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Fix residue conformational state indexing by group id #459

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Merged
harryswift01 merged 3 commits into from
Oct 14, 2026
Merged

Fix residue conformational state indexing by group id #459

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96cdd8b
fix(conformations): key residue conformational states by group id
harryswift01 Oct 14, 2026
c0ee930
test(conformations): update unit tests for group-keyed residue states
harryswift01 Oct 14, 2026
0933016
tests(regressions): update regression baselines for group-keyed resid…
harryswift01 Oct 14, 2026
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20 changes: 15 additions & 5 deletions CodeEntropy/levels/dihedrals/conformational_state_builder.py
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,12 @@ def build_conformational_states(
frame_selection: FrameSelection,
progress: _RichProgressSink | None = None,
chunk_size: int | None = None,
) -> tuple[dict[UAKey, list[str]], list[list[str]], dict[UAKey, int], list[int]]:
) -> tuple[
dict[UAKey, list[str]],
dict[int, list[str]],
dict[UAKey, int],
dict[int, int],
]:
"""Build conformational state labels from selected trajectory frames.

Args:
Expand Down Expand Up @@ -87,7 +92,12 @@ def _build_conformational_states_serial_chunked(
frame_selection: FrameSelection,
chunk_size: int,
progress: _RichProgressSink | None = None,
) -> tuple[dict[UAKey, list[str]], list[list[str]], dict[UAKey, int], list[int]]:
) -> tuple[
dict[UAKey, list[str]],
dict[int, list[str]],
dict[UAKey, int],
dict[int, int],
]:
"""Build conformational states with serial frame-chunk map-reduce.

Args:
Expand All @@ -108,11 +118,10 @@ def _build_conformational_states_serial_chunked(
if chunk_size < 1:
raise ValueError("chunk_size must be >= 1")

number_groups = len(groups)
states_ua: dict[UAKey, list[str]] = {}
states_res: list[list[str]] = [[] for _ in range(number_groups)]
states_res: dict[int, list[str]] = {}
flexible_ua: dict[UAKey, int] = {}
flexible_res: list[int] = []
flexible_res: dict[int, int] = {}

task: TaskID | None = None
if progress is not None:
Expand Down Expand Up @@ -186,6 +195,7 @@ def _build_conformational_states_serial_chunked(
state_data = self._reduce_state_partials(state_partials)

self._merge_group_state_data(
group_id=group_id,
state_data=state_data,
states_ua=states_ua,
states_res=states_res,
Expand Down
15 changes: 9 additions & 6 deletions CodeEntropy/levels/dihedrals/state_assignment.py
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Original file line number Diff line number Diff line change
Expand Up @@ -170,20 +170,23 @@ def _reduce_state_partials(

@staticmethod
def _merge_group_state_data(
group_id: int,
state_data: ConformationStateData,
states_ua: dict[UAKey, list[str]],
states_res: list[list[str]],
states_res: dict[int, list[str]],
flexible_ua: dict[UAKey, int],
flexible_res: list[int],
flexible_res: dict[int, int],
) -> None:
"""Merge one group's state data into final output accumulators.

Args:
group_id: Id of the group the state data belongs to.
state_data: Serial conformational state data for one group.
states_ua: UA state accumulator to mutate.
states_res: Residue state accumulator to mutate.
states_res: Residue state accumulator, keyed by group id, to mutate.
flexible_ua: UA flexible-dihedral accumulator to mutate.
flexible_res: Residue flexible-dihedral accumulator to mutate.
flexible_res: Residue flexible-dihedral accumulator, keyed by group id,
to mutate.

Returns:
None. Mutates the provided accumulators.
Expand All @@ -199,8 +202,8 @@ def _merge_group_state_data(
state_data.flexible_ua_updates[key],
)

states_res.append(state_data.state_res)
flexible_res.append(state_data.flex_res)
states_res[group_id] = state_data.state_res
flexible_res[group_id] = state_data.flex_res

def _process_conformations_from_angles(
self,
Expand Down
8 changes: 4 additions & 4 deletions tests/regression/baselines/benzaldehyde/axes_off.json
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Expand Up @@ -3,14 +3,14 @@
"0": {
"components": {
"united_atom:Transvibrational": 0.06950663196232491,
"united_atom:Rovibrational": 35.19655714759131,
"residue:FTmat-Transvibrational": 86.6413638447789,
"residue:FTmat-Rovibrational": 62.24303760058523,
"united_atom:Rovibrational": 35.19655714759134,
"residue:FTmat-Transvibrational": 86.64136384477892,
"residue:FTmat-Rovibrational": 62.24303760058521,
"united_atom:Conformational": 0.0,
"residue:Conformational": 0.0,
"residue:Orientational": 20.481571492615355
},
"total": 204.6320367175331
"total": 204.63203671753317
}
}
}
6 changes: 3 additions & 3 deletions tests/regression/baselines/benzaldehyde/combined_forcetorque_false.json
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Expand Up @@ -3,14 +3,14 @@
"0": {
"components": {
"united_atom:Transvibrational": 0.06817494136874551,
"united_atom:Rovibrational": 49.686697381523466,
"united_atom:Rovibrational": 49.686697381523516,
"residue:Transvibrational": 69.25273989458984,
"residue:Rovibrational": 68.64810133422232,
"residue:Rovibrational": 68.6481013342223,
"united_atom:Conformational": 0.0,
"residue:Conformational": 0.0,
"residue:Orientational": 20.481571492615355
},
"total": 208.13728504431973
"total": 208.13728504431975
}
}
}
6 changes: 3 additions & 3 deletions tests/regression/baselines/benzaldehyde/default.json
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Original file line number Diff line number Diff line change
Expand Up @@ -2,9 +2,9 @@
"groups": {
"0": {
"components": {
"united_atom:Transvibrational": 24.921822103314035,
"united_atom:Rovibrational": 27.950376507672594,
"residue:FTmat-Transvibrational": 70.97090266225699,
"united_atom:Transvibrational": 24.92182210331405,
"united_atom:Rovibrational": 27.950376507672583,
"residue:FTmat-Transvibrational": 70.97090266225698,
"residue:FTmat-Rovibrational": 59.588669973122094,
"united_atom:Conformational": 7.522643899702263,
"residue:Conformational": 0.0,
Expand Down
4 changes: 2 additions & 2 deletions tests/regression/baselines/benzaldehyde/frame_window.json
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Expand Up @@ -3,8 +3,8 @@
"0": {
"components": {
"united_atom:Transvibrational": 37.90368186636453,
"united_atom:Rovibrational": 38.219068584436165,
"residue:FTmat-Transvibrational": 73.76730786578052,
"united_atom:Rovibrational": 38.21906858443616,
"residue:FTmat-Transvibrational": 73.76730786578054,
"residue:FTmat-Rovibrational": 57.689489298548764,
"united_atom:Conformational": 0.0,
"residue:Conformational": 0.0,
Expand Down
24 changes: 12 additions & 12 deletions tests/regression/baselines/benzaldehyde/grouping_each.json
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Original file line number Diff line number Diff line change
Expand Up @@ -3,14 +3,14 @@
"0": {
"components": {
"united_atom:Transvibrational": 0.0,
"united_atom:Rovibrational": 0.062499436482478535,
"residue:FTmat-Transvibrational": 16.838570367698324,
"united_atom:Rovibrational": 0.062499436482478445,
"residue:FTmat-Transvibrational": 16.83857036769834,
"residue:FTmat-Rovibrational": 0.0,
"united_atom:Conformational": 0.0,
"residue:Conformational": 0.0,
"residue:Orientational": 31.909265242174982
},
"total": 48.81033504635579
"total": 48.8103350463558
},
"1": {
"components": {
Expand All @@ -27,26 +27,26 @@
"2": {
"components": {
"united_atom:Transvibrational": 0.0,
"united_atom:Rovibrational": 0.0022147884278620493,
"united_atom:Rovibrational": 0.0022147884278620397,
"residue:FTmat-Transvibrational": 17.449372254125855,
"residue:FTmat-Rovibrational": 0.0,
"united_atom:Conformational": 0.0,
"residue:Conformational": 0.0,
"residue:Orientational": 31.909265242174982
},
"total": 49.3608522847287
"total": 49.36085228472869
},
"3": {
"components": {
"united_atom:Transvibrational": 0.0,
"united_atom:Rovibrational": 0.001983835543157824,
"residue:FTmat-Transvibrational": 15.80397693084538,
"residue:FTmat-Transvibrational": 15.803976930845373,
"residue:FTmat-Rovibrational": 0.0,
"united_atom:Conformational": 0.0,
"residue:Conformational": 0.0,
"residue:Orientational": 0.0
},
"total": 15.805960766388537
"total": 15.80596076638853
},
"4": {
"components": {
Expand Down Expand Up @@ -88,30 +88,30 @@
"components": {
"united_atom:Transvibrational": 0.0,
"united_atom:Rovibrational": 0.004033941970593011,
"residue:FTmat-Transvibrational": 18.906768821421366,
"residue:FTmat-Transvibrational": 18.906768821421363,
"residue:FTmat-Rovibrational": 0.0,
"united_atom:Conformational": 0.0,
"residue:Conformational": 0.0,
"residue:Orientational": 0.0
},
"total": 18.91080276339196
"total": 18.910802763391956
},
"8": {
"components": {
"united_atom:Transvibrational": 0.0,
"united_atom:Rovibrational": 0.020362757918507036,
"united_atom:Rovibrational": 0.020362757918507064,
"residue:FTmat-Transvibrational": 16.13204209116967,
"residue:FTmat-Rovibrational": 0.0,
"united_atom:Conformational": 0.0,
"residue:Conformational": 0.0,
"residue:Orientational": 31.909265242174982
},
"total": 48.06167009126315
"total": 48.06167009126316
},
"9": {
"components": {
"united_atom:Transvibrational": 0.0,
"united_atom:Rovibrational": 0.00023139743934636996,
"united_atom:Rovibrational": 0.0002313974393463703,
"residue:FTmat-Transvibrational": 21.42548529236267,
"residue:FTmat-Rovibrational": 0.0,
"united_atom:Conformational": 0.0,
Expand Down
6 changes: 3 additions & 3 deletions tests/regression/baselines/benzaldehyde/rad.json
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Expand Up @@ -2,9 +2,9 @@
"groups": {
"0": {
"components": {
"united_atom:Transvibrational": 24.921822103314035,
"united_atom:Rovibrational": 27.950376507672594,
"residue:FTmat-Transvibrational": 70.97090266225699,
"united_atom:Transvibrational": 24.92182210331405,
"united_atom:Rovibrational": 27.950376507672583,
"residue:FTmat-Transvibrational": 70.97090266225698,
"residue:FTmat-Rovibrational": 59.588669973122094,
"united_atom:Conformational": 7.522643899702263,
"residue:Conformational": 0.0,
Expand Down
6 changes: 3 additions & 3 deletions tests/regression/baselines/benzaldehyde/selection_subset.json
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Expand Up @@ -3,14 +3,14 @@
"0": {
"components": {
"united_atom:Transvibrational": 0.06817494136874551,
"united_atom:Rovibrational": 49.686697381523466,
"residue:FTmat-Transvibrational": 85.94814793508023,
"united_atom:Rovibrational": 49.686697381523516,
"residue:FTmat-Transvibrational": 85.94814793508021,
"residue:FTmat-Rovibrational": 61.7256510401677,
"united_atom:Conformational": 0.0,
"residue:Conformational": 0.0,
"residue:Orientational": 20.481571492615355
},
"total": 217.9102427907555
"total": 217.91024279075552
}
}
}
8 changes: 4 additions & 4 deletions tests/regression/baselines/benzene/axes_off.json
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Expand Up @@ -2,15 +2,15 @@
"groups": {
"0": {
"components": {
"united_atom:Transvibrational": 0.17072733303436669,
"united_atom:Transvibrational": 0.17072733303436652,
"united_atom:Rovibrational": 38.707686995757996,
"residue:FTmat-Transvibrational": 78.01138885368493,
"residue:FTmat-Rovibrational": 47.12762732161061,
"residue:FTmat-Transvibrational": 78.01138885368485,
"residue:FTmat-Rovibrational": 47.127627321610596,
"united_atom:Conformational": 0.0,
"residue:Conformational": 0.0,
"residue:Orientational": 0.0
},
"total": 164.0174305040879
"total": 164.0174305040878
}
}
}
6 changes: 3 additions & 3 deletions tests/regression/baselines/benzene/combined_forcetorque_off.json
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Expand Up @@ -2,15 +2,15 @@
"groups": {
"0": {
"components": {
"united_atom:Transvibrational": 0.20056759662549248,
"united_atom:Rovibrational": 40.69581240789943,
"united_atom:Transvibrational": 0.2005675966254925,
"united_atom:Rovibrational": 40.695812407899396,
"residue:Transvibrational": 60.612932277845054,
"residue:Rovibrational": 52.53948263906845,
"united_atom:Conformational": 0.0,
"residue:Conformational": 0.0,
"residue:Orientational": 0.0
},
"total": 154.04879492143843
"total": 154.0487949214384
}
}
}
8 changes: 4 additions & 4 deletions tests/regression/baselines/benzene/default.json
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Expand Up @@ -2,10 +2,10 @@
"groups": {
"0": {
"components": {
"united_atom:Transvibrational": 9.070682016770112,
"united_atom:Rovibrational": 27.534380126250213,
"residue:FTmat-Transvibrational": 72.69407639869898,
"residue:FTmat-Rovibrational": 59.84501427492272,
"united_atom:Transvibrational": 9.070682016770117,
"united_atom:Rovibrational": 27.5343801262502,
"residue:FTmat-Transvibrational": 72.694076398699,
"residue:FTmat-Rovibrational": 59.84501427492273,
"united_atom:Conformational": 0.0,
"residue:Conformational": 0.0,
"residue:Orientational": 41.58427729275938
Expand Down
10 changes: 5 additions & 5 deletions tests/regression/baselines/benzene/frame_window.json
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Expand Up @@ -2,15 +2,15 @@
"groups": {
"0": {
"components": {
"united_atom:Transvibrational": 13.02795056227694,
"united_atom:Rovibrational": 34.98492056748487,
"residue:FTmat-Transvibrational": 75.50603474425519,
"residue:FTmat-Rovibrational": 54.88466842760241,
"united_atom:Transvibrational": 13.027950562276953,
"united_atom:Rovibrational": 34.984920567484934,
"residue:FTmat-Transvibrational": 75.50603474425517,
"residue:FTmat-Rovibrational": 54.88466842760242,
"united_atom:Conformational": 0.0,
"residue:Conformational": 0.0,
"residue:Orientational": 0.0
},
"total": 178.40357430161941
"total": 178.40357430161947
}
}
}
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