Feature 106

corelib/src/libs/SireIO/amberrst7.cpp

@@ -1175,9 +1175,15 @@ SireMaths::Vector AmberRst7::boxDimensions() const
 }
 
 /** Return the parsed box angles */
-SireMaths::Vector AmberRst7::boxAngles() const
+QVector<SireUnits::Dimension::Angle> AmberRst7::boxAngles() const
 {
-    return box_angs;
+    QVector<SireUnits::Dimension::Angle> angs(3);
+
+    angs[0] = box_angs.x() * SireUnits::degree;
+    angs[1] = box_angs.y() * SireUnits::degree;
+    angs[2] = box_angs.z() * SireUnits::degree;
+
+    return angs;
 }
 
 /** Return this parser constructed from the passed filename */

corelib/src/libs/SireIO/amberrst7.h

@@ -32,6 +32,8 @@
 
 #include "SireMaths/vector.h"
 
+#include "SireUnits/dimensions.h"
+
 SIRE_BEGIN_HEADER
 
 namespace SireIO
@@ -112,7 +114,7 @@ namespace SireIO
         QVector<SireMaths::Vector> velocities() const;
 
         SireMaths::Vector boxDimensions() const;
-        SireMaths::Vector boxAngles() const;
+        QVector<SireUnits::Dimension::Angle> boxAngles() const;
 
     protected:
         void addToSystem(SireSystem::System &system, const PropertyMap &map) const;

corelib/src/libs/SireSystem/forcefieldinfo.cpp

@@ -450,6 +450,14 @@ void ForceFieldInfo::setCutoffType(QString cutoff_type)
 void ForceFieldInfo::setCutoffType(QString s_cutoff_type,
                                    const PropertyMap &map)
 {
+    if (s_cutoff_type == "auto")
+    {
+        if (this->space().isPeriodic())
+            s_cutoff_type = "PME";
+        else
+            s_cutoff_type = "RF";
+    }
+
     auto cutoff_type = string_to_cutoff_type(s_cutoff_type);
 
     if (cutoff_type == NO_CUTOFF)

doc/source/changelog.rst

@@ -15,6 +15,24 @@ organisation on `GitHub <https://github.com/openbiosim/sire>`__.
 `2023.5.0 <https://github.com/openbiosim/sire/compare/2023.4.0...2023.5.0>`__ - December 2023
 ---------------------------------------------------------------------------------------------
 
+* Added a new :mod:`sire.options` module that contains new
+  :cls:`sire.options.Option` objects to represent configurable options.
+  These include documentation, and make it easier to validate and expose
+  possible values of configurable options. The API docs for
+  :cls:`~sire.options.Option` shows how to create your own Option type.
+  The unit test in ``tests/options/test_options.py`` show how to use
+  the options. This is integrated into the sire/OpenMM layer.
+
+* Have :cls:`~sire.io.parser.RST7` return a list of angles from the
+  ``box_angles()`` function, rather than a :cls:`~sire.maths.Vector`.
+  This prevents the confusing behaviour where the angles are wrongly
+  shown in units of angstroms... This fixes issues #106.
+
+* Please add an item to this changelog when you create your PR
+
+`2023.4.1 <https://github.com/openbiosim/sire/compare/2023.4.0...2023.4.1>`__ - October 2023
+---------------------------------------------------------------------------------------------
+
 * Fixed regression introduced in 2023.4.0 that meant that removed the constraints
   from water molecules that had no internal bonds. These waters would blow up
   as there was nothing holding them together. The need for these constraints is
@@ -35,8 +53,6 @@ organisation on `GitHub <https://github.com/openbiosim/sire>`__.
 * Fixed an issue where the vacuum dynamics and minimisation simulations still
   had a spurious periodic box added when ``.commit()`` was called.
 
-* Please add an item to this changelog when you create your PR
-
 `2023.4.0 <https://github.com/openbiosim/sire/compare/2023.3.0...2023.4.0>`__ - October 2023
 --------------------------------------------------------------------------------------------
 

recipes/sire/template.yaml

@@ -2,7 +2,7 @@
 
 package:
   name: {{ name }}
-  version: {{ environ.get('GIT_DESCRIBE_TAG', 'PR') }}
+  version: {{ environ.get('GIT_DESCRIBE_TAG', 'PR').replace('-','') }}
 
 source:
   git_url: SIRE_REMOTE

src/sire/CMakeLists.txt

@@ -103,6 +103,7 @@ add_subdirectory (mm)
 add_subdirectory (mol)
 add_subdirectory (morph)
 add_subdirectory (move)
+add_subdirectory (options)
 add_subdirectory (restraints)
 add_subdirectory (search)
 add_subdirectory (stream)

src/sire/__init__.py

@@ -697,6 +697,7 @@ def _convert(id):
     mol = _lazy_import.lazy_module("sire.mol")
     morph = _lazy_import.lazy_module("sire.morph")
     move = _lazy_import.lazy_module("sire.move")
+    options = _lazy_import.lazy_module("sire.options")
     qt = _lazy_import.lazy_module("sire.qt")
     restraints = _lazy_import.lazy_module("sire.restraints")
     search = _lazy_import.lazy_module("sire.search")

src/sire/base/__init__.py

@@ -122,6 +122,25 @@ def __propertymap_set(obj, key, value):
     PropertyMap.__orig__set = PropertyMap.set
     PropertyMap.set = __propertymap_set
 
+    def __propertymap_get_string(obj, key: str):
+        """
+        Return the string value associated with the passed 'key'
+
+        This returns 'key' if there is no value associated
+        """
+        key = str(key)
+        if obj.specified(key):
+            val = obj[key]
+
+            if val.has_value():
+                return val.value().as_string()
+            else:
+                return val.source()
+        else:
+            return key
+
+    PropertyMap.get_string = __propertymap_get_string
+
 
 def create_map(values, extras=None):
     """Construct a PropertyMap from the

src/sire/mol/__init__.py

@@ -1411,6 +1411,7 @@ def _dynamics(
     constraint=None,
     perturbable_constraint=None,
     include_constrained_energies: bool = True,
+    integrator=None,
     schedule=None,
     lambda_value=None,
     swap_end_states=None,
@@ -1486,6 +1487,13 @@ def _dynamics(
         energy of the constrained degrees of freedom are not included
         in the total energy, and their forces are not evaluated.
 
+    integrator: str
+        The type of integrator to use, e.g. `langevin`, `verlet` etc.
+        See https://sire.openbiosim.org/cheatsheet/openmm.html#choosing-options
+        for the full list of options. This will be automatically
+        set to `langevin_middle` (NVT/NPT) or `verlet` (NVE) depending
+        on the ensemble if this is not set (or is set to `auto`)
+
     schedule: sire.cas.LambdaSchedule
         The schedule used to control how perturbable forcefield parameters
         should be morphed as a function of lambda. If this is not set
@@ -1613,14 +1621,7 @@ def _dynamics(
         cutoff = 7.5 * angstrom
 
     if cutoff_type is None and not map.specified("cutoff_type"):
-        try:
-            if view.property(map["space"]).is_periodic():
-                cutoff_type = "PME"
-            else:
-                cutoff_type = "RF"
-        except Exception:
-            # no space, use RF
-            cutoff_type = "RF"
+        cutoff_type = "auto"
 
     if timestep is None and not map.specified("timestep"):
         from ..units import femtosecond
@@ -1646,27 +1647,7 @@ def _dynamics(
         map.set("save_velocities", save_velocities)
 
     if constraint is None and not map.specified("constraint"):
-        from ..units import femtosecond
-
-        if timestep is None:
-            # it must be in the map
-            timestep = map["timestep"].value()
-
-        if timestep > 4 * femtosecond:
-            # need constraint on everything
-            constraint = "bonds-h-angles"
-
-        elif timestep > 2 * femtosecond:
-            # need constraint on everything
-            constraint = "h-bonds-h-angles"
-
-        elif timestep > 1 * femtosecond:
-            # need it just on H bonds and angles
-            constraint = "h-bonds"
-
-        else:
-            # can get away with no constraints
-            constraint = "none"
+        constraint = "auto"
 
     if perturbable_constraint is not None:
         perturbable_constraint = str(perturbable_constraint).lower()
@@ -1691,6 +1672,9 @@ def _dynamics(
     if platform is not None:
         map.set("platform", str(platform))
 
+    if integrator is not None:
+        map.set("integrator", str(integrator))
+
     return Dynamics(
         view,
         cutoff=cutoff,
@@ -1878,14 +1862,7 @@ def _minimisation(
         cutoff = 7.5 * angstrom
 
     if cutoff_type is None and not map.specified("cutoff_type"):
-        try:
-            if view.property(map["space"]).is_periodic():
-                cutoff_type = "PME"
-            else:
-                cutoff_type = "RF"
-        except Exception:
-            # no space, use RF
-            cutoff_type = "RF"
+        cutoff_type = "auto"
 
     if device is not None:
         map.set("device", str(device))

src/sire/mol/_dynamics.py

@@ -381,19 +381,13 @@ def constraint(self):
         if self.is_null():
             return None
         else:
-            if self._map.specified("constraint"):
-                return self._map["constraint"].source()
-            else:
-                return "none"
+            return self._omm_mols.get_constraint()
 
     def perturbable_constraint(self):
         if self.is_null():
             return None
         else:
-            if self._map.specified("perturbable_constraint"):
-                return self._map["perturbable_constraint"].source()
-            else:
-                return self.constraint()
+            return self._omm_mols.get_perturbable_constraint()
 
     def get_schedule(self):
         if self.is_null():
@@ -427,6 +421,12 @@ def set_lambda(self, lambda_value: float):
             self._omm_mols.set_lambda(lambda_value)
             self._clear_state()
 
+    def integrator(self):
+        if self.is_null():
+            return None
+        else:
+            return self._omm_mols.getIntegrator()
+
     def info(self):
         if self.is_null():
             return None
@@ -1198,6 +1198,12 @@ def perturbable_constraint(self):
         """
         return self._d.perturbable_constraint()
 
+    def integrator(self):
+        """
+        Return the integrator that is used to run dynamics
+        """
+        return self._d.integrator()
+
     def info(self):
         """
         Return the information that describes the forcefield that will

src/sire/options/CMakeLists.txt

@@ -0,0 +1,15 @@
+########################################
+#
+# sire.options
+#
+########################################
+
+# Add your script to this list
+set ( SCRIPTS
+        __init__.py
+        _option.py
+        _dynamics_options.py
+    )
+
+# installation
+install( FILES ${SCRIPTS} DESTINATION ${SIRE_PYTHON}/sire/options )

src/sire/options/__init__.py

@@ -0,0 +1,18 @@
+__all__ = [
+    "Option",
+    "Integrator",
+    "Constraint",
+    "PerturbableConstraint",
+    "Cutoff",
+    "Platform",
+]
+
+from ._option import Option
+
+from ._dynamics_options import (
+    Integrator,
+    Constraint,
+    Cutoff,
+    PerturbableConstraint,
+    Platform,
+)