Merge pull request #404 from OpenBioSim/backport_403

Backport fixes from PRs #400 and #403

Author: lohedges

python/BioSimSpace/Parameters/_parameters.py

@@ -534,57 +534,6 @@ def _parameterise_openff(
             "must be in your PATH."
         ) from None
 
-    # Check the Antechamber version. Open Force Field requires Antechamber >= 22.0.
-    try:
-        # Antechamber returns an exit code of 1 when requesting version information.
-        # As such, we wrap the call within a try-except block in case it fails.
-
-        import shlex as _shlex
-        import subprocess as _subprocess
-
-        # Generate the command-line string. (Antechamber must be in the PATH,
-        # so no need to use AMBERHOME.
-        command = "antechamber -v"
-
-        # Run the command as a subprocess.
-        proc = _subprocess.run(
-            _Utils.command_split(command),
-            shell=False,
-            text=True,
-            stdout=_subprocess.PIPE,
-            stderr=_subprocess.STDOUT,
-        )
-
-        # Get stdout and split into lines.
-        lines = proc.stdout.split("\n")
-
-        # If present, version information is on line 1.
-        string = lines[1]
-
-        # Delete the welcome message.
-        string = string.replace("Welcome to antechamber", "")
-
-        # Extract the version and convert to float.
-        version = float(string.split(":")[0])
-
-        # The version is okay, enable Open Force Field support.
-        if version >= 22:
-            is_compatible = True
-        # Disable Open Force Field support.
-        else:
-            is_compatible = False
-
-        del _shlex
-        del _subprocess
-
-    # Something went wrong, disable Open Force Field support.
-    except:
-        is_compatible = False
-        raise
-
-    if not is_compatible:
-        raise _IncompatibleError(f"'{forcefield}' requires Antechamber >= 22.0")
-
     # Validate arguments.
 
     if not isinstance(molecule, (_Molecule, str)):

python/BioSimSpace/Process/_amber.py

@@ -732,31 +732,58 @@ def getFrame(self, index):
             # Create a copy of the existing system object.
             old_system = self._system.copy()
 
-            # Update the coordinates and velocities and return a mapping between
-            # the molecule indices in the two systems.
-            sire_system, mapping = _SireIO.updateCoordinatesAndVelocities(
-                old_system._sire_object,
-                new_system._sire_object,
-                self._mapping,
-                is_lambda1,
-                self._property_map,
-                self._property_map,
-            )
+            if isinstance(self._protocol, _Protocol._FreeEnergyMixin):
+                # Udpate the coordinates and velocities and return a mapping between
+                # the molecule indices in the two systems.
+                mapping = {
+                    _SireMol.MolIdx(x): _SireMol.MolIdx(x)
+                    for x in range(0, self._squashed_system.nMolecules())
+                }
+                (
+                    self._squashed_system._sire_object,
+                    _,
+                ) = _SireIO.updateCoordinatesAndVelocities(
+                    self._squashed_system._sire_object,
+                    new_system._sire_object,
+                    mapping,
+                    is_lambda1,
+                    self._property_map,
+                    self._property_map,
+                )
+
+                # Update the unsquashed system based on the updated squashed system.
+                old_system = _unsquash(
+                    old_system,
+                    self._squashed_system,
+                    self._mapping,
+                    explicit_dummies=self._explicit_dummies,
+                )
+
+            else:
+                # Update the coordinates and velocities and return a mapping between
+                # the molecule indices in the two systems.
+                sire_system, mapping = _SireIO.updateCoordinatesAndVelocities(
+                    old_system._sire_object,
+                    new_system._sire_object,
+                    self._mapping,
+                    is_lambda1,
+                    self._property_map,
+                    self._property_map,
+                )
 
-            # Update the underlying Sire object.
-            old_system._sire_object = sire_system
+                # Update the underlying Sire object.
+                old_system._sire_object = sire_system
 
-            # Store the mapping between the MolIdx in both systems so we don't
-            # need to recompute it next time.
-            self._mapping = mapping
+                # Store the mapping between the MolIdx in both systems so we don't
+                # need to recompute it next time.
+                self._mapping = mapping
 
             # Update the box information in the original system.
-            if self._has_box:
-                if "space" in new_system._sire_object.propertyKeys():
-                    box = new_system._sire_object.property("space")
-                    old_system._sire_object.setProperty(
-                        self._property_map.get("space", "space"), box
-                    )
+            if "space" in new_system._sire_object.propertyKeys():
+                box = new_system._sire_object.property("space")
+                old_system._sire_object.setProperty(
+                    self._property_map.get("space", "space"), box
+                )
 
             return old_system
 

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

@@ -534,57 +534,6 @@ def _parameterise_openff(
             "must be in your PATH."
         ) from None
 
-    # Check the Antechamber version. Open Force Field requires Antechamber >= 22.0.
-    try:
-        # Antechamber returns an exit code of 1 when requesting version information.
-        # As such, we wrap the call within a try-except block in case it fails.
-
-        import shlex as _shlex
-        import subprocess as _subprocess
-
-        # Generate the command-line string. (Antechamber must be in the PATH,
-        # so no need to use AMBERHOME.
-        command = "antechamber -v"
-
-        # Run the command as a subprocess.
-        proc = _subprocess.run(
-            _Utils.command_split(command),
-            shell=False,
-            text=True,
-            stdout=_subprocess.PIPE,
-            stderr=_subprocess.STDOUT,
-        )
-
-        # Get stdout and split into lines.
-        lines = proc.stdout.split("\n")
-
-        # If present, version information is on line 1.
-        string = lines[1]
-
-        # Delete the welcome message.
-        string = string.replace("Welcome to antechamber", "")
-
-        # Extract the version and convert to float.
-        version = float(string.split(":")[0])
-
-        # The version is okay, enable Open Force Field support.
-        if version >= 22:
-            is_compatible = True
-        # Disable Open Force Field support.
-        else:
-            is_compatible = False
-
-        del _shlex
-        del _subprocess
-
-    # Something went wrong, disable Open Force Field support.
-    except:
-        is_compatible = False
-        raise
-
-    if not is_compatible:
-        raise _IncompatibleError(f"'{forcefield}' requires Antechamber >= 22.0")
-
     # Validate arguments.
 
     if not isinstance(molecule, (_Molecule, str)):

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

@@ -1930,6 +1930,29 @@ def getCurrentPressure(self, time_series=False):
         """
         return self.getPressure(time_series, block=False)
 
+    def getDensity(self, time_series=False, block="AUTO"):
+        """
+        Get the Density.
+
+        Parameters
+        ----------
+
+        time_series : bool
+            Whether to return a list of time series records.
+
+        block : bool
+            Whether to block until the process has finished running.
+
+        Returns
+        -------
+
+        density : :class:`GeneralUnit <BioSimSpace.Units.Mass.kilogram / BioSimSpace.Units.Volume.meter3>`
+            The Density.
+        """
+        return self.getRecord(
+            "DENSITY", time_series, _Units.Mass.kilogram / _Units.Volume.meter3, block
+        )
+
     def getPressureDC(self, time_series=False, block="AUTO"):
         """
         Get the DC pressure.
@@ -2489,7 +2512,7 @@ def _parse_energy_units(text):
                 elif unit == "nm/ps":
                     units.append(_Units.Length.nanometer / _Units.Time.picosecond)
                 elif unit == "kg/m^3":
-                    units.append(_Types._GeneralUnit("kg/m3"))
+                    units.append(_Units.Mass.kilogram / _Units.Volume.meter3)
                 else:
                     units.append(1.0)
                     _warnings.warn(
@@ -2935,6 +2958,11 @@ def _saveMetric(
                             _Units.Temperature.kelvin,
                             "getTemperature",
                         ),
+                        (
+                            "Density (g/cm^3)",
+                            _Units.Mass.gram / _Units.Volume.centimeter3,
+                            "getDensity",
+                        ),
                     ]
                 )
             df = self._convert_datadict_keys(datadict_keys)

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

@@ -32,6 +32,7 @@
 import traceback
 
 import pandas as pd
+from loguru import logger
 
 from .._Utils import _try_import
 
@@ -53,6 +54,7 @@
 from ..Protocol._protocol import Protocol as _Protocol
 from .._SireWrappers import System as _System
 from ..Types._type import Type as _Type
+from ..Types import Time as _Time
 from .. import Units as _Units
 from .. import _Utils
 from ..FreeEnergy._restraint import Restraint as _Restraint
@@ -898,7 +900,7 @@ def setSeed(self, seed):
         else:
             self._seed = seed
 
-    def wait(self, max_time=None):
+    def wait(self, max_time=None, inactivity_timeout: None | _Time = None):
         """
         Wait for the process to finish.
 
@@ -939,11 +941,52 @@ def wait(self, max_time=None):
             self._process.wait(max_time)
 
         else:
-            # Wait for the process to finish.
-            self._process.wait()
+            if inactivity_timeout is None:
+                # Wait for the process to finish.
+                self._process.wait()
 
-            # Store the final run time.
-            self.runTime()
+                # Store the final run time.
+                self.runTime()
+            else:
+                inactivity_timeout = int(inactivity_timeout.milliseconds().value())
+                last_time = self._getLastTime()
+                if last_time is None:
+                    # Wait for the process to finish.
+                    self._process.wait()
+
+                    # Store the final run time.
+                    self.runTime()
+                else:
+                    while self.isRunning():
+                        self._process.wait(inactivity_timeout)
+                        if self.isRunning():
+                            current_time = self._getLastTime()
+                            if current_time > last_time:
+                                logger.info(
+                                    f"Current simulation time ({current_time})."
+                                )
+                                last_time = current_time
+                            else:
+                                logger.warning(
+                                    f"Current simulation time ({current_time}) has not advanced compared "
+                                    f"to the last time ({last_time}). The process "
+                                    f"might have hung and will be killed."
+                                )
+                                with open(
+                                    f"{self.workDir()}/{self._name}.out", "a+"
+                                ) as f:
+                                    f.write("Process Hung. Killed.")
+                                self.kill()
+
+    def _getLastTime(self) -> float | None:
+        """This is the base method in the Process base class.
+        Each subclass, such as AMBER or GROMACS, is expected to override this method
+        to provide their own implementation for returning the current time.
+
+        If this method is not overridden, it will return None,
+        and the `inactivity_timeout` feature will be skipped.
+        """
+        return None
 
     def isQueued(self):
         """

python/BioSimSpace/Sandpit/Exscientia/Units/Volume/__init__.py

@@ -24,11 +24,12 @@
 __author__ = "Lester Hedges"
 __email__ = "lester.hedges@gmail.com"
 
-__all__ = ["meter3", "nanometer3", "angstrom3", "picometer3"]
+__all__ = ["meter3", "nanometer3", "angstrom3", "picometer3", "centimeter3"]
 
 from ...Types import Volume as _Volume
 
 meter3 = _Volume(1, "meter3")
 nanometer3 = _Volume(1, "nanometer3")
 angstrom3 = _Volume(1, "angstrom3")
 picometer3 = _Volume(1, "picometer3")
+centimeter3 = _Volume(1e-6, "meter3")

tests/Parameters/test_parameters.py

@@ -169,8 +169,11 @@ def test_smiles_stereo():
     assert rdmol0_smiles == rdmol1_smiles
 
 
+# This test is currently skipped since it fails with AnteChamber verssion
+# 24.0 and above and there is no way to query the version number from
+# the command-line. (The version output has been removed.)
 @pytest.mark.skipif(
-    has_antechamber is False or has_tleap is False,
+    True or has_antechamber is False or has_tleap is False,
     reason="Requires AmberTools/antechamber and tLEaP to be installed.",
 )
 def test_acdoctor():

tests/Sandpit/Exscientia/Parameters/test_parameters.py

@@ -174,8 +174,11 @@ def test_smiles_stereo():
     assert rdmol0_smiles == rdmol1_smiles
 
 
+# This test is currently skipped since it fails with AnteChamber verssion
+# 24.0 and above and there is no way to query the version number from
+# the command-line. (The version output has been removed.)
 @pytest.mark.skipif(
-    has_antechamber is False or has_tleap is False,
+    True or has_antechamber is False or has_tleap is False,
     reason="Requires AmberTools/antechamber and tLEaP to be installed.",
 )
 def test_acdoctor():

tests/Sandpit/Exscientia/Process/test_gromacs.py

@@ -12,10 +12,11 @@
 from BioSimSpace.Sandpit.Exscientia.Units.Angle import radian
 from BioSimSpace.Sandpit.Exscientia.Units.Energy import kcal_per_mol, kj_per_mol
 from BioSimSpace.Sandpit.Exscientia.Units.Length import angstrom
+from BioSimSpace.Sandpit.Exscientia.Units.Mass import gram
 from BioSimSpace.Sandpit.Exscientia.Units.Pressure import bar
 from BioSimSpace.Sandpit.Exscientia.Units.Temperature import kelvin
 from BioSimSpace.Sandpit.Exscientia.Units.Time import picosecond
-from BioSimSpace.Sandpit.Exscientia.Units.Volume import nanometer3
+from BioSimSpace.Sandpit.Exscientia.Units.Volume import centimeter3, nanometer3
 from tests.Sandpit.Exscientia.conftest import (
     has_alchemtest,
     has_amber,
@@ -359,6 +360,8 @@ def setup(perturbable_system):
             ("getPressureDC", False, -215.590363, bar),
             ("getVolume", True, 44.679958, nanometer3),
             ("getVolume", False, 44.523510, nanometer3),
+            ("getDensity", False, 1.027221558, gram / centimeter3),
+            ("getDensity", True, 1.023624695, gram / centimeter3),
         ],
     )
     def test_get(self, setup, func, time_series, value, unit):
@@ -378,6 +381,7 @@ def test_metric_parquet(self, setup):
         assert np.isclose(df["Volume (nm^3)"][0.0], 44.679958)
         assert np.isclose(df["Pressure (bar)"][0.0], 119.490417)
         assert np.isclose(df["Temperature (kelvin)"][0.0], 306.766907)
+        assert np.isclose(df["Density (g/cm^3)"][0.0], 1.023624695)
 
     def test_dhdl_parquet_exist(self, setup):
         assert Path(f"{setup.workDir()}/dHdl.parquet").exists()