Merge pull request #469 from OpenBioSim/release_2025.3.0

Release 2025.3.0

Author: lohedges

README.rst

@@ -17,16 +17,6 @@
    :target: https://joss.theoj.org/papers/4ba84ad443693b5dded90e35bf5f8225
    :alt: Paper
 
-Survey
-------
-
-We are currently conducting a
-`survey <https://docs.google.com/forms/d/1zY0i3lLR9MhmohKjcu0wJp_CXJvBwcWoj6iG4p9LNKk/edit?ts=6836f566>`__
-to help us understand how BioSimSpace is being used and how we can improve it.
-The survey explores your molecular simulation tools and practices, identifies workflow challenges, and
-gathers feedback on the BioSimSpace simulation framework to guide its future development. If you have
-a few minutes, please fill it out!
-
 About
 -----
 

doc/source/changelog.rst

@@ -9,7 +9,18 @@ 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.
 
-`2025.2.0 <https://github.com/openbiosim/biosimspace/compare/2024.5.0...2025.2.0>`_ - Oct 08 2025
+`2025.3.0 <https://github.com/openbiosim/biosimspace/compare/2025.2.0...2025.3.0>`_ - Nov 10 2025
+-------------------------------------------------------------------------------------------------
+
+* Fixed bug that caused trajectory frame reconstruction to be skipped for perturbable systems (`#460 <https://github.com/OpenBioSim/biosimspace/pull/460>`__).
+* Fixed typo in RDKit ``rdMolDraw2D`` attribute name (`#463 <https://github.com/OpenBioSim/biosimspace/pull/463>`__).
+* Fix incorrect context manager name in node runner (`#463 <https://github.com/OpenBioSim/biosimspace/pull/463>`__).
+* Added functionality for quickly getting and setting the coordinates array of a :class:`System <BioSimSpace._SireWrappers.System>` (`#465 <https://github.com/OpenBioSim/biosimspace/pull/465>`__).
+* Reduce depdency import overheads by switching from module level imports to function and method level (`#466 <https://github.com/OpenBioSim/biosimspace/pull/466>`__).
+* Fully switch over to using the new Sire Python API naming convention, allowing BioSimSpace to be used within Sire (`#466 <https://github.com/OpenBioSim/biosimspace/pull/466>`__).
+* Fixed logic used for setting the GPU device index for :class:`Process.OpenMM <BioSimSpace.Process.OpenMM>` (`#468 <https://github.com/OpenBioSim/biosimspace/pull/468>`__).
+
+`2025.2.0 <https://github.com/openbiosim/biosimspace/compare/2025.1.0...2025.2.0>`_ - Oct 08 2025
 -------------------------------------------------------------------------------------------------
 
 * Add support for ``SOMD2`` FEP analysis using data frames with different numbers of samples (`#415 <https://github.com/OpenBioSim/biosimspace/pull/415>`__).

doc/source/tutorials/crystal_water.rst

@@ -20,7 +20,7 @@ Firstly, let's load the PDB structure:
 >>> import BioSimSpace as BSS
 >>> tyk2_xtal = BSS.IO.readMolecules(
 ...    BSS.IO.expand(
-...        BSS.IO.tutorialUrl(), "tyk2_xtal.pdb"
+...        BSS.tutorialUrl(), "tyk2_xtal.pdb"
 ...    )
 ...)[0]
 

doc/source/tutorials/molecular_editing.rst

@@ -108,8 +108,8 @@ SireMol::AtomCharges( size=9
 
 .. Note::
    To see the full list of properties available for a molecule, you can use the
-   ``propertyKeys()`` method on the underlying Sire molecule object, e.g.
-   ``ethanol._sire_object.propertyKeys()``.
+   ``property_keys()`` method on the underlying Sire molecule object, e.g.
+   ``ethanol._sire_object.property_keys()``.
 
 Editing bonds
 -------------
@@ -122,7 +122,7 @@ constant for all existing bonds:
 >>> bonds = TwoAtomFunctions(ethanol._sire_object.info())
 >>> for bond in ethanol._sire_object.property("bond").potentials():
 ...     amber_bond = AmberBond(0, 0)
-...     bonds.set(bond.atom0(), bond.atom1(), amber_bond.toExpression(Symbol("r")))
+...     bonds.set(bond.atom0(), bond.atom1(), amber_bond.to_expression(Symbol("r")))
 >>> cursor = ethanol._sire_object.cursor()
 >>> cursor["bond"] = bonds
 >>> ethanol._sire_object = cursor.commit()
@@ -163,7 +163,7 @@ and modifying the desired angle:
 >>> for angle in ethanol._sire_object.property("angle").potentials():
 ...     if ethanol._sire_object.atom(angle.atom1()).name().value() == "O3":
 ...         amber_angle = AmberAngle(100, 1.5)
-...         angles.set(angle.atom0(), angle.atom1(), angle.atom2(), amber_angle.toExpression(Symbol("theta")))
+...         angles.set(angle.atom0(), angle.atom1(), angle.atom2(), amber_angle.to_expression(Symbol("theta")))
 ...     else:
 ...         angles.set(angle.atom0(), angle.atom1(), angle.atom2(), angle.function())
 
@@ -247,7 +247,7 @@ A regular AMBER-style dihedral series where all terms have positive cosine facto
 >>> d = AmberDihedral(f, Phi)
 >>> print("AMBER:", d)
 AMBER: AmberDihedral( k[0] = 0.3, periodicity[0] = 1, phase[0] = 0, k[1] = 0.8, periodicity[1] = 4, phase[1] = 0 )
->>> assert d.toExpression(Phi) == f
+>>> assert d.to_expression(Phi) == f
 
 An AMBER-style dihedral containing positive and negative cosine factors, which
 can appear in the CHARMM force field:
@@ -256,7 +256,7 @@ can appear in the CHARMM force field:
 >>> d = AmberDihedral(f, Phi)
 >>> print("CHARMM:", d)
 CHARMM: AmberDihedral( k[0] = 0.3, periodicity[0] = 1, phase[0] = 0, k[1] = -0.8, periodicity[1] = 4, phase[1] = 0 )
->>> assert d.toExpression(Phi) == f
+>>> assert d.to_expression(Phi) == f
 
 An AMBER-style dihedral containing positive and negative cosine factors, with
 the negative of the form ``k [1 - Cos(Phi)]`` rather than ``-k [1 + Cos(Phi)]``.
@@ -269,7 +269,7 @@ GROMACS: AmberDihedral( k[0] = 0.3, periodicity[0] = 1, phase[0] = 0, k[1] = 0.8
 >>> from math import isclose
 >>> from sire.legacy.CAS import SymbolValue, Values
 >>> val = Values(SymbolValue(Phi.ID(), 2.0))
->>> assert isclose(f.evaluate(val), d.toExpression(Phi).evaluate(val))
+>>> assert isclose(f.evaluate(val), d.to_expression(Phi).evaluate(val))
 
 Finally, a three-term expression that mixes all formats:
 
@@ -280,7 +280,7 @@ Finally, a three-term expression that mixes all formats:
 ...     + 0.8 * (1 - Cos(4 * Phi))
 ... )
 >>> d = AmberDihedral(f, Phi)
->>> assert isclose(f.evaluate(val), d.toExpression(Phi).evaluate(val))
+>>> assert isclose(f.evaluate(val), d.to_expression(Phi).evaluate(val))
 
 .. Note::
    Impropers are also stored as ``FourAtomFunction`` objects, which can be
@@ -428,17 +428,17 @@ the editor, reparenting them to the appropriate chain, then adding the atoms:
 ...     cg = editor.add(sr.legacy.Mol.CGName(str(i)))
 ...     new_res = editor.add(res.number())
 ...     new_res.rename(res.name())
-...     new_res.reparent(chain_ids[i // 3])
-...     for j, atom in enumerate(res.atoms()):
+...     new_res.reparent(sr.legacy.Mol.ChainName(chain_ids[i]))
+...     for atom in res.atoms():
 ...         new_atom = cg.add(atom.number())
 ...         new_atom.rename(atom.name())
 ...         new_atom.reparent(res.index())
 ... editor = editor.commit().edit()
 
 Next we need to copy across the molecular properties, e.g. charges and bonded terms.
 
->>> for prop in ala._sire_object.propertKeys():
-...     editor = editor.setProperty(prop, ala._sire_object.property(prop)).molecule()
+>>> for prop in ala._sire_object.property_keys():
+...     editor = editor.set_property(prop, ala._sire_object.property(prop)).molecule()
 
 Finally, we can commit the changes to create the new molecule:
 

python/BioSimSpace/Align/__init__.py

@@ -40,4 +40,10 @@
     viewMapping
 """
 
+import sire as _sr
+
+_sr.use_new_api()
+del _sr
+
 from ._align import *
+from . import _squash