processes to single point calculations with GROMACS.
-    p0 = BSS.Process.Gromacs(m0.toSystem(), protocol, extra_options={"nsteps" : 0})
-    p1 = BSS.Process.Gromacs(m1.toSystem(), protocol, extra_options={"nsteps" : 0})
+    p0 = BSS.Process.Gromacs(m0.toSystem(), protocol, extra_options={"nsteps": 0})
+    p1 = BSS.Process.Gromacs(m1.toSystem(), protocol, extra_options={"nsteps": 0})
     p01 = BSS.Process.Gromacs(
         (m0 + m1).toSystem(), protocol, extra_options={"nsteps": 0}
     )

test/Sandpit/Exscientia/Process/test_gromacs.py

@@ -1,4 +1,5 @@
 import numpy as np
+import shutil
 import pytest
 
 import BioSimSpace.Sandpit.Exscientia as BSS
@@ -214,17 +215,17 @@ def run_process(system, protocol, **kwargs):
 class TestGetRecord:
     @staticmethod
     @pytest.fixture()
-    def setup(system, tmpdir_factory):
-        workdir = tmpdir_factory.mktemp("out")
-        (workdir / "gromacs.edr").mklinkto(
-            "test/Sandpit/Exscientia/output/gromacs/gromacs.edr"
-        )
+    def setup(system):
         protocol = BSS.Protocol.Production(
             runtime=BSS.Types.Time(60, "picosecond"),
             timestep=BSS.Types.Time(4, "femtosecond"),
             report_interval=200,
         )
-        process = BSS.Process.Gromacs(system, protocol, work_dir=str(workdir))
+        process = BSS.Process.Gromacs(system, protocol)
+        shutil.copyfile(
+            "test/Sandpit/Exscientia/output/gromacs.edr",
+            process.workDir() + "/gromacs.edr",
+        )
         process._update_energy_dict()
         return process