Skip to content

Use set operations for unique atom detection in HybridTopologyFactory #1911

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Closed
kokishimada wants to merge 2 commits into from
Closed

Use set operations for unique atom detection in HybridTopologyFactory #1911

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
b10e54e
Use set operations for unique atom detection in HybridTopologyFactory
kokishimada Apr 1, 2026
bfd99e4
Remove redundant _find_bond_parameters call in _handle_harmonic_bonds
kokishimada Apr 1, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
29 changes: 13 additions & 16 deletions src/openfe/protocols/openmm_rfe/_rfe_utils/relative.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -437,22 +437,21 @@ def _set_mappings(self, old_to_new_map, core_old_to_new_map):
self._new_to_hybrid_map = {}

# Get unique atoms
# old system first
self._unique_old_atoms = []
for particle_idx in range(self._old_system.getNumParticles()):
if particle_idx not in self._old_to_new_map.keys():
self._unique_old_atoms.append(particle_idx)
old_mapped = self._old_to_new_map.keys()
self._unique_old_atoms = sorted(
set(range(self._old_system.getNumParticles())) - old_mapped
)

self._unique_new_atoms = []
for particle_idx in range(self._new_system.getNumParticles()):
if particle_idx not in self._new_to_old_map.keys():
self._unique_new_atoms.append(particle_idx)
new_mapped = self._new_to_old_map.keys()
self._unique_new_atoms = sorted(
set(range(self._new_system.getNumParticles())) - new_mapped
)

# Get env atoms (i.e. atoms mapped not in core)
self._env_old_to_new_map = {}
for key, value in old_to_new_map.items():
if key not in self._core_old_to_new_map.keys():
self._env_old_to_new_map[key] = value
self._env_old_to_new_map = {
k: v for k, v in old_to_new_map.items()
if k not in self._core_old_to_new_map
}

self._env_new_to_old_map = self._invert_dict(self._env_old_to_new_map)

Expand Down Expand Up @@ -1221,9 +1220,7 @@ def _handle_harmonic_bonds(self):
r0_new = r0_old
k_new = 0.0*unit.kilojoule_per_mole/unit.angstrom**2
else:
# TODO - why is this being recalculated?
[index1, index2, r0_new, k_new] = self._find_bond_parameters(
new_system_bond_force, index1_new, index2_new)
[_, _, r0_new, k_new] = new_bond_parameters
self._hybrid_system_forces['core_bond_force'].addBond(
index1_hybrid, index2_hybrid,
[r0_old, k_old, r0_new, k_new])
Expand Down
Loading