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Fix complex alignment

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hannahbaumann
2026-05-29 12:42:02 +02:00
parent 14381f9abc
commit 811a1b675a
1 changed files with 4 additions and 4 deletions
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8
src/openfe/protocols/openmm_septop/base_units.py
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@@ -1549,7 +1549,7 @@ class BaseSepTopAnalysisUnit(gufe.ProtocolUnit, SepTopUnitMixin):
SymmetryCorrectedLigandRMSD,
)
from openfe_analysis.utils.apply_transformations import (
apply_alignment_transformations,
apply_complex_alignment_transformations,
)
from openfe_analysis.utils.universe_utils import create_universe_single_state
@@ -1568,7 +1568,7 @@ class BaseSepTopAnalysisUnit(gufe.ProtocolUnit, SepTopUnitMixin):
prot = u.select_atoms("protein and name CA")
lig_A = u.atoms[ligand_A_indices]
lig_B = u.atoms[ligand_B_indices]
apply_alignment_transformations(u, protein=prot, ligand=lig_A + lig_B)
apply_complex_alignment_transformations(u, protein=prot, ligand=[lig_A, lig_B])
if prot:
prot_rmsd2d = Protein2DRMSD(prot).run(step=skip)
@@ -1628,7 +1628,7 @@ class BaseSepTopAnalysisUnit(gufe.ProtocolUnit, SepTopUnitMixin):
"""
from openfe_analysis.rmsd import SymmetryCorrectedLigandRMSD
from openfe_analysis.utils.apply_transformations import (
apply_alignment_transformations,
apply_ligand_alignment_transformations,
)
from openfe_analysis.utils.universe_utils import create_universe_single_state
@@ -1646,7 +1646,7 @@ class BaseSepTopAnalysisUnit(gufe.ProtocolUnit, SepTopUnitMixin):
]:
u = create_universe_single_state(pdb_file, ds, state=state_idx)
lig = u.atoms[indices]
apply_alignment_transformations(u, ligand=lig)
apply_ligand_alignment_transformations(u, ligand=lig)
lig_rmsd = SymmetryCorrectedLigandRMSD(lig, rdmol=rdmol).run(step=skip)
data[f"{label}_RMSD"].append(lig_rmsd.results.rmsd)