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Fix issue #437 #436

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Merged
lohedges merged 1 commit into from
Apr 21, 2026
Merged

Fix issue #437 #436

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4 changes: 4 additions & 0 deletions doc/source/changelog.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -62,6 +62,10 @@ organisation on `GitHub <https://github.com/openbiosim/sire>`__.
raising a ``KeyError``. Out-of-bounds positive and negative single-index values now
behave consistently with ``residx`` and ``atomidx``.

* Reassign end-state mass and element properties in the ``sire.morph.create_from_pertfile``
to undo ``SOMD`` modifications.


`2025.4.0 <https://github.com/openbiosim/sire/compare/2025.3.0...2025.4.0>`__ - February 2026
---------------------------------------------------------------------------------------------

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18 changes: 16 additions & 2 deletions src/sire/morph/_pertfile.py
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Expand Up @@ -67,6 +67,7 @@ def create_from_pertfile(mol, pertfile, map=None):
lj_prop = map["LJ"].source()
typ_prop = map["ambertype"].source()
elem_prop = map["element"].source()
mass_prop = map["mass"].source()

c["charge0"] = c[chg_prop]
c["charge1"] = c[chg_prop]
Expand All @@ -80,6 +81,9 @@ def create_from_pertfile(mol, pertfile, map=None):
c["element0"] = c[elem_prop]
c["element1"] = c[elem_prop]

c["mass0"] = c[mass_prop]
c["mass1"] = c[mass_prop]

for atom in c.atoms():
atomname = atom.name

Expand All @@ -90,7 +94,7 @@ def create_from_pertfile(mol, pertfile, map=None):
lj1 = template.get_final_lj(atomname)
typ0 = template.get_init_type(atomname)
typ1 = template.get_final_type(atomname)
except Exception as e:
except Exception:
continue

atom["charge0"] = q0
Expand All @@ -102,8 +106,18 @@ def create_from_pertfile(mol, pertfile, map=None):
atom["ambertype0"] = typ0
atom["ambertype1"] = typ1

# IMPORTANT: The pert file will already include modifications to the element
# and mass properties of the end states, i.e. when perturbing, elements are
# set to the mass/eelement of the heaviest end state. As such, we need to
# infer the element from the ambertype, then reset the mass. This also
# removes any existing hydrogen mass repartitioning.

atom["element0"] = Element.biological_element(typ0)
atom["element1"] = Element.biological_element(typ1)

atom["mass0"] = atom["element0"].mass()
atom["mass1"] = atom["element1"].mass()

# now update all of the internals
bond_prop = map["bond"].source()
ang_prop = map["angle"].source()
Expand Down Expand Up @@ -259,7 +273,7 @@ def create_from_pertfile(mol, pertfile, map=None):
c["improper1"] = impropers1

# duplicate unperturbed properties
for prop in ["coordinates", "mass", "forcefield", "intrascale"]:
for prop in ["coordinates", "forcefield", "intrascale"]:
orig_prop = map[prop].source()
c[prop + "0"] = c[orig_prop]
c[prop + "1"] = c[orig_prop]
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