Merge pull request #263 from OpenBioSim/backport_2023.5.1

Backport 2023.5.1

doc/source/changelog.rst

@@ -9,6 +9,19 @@ company supporting open-source development of fostering academic/industrial coll
 within the biomolecular simulation community. Our software is hosted via the `OpenBioSim`
 `GitHub <https://github.com/OpenBioSim/biosimspace>`__ organisation.
 
+`2023.5.1 <https://github.com/openbiosim/biosimspace/compare/2023.5.0...2023.5.1>`_ - Mar 20 2024
+-------------------------------------------------------------------------------------------------
+
+* Fixed path to user links file in the :func:`generateNetwork <BioSimSpace.Align.generateNetwork>` function (`#233 <https://github.com/OpenBioSim/biosimspace/pull/233>`__).
+* Fixed redirection of stderr (`#233 <https://github.com/OpenBioSim/biosimspace/pull/233>`__).
+* Switched to using ``AtomCoordMatcher`` to map parameterised molecules back to their original topology. This resolves issues where atoms moved between residues following parameterisation (`#235 <https://github.com/OpenBioSim/biosimspace/pull/235>`__).
+* Make the GROMACS ``_generate_binary_run_file`` function static so that it can be used when initialising free energy simulations in setup-only mode (`#237 <https://github.com/OpenBioSim/biosimspace/pull/237>`__).
+* Improve error handling and message when attempting to extract an all dummy atom selection (`#251 <https://github.com/OpenBioSim/biosimspace/pull/251>`__).
+* Don't set SOMD specific end-state properties when decoupling a molecule (`#253 <https://github.com/OpenBioSim/biosimspace/pull/253>`__).
+* Only convert to a end-state system when not running a free energy protocol with GROMACS so that hybrid topology isn't lost when using position restraints (`#257 <https://github.com/OpenBioSim/biosimspace/pull/257>`__).
+* Exclude standard free ions from the AMBER position restraint mask (`#260 <https://github.com/OpenBioSim/biosimspace/pull/260>`__).
+* Update the ``BioSimSpace.Types._GeneralUnit.__pow__`` operator to support fractional exponents (`#260 <https://github.com/OpenBioSim/biosimspace/pull/260>`__).
+
 `2023.5.0 <https://github.com/openbiosim/biosimspace/compare/2023.4.1...2023.5.0>`_ - Dec 16 2023
 -------------------------------------------------------------------------------------------------
 

python/BioSimSpace/Process/_gromacs.py

@@ -1995,8 +1995,10 @@ def _add_position_restraints(self):
             # Create a copy of the system.
             system = self._system.copy()
 
-            # Convert to the lambda = 0 state if this is a perturbable system.
-            system = self._checkPerturbable(system)
+            # Convert to the lambda = 0 state if this is a perturbable system and this
+            # isn't a free energy protocol.
+            if not isinstance(self._protocol, _FreeEnergyMixin):
+                system = self._checkPerturbable(system)
 
             # Convert the water model topology so that it matches the GROMACS naming convention.
             system._set_water_topology("GROMACS")

python/BioSimSpace/Protocol/_position_restraint_mixin.py

@@ -1,7 +1,7 @@
 ######################################################################
 # BioSimSpace: Making biomolecular simulation a breeze!
 #
-# Copyright: 2017-2023
+# Copyright: 2017-2024
 #
 # Authors: Lester Hedges <[email protected]>
 #
@@ -214,7 +214,7 @@ def setForceConstant(self, force_constant):
                 )
 
             # Validate the dimensions.
-            if force_constant.dimensions() != (0, 0, 0, 1, -1, 0, -2):
+            if force_constant.dimensions() != (1, 0, -2, 0, 0, -1, 0):
                 raise ValueError(
                     "'force_constant' has invalid dimensions! "
                     f"Expected dimensions are 'M Q-1 T-2', found '{force_constant.unit()}'"

python/BioSimSpace/Sandpit/Exscientia/FreeEnergy/_restraint.py

@@ -1,7 +1,7 @@
 ######################################################################
 # BioSimSpace: Making biomolecular simulation a breeze!
 #
-# Copyright: 2017-2023
+# Copyright: 2017-2024
 #
 # Authors: Lester Hedges <[email protected]>
 #
@@ -174,7 +174,7 @@ def __init__(self, system, restraint_dict, temperature, restraint_type="Boresch"
             for key in ["kthetaA", "kthetaB", "kphiA", "kphiB", "kphiC"]:
                 if restraint_dict["force_constants"][key] != 0:
                     dim = restraint_dict["force_constants"][key].dimensions()
-                    if dim != (-2, 0, 2, 1, -1, 0, -2):
+                    if dim != (1, 2, -2, 0, 0, -1, -2):
                         raise ValueError(
                             f"restraint_dict['force_constants']['{key}'] must be of type "
                             f"'BioSimSpace.Types.Energy'/'BioSimSpace.Types.Angle^2'"
@@ -202,7 +202,7 @@ def __init__(self, system, restraint_dict, temperature, restraint_type="Boresch"
             # Test if the force constant of the bond r1-l1 is the correct unit
             # Such as kcal/mol/angstrom^2
             dim = restraint_dict["force_constants"]["kr"].dimensions()
-            if dim != (0, 0, 0, 1, -1, 0, -2):
+            if dim != (1, 0, -2, 0, 0, -1, 0):
                 raise ValueError(
                     "restraint_dict['force_constants']['kr'] must be of type "
                     "'BioSimSpace.Types.Energy'/'BioSimSpace.Types.Length^2'"
@@ -290,13 +290,13 @@ def __init__(self, system, restraint_dict, temperature, restraint_type="Boresch"
                             "'BioSimSpace.Types.Length'"
                         )
                 if not single_restraint_dict["kr"].dimensions() == (
+                    1,
                     0,
+                    -2,
                     0,
                     0,
-                    1,
                     -1,
                     0,
-                    -2,
                 ):
                     raise ValueError(
                         "distance_restraint_dict['kr'] must be of type "

python/BioSimSpace/Sandpit/Exscientia/FreeEnergy/_restraint_search.py

@@ -1,7 +1,7 @@
 ######################################################################
 # BioSimSpace: Making biomolecular simulation a breeze!
 #
-# Copyright: 2017-2023
+# Copyright: 2017-2024
 #
 # Authors: Lester Hedges <[email protected]>
 #
@@ -641,7 +641,7 @@ def analyse(
 
         if force_constant:
             dim = force_constant.dimensions()
-            if dim != (0, 0, 0, 1, -1, 0, -2):
+            if dim != (1, 0, -2, 0, 0, -1, 0):
                 raise ValueError(
                     "force_constant must be of type "
                     "'BioSimSpace.Types.Energy'/'BioSimSpace.Types.Length^2'"

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

@@ -2099,8 +2099,10 @@ def _add_position_restraints(self, config_options):
             # Create a copy of the system.
             system = self._system.copy()
 
-            # Convert to the lambda = 0 state if this is a perturbable system.
-            system = self._checkPerturbable(system)
+            # Convert to the lambda = 0 state if this is a perturbable system and this
+            # isn't a free energy protocol.
+            if not isinstance(self._protocol, _Protocol._FreeEnergyMixin):
+                system = self._checkPerturbable(system)
 
             # Convert the water model topology so that it matches the GROMACS naming convention.
             system._set_water_topology("GROMACS")

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

@@ -293,9 +293,9 @@ def generateAmberConfig(self, extra_options=None, extra_lines=None):
                                     ]
                                 restraint_mask = "@" + ",".join(restraint_atom_names)
                             elif restraint == "heavy":
-                                restraint_mask = "!:WAT & !@H="
+                                restraint_mask = "!:WAT & !@%NA,CL & !@H="
                             elif restraint == "all":
-                                restraint_mask = "!:WAT"
+                                restraint_mask = "!:WAT & !@%NA,CL"
 
                         # We can't do anything about a custom restraint, since we don't
                         # know anything about the atoms.

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

@@ -185,7 +185,7 @@ def setForceConstant(self, force_constant):
                 )
 
             # Validate the dimensions.
-            if force_constant.dimensions() != (0, 0, 0, 1, -1, 0, -2):
+            if force_constant.dimensions() != (1, 0, -2, 0, 0, -1, 0):
                 raise ValueError(
                     "'force_constant' has invalid dimensions! "
                     f"Expected dimensions are 'M Q-1 T-2', found '{force_constant.unit()}'"

python/BioSimSpace/Sandpit/Exscientia/Types/_angle.py

@@ -1,7 +1,7 @@
 ######################################################################
 # BioSimSpace: Making biomolecular simulation a breeze!
 #
-# Copyright: 2017-2023
+# Copyright: 2017-2024
 #
 # Authors: Lester Hedges <[email protected]>
 #
@@ -52,9 +52,8 @@ class Angle(_Type):
     # Null type unit for avoiding issue printing configargparse help.
     _default_unit = "RADIAN"
 
-    # The dimension mask:
-    #     Angle, Charge, Length, Mass, Quantity, Temperature, Time
-    _dimensions = (1, 0, 0, 0, 0, 0, 0)
+    # The dimension mask.
+    _dimensions = tuple(list(_supported_units.values())[0].dimensions())
 
     def __init__(self, *args):
         """
@@ -188,7 +187,8 @@ def _convert_to(self, unit):
                 "Supported units are: '%s'" % list(self._supported_units.keys())
             )
 
-    def _validate_unit(self, unit):
+    @classmethod
+    def _validate_unit(cls, unit):
         """Validate that the unit are supported."""
 
         # Strip whitespace and convert to upper case.
@@ -210,13 +210,13 @@ def _validate_unit(self, unit):
         unit = unit.replace("AD", "")
 
         # Check that the unit is supported.
-        if unit in self._supported_units:
+        if unit in cls._supported_units:
             return unit
-        elif unit in self._abbreviations:
-            return self._abbreviations[unit]
+        elif unit in cls._abbreviations:
+            return cls._abbreviations[unit]
         else:
             raise ValueError(
-                "Supported units are: '%s'" % list(self._supported_units.keys())
+                "Supported units are: '%s'" % list(cls._supported_units.keys())
             )
 
     @staticmethod

python/BioSimSpace/Sandpit/Exscientia/Types/_area.py

@@ -1,7 +1,7 @@
 ######################################################################
 # BioSimSpace: Making biomolecular simulation a breeze!
 #
-# Copyright: 2017-2023
+# Copyright: 2017-2024
 #
 # Authors: Lester Hedges <[email protected]>
 #
@@ -72,9 +72,8 @@ class Area(_Type):
     # Null type unit for avoiding issue printing configargparse help.
     _default_unit = "ANGSTROM2"
 
-    # The dimension mask:
-    #     Angle, Charge, Length, Mass, Quantity, Temperature, Time
-    _dimensions = (0, 0, 2, 0, 0, 0, 0)
+    # The dimension mask.
+    _dimensions = tuple(list(_supported_units.values())[0].dimensions())
 
     def __init__(self, *args):
         """
@@ -330,7 +329,8 @@ def _convert_to(self, unit):
                 "Supported units are: '%s'" % list(self._supported_units.keys())
             )
 
-    def _validate_unit(self, unit):
+    @classmethod
+    def _validate_unit(cls, unit):
         """Validate that the unit is supported."""
 
         # Strip whitespace and convert to upper case.
@@ -360,13 +360,13 @@ def _validate_unit(self, unit):
             unit = unit[0:index] + unit[index + 1 :] + "2"
 
         # Check that the unit is supported.
-        if unit in self._supported_units:
+        if unit in cls._supported_units:
             return unit
-        elif unit in self._abbreviations:
-            return self._abbreviations[unit]
+        elif unit in cls._abbreviations:
+            return cls._abbreviations[unit]
         else:
             raise ValueError(
-                "Supported units are: '%s'" % list(self._supported_units.keys())
+                "Supported units are: '%s'" % list(cls._supported_units.keys())
             )
 
     @staticmethod

python/BioSimSpace/Sandpit/Exscientia/Types/_charge.py

@@ -1,7 +1,7 @@
 ######################################################################
 # BioSimSpace: Making biomolecular simulation a breeze!
 #
-# Copyright: 2017-2023
+# Copyright: 2017-2024
 #
 # Authors: Lester Hedges <[email protected]>
 #
@@ -58,9 +58,8 @@ class Charge(_Type):
     # Null type unit for avoiding issue printing configargparse help.
     _default_unit = "ELECTRON CHARGE"
 
-    # The dimension mask:
-    #     Angle, Charge, Length, Mass, Quantity, Temperature, Time
-    _dimensions = (0, 1, 0, 0, 0, 0, 0)
+    # The dimension mask.
+    _dimensions = tuple(list(_supported_units.values())[0].dimensions())
 
     def __init__(self, *args):
         """
@@ -182,7 +181,8 @@ def _convert_to(self, unit):
                 "Supported units are: '%s'" % list(self._supported_units.keys())
             )
 
-    def _validate_unit(self, unit):
+    @classmethod
+    def _validate_unit(cls, unit):
         """Validate that the unit are supported."""
 
         # Strip whitespace and convert to upper case.
@@ -213,11 +213,11 @@ def _validate_unit(self, unit):
         unit = unit.replace("COUL", "C")
 
         # Check that the unit is supported.
-        if unit in self._abbreviations:
-            return self._abbreviations[unit]
+        if unit in cls._abbreviations:
+            return cls._abbreviations[unit]
         else:
             raise ValueError(
-                "Supported units are: '%s'" % list(self._supported_units.keys())
+                "Supported units are: '%s'" % list(cls._supported_units.keys())
             )
 
     @staticmethod

python/BioSimSpace/Sandpit/Exscientia/Types/_energy.py

@@ -1,7 +1,7 @@
 ######################################################################
 # BioSimSpace: Making biomolecular simulation a breeze!
 #
-# Copyright: 2017-2023
+# Copyright: 2017-2024
 #
 # Authors: Lester Hedges <[email protected]>
 #
@@ -68,9 +68,8 @@ class Energy(_Type):
     # Null type unit for avoiding issue printing configargparse help.
     _default_unit = "KILO CALORIES PER MOL"
 
-    # The dimension mask:
-    #     Angle, Charge, Length, Mass, Quantity, Temperature, Time
-    _dimensions = (0, 0, 2, 1, -1, 0, -2)
+    # The dimension mask.
+    _dimensions = tuple(list(_supported_units.values())[0].dimensions())
 
     def __init__(self, *args):
         """
@@ -213,7 +212,8 @@ def _convert_to(self, unit):
                 "Supported units are: '%s'" % list(self._supported_units.keys())
             )
 
-    def _validate_unit(self, unit):
+    @classmethod
+    def _validate_unit(cls, unit):
         """Validate that the unit are supported."""
 
         # Strip whitespace and convert to upper case.
@@ -235,11 +235,11 @@ def _validate_unit(self, unit):
         unit = unit.replace("JOULES", "J")
 
         # Check that the unit is supported.
-        if unit in self._abbreviations:
-            return self._abbreviations[unit]
+        if unit in cls._abbreviations:
+            return cls._abbreviations[unit]
         else:
             raise ValueError(
-                "Supported units are: '%s'" % list(self._supported_units.keys())
+                "Supported units are: '%s'" % list(cls._supported_units.keys())
             )
 
     @staticmethod