Release 2026.2.0

README.rst

@@ -36,8 +36,8 @@ It is used as a key component of `BioSimSpace <https://biosimspace.org>`__,
 and is distributed and supported as an open source community project by
 `OpenBioSim <https://openbiosim.org>`__.
 
-For more information about how to use Sire, and about application
-built with Sire, please `visit the Sire website <https://sire.openbiosim.org>`__.
+For more information about how to use sire, and about applications
+built with sire, please `visit the sire website <https://sire.openbiosim.org>`__.
 
 * `Features <https://sire.openbiosim.org/features.html>`__
 * `Quick start guide <https://sire.openbiosim.org/quickstart/index.html>`__
@@ -46,7 +46,7 @@ built with Sire, please `visit the Sire website <https://sire.openbiosim.org>`__
 Installation
 ============
 
-The easiest way to install Sire is using our `conda channel <https://anaconda.org/openbiosim/repo>`__.
+The easiest way to install sire is using our `conda channel <https://anaconda.org/openbiosim/repo>`__.
 Sire is built using dependencies from `conda-forge <https://conda-forge.org/>`__,
 so please ensure that the channel takes strict priority. We recommend using
 `miniforge3 <https://github.com/conda-forge/miniforge#miniforge3>`__.
@@ -135,7 +135,9 @@ Other pixi environments are available depending on your needs:
 * ``pixi install -e default`` - core sire dependencies only
 * ``pixi install -e obs`` - include downstream OpenBioSim package dependencies
 * ``pixi install -e emle`` - include `emle-engine <https://github.com/chemle/emle-engine>`__ dependencies
-* ``pixi install -e dev`` - all of the above plus test dependencies
+* ``pixi install -e test`` - include test dependencies
+* ``pixi install -e full`` - include both the ``obs`` and ``emle`` dependencies
+* ``pixi install -e dev`` - all of the above, plus linting tools
 
 Any additional startup commands can be specified in the ``pixi.sh`` file
 in the root of the sire repository. This file is automatically sourced when
@@ -153,13 +155,28 @@ this:
     pixi shell -e dev
     ln -s /etc/OpenCL/vendors "${CONDA_PREFIX}/etc/OpenCL/vendors/ocl-icd-system"
 
+Note that we don't pin ``cuda-version`` in ``pixi.toml``, which is pulled in
+as a transitive dependency of OpenMM. This means that the version you end up
+with might not be compatible with the CUDA driver installed on your system. If
+you need a specific version, then add it to the ``[dependencies]`` section of
+``pixi.toml`` before creating the environment, e.g.:
+
+.. code-block:: toml
+
+    [dependencies]
+    cuda-version = "==12.6"
+
+This is intended as a local development tweak only and shouldn't be committed,
+since ``actions/generate_recipe.py`` reads the ``[dependencies]`` section when
+generating the conda recipe, so the pin would also end up in our packages.
+
 Support and Development
 =======================
 
 Bugs, Comments, Questions
 -------------------------
 For bug reports/suggestions/complaints please file an issue on
-`GitHub <http://github.com/OpenBioSim/sire/issues>`__.
+`GitHub <https://github.com/OpenBioSim/sire/issues>`__.
 
 Developers guide
 ----------------
@@ -184,14 +201,14 @@ a consistent style without a blanket one-time reformatting.
 
 GitHub actions
 --------------
-Since sire is quite large, a build can take quite long and might not be neccessary
-if a commit is only fixing a couple of typos. Simply add ``ci skip``
+Since sire is quite large, a build can take quite a long time and might not be
+necessary if a commit is only fixing a couple of typos. Simply add ``ci skip``
 to your commit message and GitHub actions will not invoke an autobuild.
 
 Note that every time you commit to devel, it will trigger a build of sire,
 full testing, construction of a Conda package and upload to our Anaconda
 channel. Please think twice before committing directly to devel. You should
-ideally be working in a _feature_ branch, and only commit to devel once you are
+ideally be working in a *feature* branch, and only commit to devel once you are
 happy the code works on your branch. Use ``ci skip`` until you are happy that
 you want to trigger a full build, test and deployment. This full pipeline will
 take several hours to complete.

actions/generate_recipe.py

@@ -37,7 +37,6 @@
 
 RUN_DEPS = {
     "gsl",
-    "lazy_import",
     "libnetcdf",
     "openmm",
     "pandas",

corelib/src/libs/SireMM/boreschrestraints.cpp

@@ -74,9 +74,7 @@ QDataStream &operator>>(QDataStream &ds, BoreschRestraint &borrest)
     {
         SharedDataStream sds(ds);
 
-        sds >> borrest.receptor_atms >> borrest.ligand_atms >> borrest._r0
-            >> borrest._theta0 >> borrest._phi0 >> borrest._kr >> borrest._ktheta
-            >> borrest._kphi >> static_cast<Property &>(borrest);
+        sds >> borrest.receptor_atms >> borrest.ligand_atms >> borrest._r0 >> borrest._theta0 >> borrest._phi0 >> borrest._kr >> borrest._ktheta >> borrest._kphi >> static_cast<Property &>(borrest);
     }
     else
         throw version_error(v, "1", r_borrest, CODELOC);
@@ -285,7 +283,7 @@ QString BoreschRestraint::toString() const
             .arg(k.join(", "))
             .arg(_r0.toString())
             .arg(t.join(", "))
-            .arg(p.join(', '));
+            .arg(p.join(", "));
     }
 }
 
@@ -345,11 +343,11 @@ static const RegisterMetaType<BoreschRestraints> r_borrests;
 
 QDataStream &operator<<(QDataStream &ds, const BoreschRestraints &borrests)
 {
-    writeHeader(ds, r_borrests, 2);
+    writeHeader(ds, r_borrests, 3);
 
     SharedDataStream sds(ds);
 
-    sds << borrests.r << borrests.use_pbc
+    sds << borrests.r << borrests.use_pbc << borrests.angle_potential << borrests.restraint_lever
         << static_cast<const Restraints &>(borrests);
 
     return ds;
@@ -364,16 +362,29 @@ QDataStream &operator>>(QDataStream &ds, BoreschRestraints &borrests)
         SharedDataStream sds(ds);
 
         sds >> borrests.r >> static_cast<Restraints &>(borrests);
+
+        borrests.use_pbc = false;
+        borrests.angle_potential = "harmonic";
+        borrests.restraint_lever = "combined";
     }
     else if (v == 2)
     {
         SharedDataStream sds(ds);
 
-        sds >> borrests.r >> borrests.use_pbc
-            >> static_cast<Restraints &>(borrests);
+        sds >> borrests.r >> borrests.use_pbc >> static_cast<Restraints &>(borrests);
+
+        borrests.angle_potential = "harmonic";
+        borrests.restraint_lever = "combined";
+    }
+    else if (v == 3)
+    {
+        SharedDataStream sds(ds);
+
+        sds >> borrests.r >> borrests.use_pbc >> borrests.angle_potential >> borrests.restraint_lever >>
+            static_cast<Restraints &>(borrests);
     }
     else
-        throw version_error(v, "1,2", r_borrests, CODELOC);
+        throw version_error(v, "1,2,3", r_borrests, CODELOC);
 
     return ds;
 }
@@ -426,7 +437,8 @@ BoreschRestraints::BoreschRestraints(const QString &name,
 }
 
 BoreschRestraints::BoreschRestraints(const BoreschRestraints &other)
-    : ConcreteProperty<BoreschRestraints, Restraints>(other), r(other.r), use_pbc(other.use_pbc)
+    : ConcreteProperty<BoreschRestraints, Restraints>(other), r(other.r), use_pbc(other.use_pbc),
+      angle_potential(other.angle_potential), restraint_lever(other.restraint_lever)
 {
 }
 
@@ -438,14 +450,17 @@ BoreschRestraints &BoreschRestraints::operator=(const BoreschRestraints &other)
 {
     r = other.r;
     use_pbc = other.use_pbc;
+    angle_potential = other.angle_potential;
+    restraint_lever = other.restraint_lever;
     Restraints::operator=(other);
     return *this;
 }
 
 bool BoreschRestraints::operator==(const BoreschRestraints &other) const
 {
     return r == other.r and Restraints::operator==(other) and
-           use_pbc == other.use_pbc;
+           use_pbc == other.use_pbc and angle_potential == other.angle_potential and
+           restraint_lever == other.restraint_lever;
 }
 
 bool BoreschRestraints::operator!=(const BoreschRestraints &other) const
@@ -499,11 +514,14 @@ QString BoreschRestraints::toString() const
         }
     }
 
-    return QObject::tr("BoreschRestraints( name=%1, size=%2, use_pbc=%3\n%4\n)")
-            .arg(this->name())
-            .arg(n)
-            .arg(this->use_pbc ? "true" : "false")
-            .arg(parts.join("\n"));
+    return QObject::tr("BoreschRestraints( name=%1, size=%2, use_pbc=%3, angle_potential=%4, "
+                       "restraint_lever=%5\n%6\n)")
+        .arg(this->name())
+        .arg(n)
+        .arg(this->use_pbc ? "true" : "false")
+        .arg(this->angle_potential)
+        .arg(this->restraint_lever)
+        .arg(parts.join("\n"));
 }
 
 /** Return whether or not this is empty */
@@ -610,3 +628,50 @@ bool BoreschRestraints::usesPbc() const
 {
     return this->use_pbc;
 }
+
+/** Set the functional form used for the two Boresch angle restraint terms.
+ *  Must be either "harmonic" (the default) or "restricted_bending". */
+void BoreschRestraints::setAnglePotential(const QString &angle_potential)
+{
+    if (angle_potential != "harmonic" and angle_potential != "restricted_bending")
+    {
+        throw SireError::invalid_arg(QObject::tr(
+                                         "'angle_potential' must be either 'harmonic' or "
+                                         "'restricted_bending', got '%1'.")
+                                         .arg(angle_potential),
+                                     CODELOC);
+    }
+
+    this->angle_potential = angle_potential;
+}
+
+/** Return the functional form used for the two Boresch angle restraint terms,
+ *  either "harmonic" or "restricted_bending". */
+QString BoreschRestraints::anglePotential() const
+{
+    return this->angle_potential;
+}
+
+/** Set how the restraint's six degrees of freedom are grouped into
+ *  lambda-addressable OpenMM Forces. Must be either "combined" (the
+ *  default) or "split". */
+void BoreschRestraints::setRestraintLever(const QString &restraint_lever)
+{
+    if (restraint_lever != "combined" and restraint_lever != "split")
+    {
+        throw SireError::invalid_arg(QObject::tr(
+                                         "'restraint_lever' must be either 'combined' or "
+                                         "'split', got '%1'.")
+                                         .arg(restraint_lever),
+                                     CODELOC);
+    }
+
+    this->restraint_lever = restraint_lever;
+}
+
+/** Return how the restraint's six degrees of freedom are grouped into
+ *  lambda-addressable OpenMM Forces, either "combined" or "split". */
+QString BoreschRestraints::restraintLever() const
+{
+    return this->restraint_lever;
+}

corelib/src/libs/SireMM/boreschrestraints.h

@@ -197,12 +197,35 @@ namespace SireMM
         void setUsesPbc(bool use_pbc);
         bool usesPbc() const;
 
+        void setAnglePotential(const QString &angle_potential);
+        QString anglePotential() const;
+
+        void setRestraintLever(const QString &restraint_lever);
+        QString restraintLever() const;
+
     private:
         /** The actual list of restraints*/
         QList<BoreschRestraint> r;
 
         /** Whether the restraints use periodic boundary conditions */
         bool use_pbc = false;
+
+        /** The functional form used for the two Boresch angle restraint
+         *  terms (thetaA, thetaB). Either "harmonic" (default) or
+         *  "restricted_bending" - the latter uses
+         *  k*(cos(theta)-cos(theta0))^2/sin(theta)^2, which diverges as
+         *  theta approaches 0 or pi, preventing the restraint angles from
+         *  ever reaching the Boresch collinearity singularity. */
+        QString angle_potential = "harmonic";
+
+        /** How the restraint's six degrees of freedom are grouped into
+         *  lambda-addressable OpenMM Forces. Either "combined" (default,
+         *  all six terms share a single scale factor / lever) or "split"
+         *  (the distance and two angle terms share one scale factor, the
+         *  three dihedral terms share a second, independent scale factor -
+         *  allowing them to be turned on according to different lambda
+         *  schedules). */
+        QString restraint_lever = "combined";
     };
 
 }

doc/source/acknowledgements.rst

@@ -475,12 +475,6 @@ The header documentation reads;
      imshow does not plot axis yet.
      make a correct documentation
 
-lazy_import
------------
-
-:mod:`sire` uses `lazy_import <https://github.com/mnmelo/lazy_import>`__ to
-lazy load the modules. This is licensed under the GPLv3.
-
 rich
 ----