From 27805df9311c0962a41e16d218500b653a355b48 Mon Sep 17 00:00:00 2001 From: skfegan Date: Wed, 8 Apr 2026 14:18:10 +0100 Subject: [PATCH 1/5] Fixing trajectory slicing. --- CodeEntropy/entropy/workflow.py | 30 ++++--- CodeEntropy/levels/dihedrals.py | 43 ---------- CodeEntropy/levels/level_dag.py | 24 ++---- CodeEntropy/levels/mda.py | 24 ++++++ CodeEntropy/levels/neighbors.py | 17 ++-- CodeEntropy/levels/nodes/conformations.py | 36 ++------- CodeEntropy/levels/nodes/find_neighbors.py | 4 +- CodeEntropy/levels/search.py | 17 +++- .../unit/CodeEntropy/entropy/test_workflow.py | 23 +++++- .../levels/nodes/test_conformations_node.py | 1 + .../levels/nodes/test_find_neighbors.py | 1 + .../unit/CodeEntropy/levels/test_dihedrals.py | 80 ------------------- .../levels/test_level_dag_orchestration.py | 50 ++---------- .../levels/test_level_dag_reduction.py | 2 +- .../unit/CodeEntropy/levels/test_neighbors.py | 12 ++- tests/unit/CodeEntropy/levels/test_search.py | 10 +-- 16 files changed, 116 insertions(+), 258 deletions(-) diff --git a/CodeEntropy/entropy/workflow.py b/CodeEntropy/entropy/workflow.py index fe50e516..7f368ad3 100644 --- a/CodeEntropy/entropy/workflow.py +++ b/CodeEntropy/entropy/workflow.py @@ -96,7 +96,7 @@ def execute(self) -> None: This orchestrates the complete entropy pipeline: 1. Build trajectory slice. - 2. Apply atom selection to create a reduced universe. + 2. Apply atom and frame selection to create a reduced universe. 3. Detect hierarchy levels. 4. Group molecules. 5. Split groups into water and non-water. @@ -233,21 +233,31 @@ def _get_number_frames(self, start: int, end: int, step: int) -> int: return math.floor((end - start) / step) def _build_reduced_universe(self) -> Any: - """Apply atom selection and return the reduced universe. - - If `selection_string` is "all", the original universe is returned. + """Apply atom and frame selection and return the reduced universe. Returns: - MDAnalysis Universe (original or reduced). + MDAnalysis Universe (reduced according to user selections). """ selection = self._args.selection_string + start = self._args.start + end = self._args.end + step = self._args.step if selection == "all": - return self._universe + reduced_atoms = self._universe + else: + reduced_atoms = self._universe_operations.select_atoms( + self._universe, selection + ) + name = f"{len(reduced_atoms.trajectory)}_frame_dump_atom_selection" + self._run_manager.write_universe(reduced_atoms, name) + + reduced_frames = self._universe_operations.select_frames( + reduced_atoms, start, end, step + ) + name = f"{len(reduced_frames.trajectory)}_frame_dump_frame_selection" + self._run_manager.write_universe(reduced_frames, name) - reduced = self._universe_operations.select_atoms(self._universe, selection) - name = f"{len(reduced.trajectory)}_frame_dump_atom_selection" - self._run_manager.write_universe(reduced, name) - return reduced + return reduced_frames def _detect_levels(self, reduced_universe: Any) -> Any: """Detect hierarchy levels for each molecule in the reduced universe. diff --git a/CodeEntropy/levels/dihedrals.py b/CodeEntropy/levels/dihedrals.py index 0b402789..03fd2dbb 100644 --- a/CodeEntropy/levels/dihedrals.py +++ b/CodeEntropy/levels/dihedrals.py @@ -39,9 +39,6 @@ def build_conformational_states( data_container: Any, levels: dict[Any, list[str]], groups: dict[int, list[Any]], - start: int, - end: int, - step: int, bin_width: float, progress: _RichProgressSink | None = None, ) -> tuple[dict[UAKey, list[str]], list[list[str]], dict[UAKey, int], list[int]]: @@ -62,9 +59,6 @@ def build_conformational_states( levels: Mapping of molecule_id -> iterable of enabled level names (e.g., ["united_atom", "residue"]). groups: Mapping of group_id -> list of molecule_ids. - start: Inclusive start frame index. - end: Exclusive end frame index. - step: Frame stride. bin_width: Histogram bin width in degrees used when identifying peak dihedral populations. progress: Optional progress sink (e.g., from @@ -81,7 +75,6 @@ def build_conformational_states( Notes: - This function advances progress once per group_id. - - Frame slicing arguments (start/end/step) are forwarded to downstream helpers as implemented in this module. """ number_groups = len(groups) @@ -131,9 +124,6 @@ def build_conformational_states( dihedrals_ua=dihedrals_ua, dihedrals_res=dihedrals_res, bin_width=bin_width, - start=start, - end=end, - step=step, level_list=levels[molecules[0]], ) @@ -145,9 +135,6 @@ def build_conformational_states( peaks_ua=peaks_ua, dihedrals_res=dihedrals_res, peaks_res=peaks_res, - start=start, - end=end, - step=step, level_list=levels[molecules[0]], states_ua=states_ua, states_res=states_res, @@ -252,9 +239,6 @@ def _collect_peaks_for_group( dihedrals_ua: list[list[Any]], dihedrals_res: list[Any], bin_width: float, - start: int, - end: int, - step: int, level_list: list[str], ) -> tuple[list[list[Any]], list[Any]]: """Compute histogram peaks for UA and residue dihedral sets. @@ -280,9 +264,6 @@ def _collect_peaks_for_group( molecules=molecules, dihedrals=dihedrals_ua[res_id], bin_width=bin_width, - start=start, - end=end, - step=step, ) elif level == "residue": @@ -295,9 +276,6 @@ def _collect_peaks_for_group( molecules=molecules, dihedrals=dihedrals_res, bin_width=bin_width, - start=start, - end=end, - step=step, ) return peaks_ua, peaks_res @@ -308,9 +286,6 @@ def _identify_peaks( molecules: list[Any], dihedrals: list[Any], bin_width: float, - start: int, - end: int, - step: int, ) -> list[list[float]]: """Identify histogram peaks ("convex turning points") for each dihedral. @@ -324,9 +299,6 @@ def _identify_peaks( molecules: Molecule ids in the group. dihedrals: Dihedral AtomGroups. bin_width: Histogram bin width (degrees). - start: Unused in legacy sampling. - end: Unused in legacy sampling. - step: Unused in legacy sampling. Returns: List of peaks per dihedral (peak_values[dihedral_index] -> list of peaks). @@ -406,9 +378,6 @@ def _assign_states_for_group( peaks_ua: list[list[Any]], dihedrals_res: list[Any], peaks_res: list[Any], - start: int, - end: int, - step: int, level_list: list[str], states_ua: dict[UAKey, list[str]], states_res: list[list[str]], @@ -429,9 +398,6 @@ def _assign_states_for_group( molecules=molecules, dihedrals=dihedrals_ua[res_id], peaks=peaks_ua[res_id], - start=start, - end=end, - step=step, ) elif level == "residue": @@ -444,9 +410,6 @@ def _assign_states_for_group( molecules=molecules, dihedrals=dihedrals_res, peaks=peaks_res, - start=start, - end=end, - step=step, ) def _assign_states( @@ -455,9 +418,6 @@ def _assign_states( molecules: list[Any], dihedrals: list[Any], peaks: list[list[Any]], - start: int, - end: int, - step: int, ) -> list[str]: """Assign discrete state labels for the provided dihedrals. @@ -471,9 +431,6 @@ def _assign_states( molecules: Molecule ids in the group. dihedrals: Dihedral AtomGroups. peaks: Peaks per dihedral. - start: Unused in legacy sampling. - end: Unused in legacy sampling. - step: Unused in legacy sampling. Returns: List of state labels (strings). diff --git a/CodeEntropy/levels/level_dag.py b/CodeEntropy/levels/level_dag.py index f43f1efc..7b1388ed 100644 --- a/CodeEntropy/levels/level_dag.py +++ b/CodeEntropy/levels/level_dag.py @@ -179,28 +179,14 @@ def _run_frame_stage( Notes: The task title shows the current frame index being processed. """ - u = shared_data["reduced_universe"] - start, end, step = shared_data["start"], shared_data["end"], shared_data["step"] + n_frames = shared_data["n_frames"] task: TaskID | None = None total_frames: int | None = None if progress is not None: try: - n_frames = len(u.trajectory) - - s = 0 if start is None else int(start) - e = n_frames if end is None else int(end) - - if e < 0: - e = n_frames + e - - e = max(0, min(e, n_frames)) - s = max(0, min(s, e)) - - st = 1 if step is None else int(step) - if st > 0: - total_frames = max(0, (e - s + st - 1) // st) + total_frames = n_frames except Exception: total_frames = None @@ -210,11 +196,11 @@ def _run_frame_stage( title="Initializing", ) - for ts in u.trajectory[start:end:step]: + for ts in range(n_frames): if progress is not None and task is not None: - progress.update(task, title=f"Frame {ts.frame}") + progress.update(task, title=f"Frame {ts}") - frame_out = self._frame_dag.execute_frame(shared_data, ts.frame) + frame_out = self._frame_dag.execute_frame(shared_data, ts) self._reduce_one_frame(shared_data, frame_out) if progress is not None and task is not None: diff --git a/CodeEntropy/levels/mda.py b/CodeEntropy/levels/mda.py index f8cdec40..b28cb3cb 100644 --- a/CodeEntropy/levels/mda.py +++ b/CodeEntropy/levels/mda.py @@ -121,6 +121,30 @@ def extract_fragment( selection_string = f"index {frag.indices[0]}:{frag.indices[-1]}" return self.select_atoms(universe, selection_string) + def extract_fragments( + self, universe: mda.Universe, molecule_ids: list[int] + ) -> mda.Universe: + """Extract a single molecule (fragment) as a standalone reduced universe. + + Args: + universe: The source universe. + molecule_id: Fragment index in `universe.atoms.fragments`. + + Returns: + A reduced universe containing only the atoms of the selected fragment. + """ + group_indices = [] + for mol_id in molecule_ids: + frag = universe.atoms.fragments[mol_id] + group_indices.extend(frag.indices) + + selection_string = "index " + for i in group_indices: + group_indices[i] = int(group_indices[i]) + selection_string += f"{group_indices[i]} " + + return self.select_atoms(universe, selection_string) + def merge_forces( self, tprfile: str, diff --git a/CodeEntropy/levels/neighbors.py b/CodeEntropy/levels/neighbors.py index a91b3950..7f77fc98 100644 --- a/CodeEntropy/levels/neighbors.py +++ b/CodeEntropy/levels/neighbors.py @@ -32,7 +32,7 @@ def __init__(self): self._levels = None self._search = Search() - def get_neighbors(self, universe, levels, groups, search_type): + def get_neighbors(self, universe, levels, groups, n_frames, search_type): """ Find the neighbors relative to the central molecule. @@ -54,22 +54,16 @@ def get_neighbors(self, universe, levels, groups, search_type): number_neighbors = {} average_number_neighbors = {} - number_frames = len(universe.trajectory) - for group_id in groups.keys(): molecules = groups[group_id] highest_level = levels[molecules[0]][-1] for mol_id in molecules: - for timestep in range(number_frames): - # This is to get MDAnalysis to get the information from the - # correct frame of the trajectory - universe.trajectory[timestep] - + for timestep in range(n_frames): if search_type == "RAD": # Use the relative angular distance method to find neighbors neighbors = self._search.get_RAD_neighbors( - universe=universe, mol_id=mol_id + universe=universe, mol_id=mol_id, timestep=timestep ) elif search_type == "grid": @@ -78,6 +72,7 @@ def get_neighbors(self, universe, levels, groups, search_type): universe=universe, mol_id=mol_id, highest_level=highest_level, + timestep=timestep, ) else: # Raise error for unavailale search_type @@ -91,9 +86,7 @@ def get_neighbors(self, universe, levels, groups, search_type): # Get the average number of neighbors: # dividing the sum by the number of molecules and number of frames number = np.sum(number_neighbors[group_id]) - average_number_neighbors[group_id] = number / ( - len(molecules) * number_frames - ) + average_number_neighbors[group_id] = number / (len(molecules) * n_frames) logger.debug( f"group: {group_id}" f"number neighbors {average_number_neighbors[group_id]}" diff --git a/CodeEntropy/levels/nodes/conformations.py b/CodeEntropy/levels/nodes/conformations.py index 89eb63a5..5e84be21 100644 --- a/CodeEntropy/levels/nodes/conformations.py +++ b/CodeEntropy/levels/nodes/conformations.py @@ -23,15 +23,11 @@ class ConformationalStateConfig: """Configuration for conformational state construction. Attributes: - start: Start frame index (inclusive). - end: End frame index (exclusive). - step: Frame stride. + n_frames: Number of frames to be analyised. bin_width: Histogram bin width in degrees. """ - start: int - end: int - step: int + n_frames: int bin_width: int @@ -70,7 +66,7 @@ def run( - "reduced_universe" - "levels" - "groups" - - "start", "end", "step" + - "n_frames" - "args" with attribute "bin_width" progress: Optional progress sink provided by ResultsReporter.progress(). @@ -80,18 +76,14 @@ def run( u = shared_data["reduced_universe"] levels = shared_data["levels"] groups = shared_data["groups"] - - cfg = self._build_config(shared_data) + bin_width = int(shared_data["args"].bin_width) states_ua, states_res, flexible_ua, flexible_res = ( self._dihedral_analysis.build_conformational_states( data_container=u, levels=levels, groups=groups, - start=cfg.start, - end=cfg.end, - step=cfg.step, - bin_width=cfg.bin_width, + bin_width=bin_width, progress=progress, ) ) @@ -111,21 +103,3 @@ def run( shared_data["flexible_dihedrals"] = flexible_states return {"conformational_states": conformational_states} - - @staticmethod - def _build_config(shared_data: SharedData) -> ConformationalStateConfig: - """Extract and validate configuration from shared_data. - - Args: - shared_data: Shared data dictionary. - - Returns: - ConformationalStateConfig with normalized integer fields. - """ - start = int(shared_data["start"]) - end = int(shared_data["end"]) - step = int(shared_data["step"]) - bin_width = int(shared_data["args"].bin_width) - return ConformationalStateConfig( - start=start, end=end, step=step, bin_width=bin_width - ) diff --git a/CodeEntropy/levels/nodes/find_neighbors.py b/CodeEntropy/levels/nodes/find_neighbors.py index 3c9bd80f..36cb0b2c 100644 --- a/CodeEntropy/levels/nodes/find_neighbors.py +++ b/CodeEntropy/levels/nodes/find_neighbors.py @@ -59,7 +59,7 @@ def run( - "reduced_universe" - "levels" - "groups" - - "start", "end", "step" + - "n_frames" - "args" with attribute "bin_width" progress: Optional progress sink provided by ResultsReporter.progress(). @@ -69,6 +69,7 @@ def run( u = shared_data["reduced_universe"] levels = shared_data["levels"] groups = shared_data["groups"] + n_frames = int(shared_data["n_frames"]) search_type = shared_data["args"].search_type # Get average number of neighbors @@ -76,6 +77,7 @@ def run( universe=u, levels=levels, groups=groups, + n_frames=n_frames, search_type=search_type, ) diff --git a/CodeEntropy/levels/search.py b/CodeEntropy/levels/search.py index 0e54e772..71c5160f 100644 --- a/CodeEntropy/levels/search.py +++ b/CodeEntropy/levels/search.py @@ -22,7 +22,7 @@ def __init__(self): self._universe = None self._mol_id = None - def get_RAD_neighbors(self, universe, mol_id): + def get_RAD_neighbors(self, universe, mol_id, timestep): """ Find the neighbors of molecule with index mol_id. @@ -34,6 +34,7 @@ def get_RAD_neighbors(self, universe, mol_id): neighbor_indices (list of ints): the list of neighboring molecule indices. """ + universe.trajectory[timestep] number_molecules = len(universe.atoms.fragments) central_position = universe.atoms.fragments[mol_id].center_of_mass() @@ -52,12 +53,18 @@ def get_RAD_neighbors(self, universe, mol_id): # Get indices of neighbors neighbor_indices = self._get_RAD_indices( - central_position, sorted_dist, universe, number_molecules + central_position, + sorted_dist, + universe, + number_molecules, + timestep, ) return neighbor_indices - def _get_RAD_indices(self, i_coords, sorted_distances, system, number_molecules): + def _get_RAD_indices( + self, i_coords, sorted_distances, system, number_molecules, timestep + ): # pylint: disable=too-many-locals r""" For a given set of atom coordinates, find its RAD shell from the distance @@ -85,6 +92,7 @@ def _get_RAD_indices(self, i_coords, sorted_distances, system, number_molecules) Returns: shell: list of indices of particles in the RAD shell of neighbors. """ + system.trajectory[timestep] # 1. truncate neighbor list to closest 30 united atoms and iterate # through neighbors from closest to furthest/ shell = [] @@ -186,7 +194,7 @@ def get_distance(self, j_position, i_position, dimensions): return distance - def get_grid_neighbors(self, universe, mol_id, highest_level): + def get_grid_neighbors(self, universe, mol_id, highest_level, timestep): """ Use MDAnalysis neighbor search to find neighbors. @@ -205,6 +213,7 @@ def get_grid_neighbors(self, universe, mol_id, highest_level): Returns: neighbors: MDAnalysis atomgroup of the neighboring particles. """ + universe.trajectory[timestep] search_object = mda.lib.NeighborSearch.AtomNeighborSearch(universe.atoms) fragment = universe.atoms.fragments[mol_id] selection_string = f"index {fragment.indices[0]}:{fragment.indices[-1]}" diff --git a/tests/unit/CodeEntropy/entropy/test_workflow.py b/tests/unit/CodeEntropy/entropy/test_workflow.py index eb87e394..8e7e27bc 100644 --- a/tests/unit/CodeEntropy/entropy/test_workflow.py +++ b/tests/unit/CodeEntropy/entropy/test_workflow.py @@ -211,8 +211,12 @@ def test_build_reduced_universe_non_all_selects_and_writes_universe(): reduced = MagicMock() reduced.trajectory = list(range(2)) + reduced2 = MagicMock() + reduced2.trajectory = list(range(2)) + uops = MagicMock() uops.select_atoms.return_value = reduced + uops.select_frames.return_value = reduced2 run_manager = MagicMock() reporter = MagicMock() @@ -229,9 +233,9 @@ def test_build_reduced_universe_non_all_selects_and_writes_universe(): out = wf._build_reduced_universe() - assert out is reduced + assert out is reduced2 uops.select_atoms.assert_called_once_with(universe, "protein") - run_manager.write_universe.assert_called_once() + uops.select_frames.assert_called_once_with(reduced, 0, -1, 1) def test_compute_water_entropy_updates_selection_string_and_calls_internal_method(): @@ -303,7 +307,17 @@ def test_build_reduced_universe_all_returns_original_universe(): output_file="out.json", ) universe = MagicMock() + + reduced = MagicMock() + reduced.trajectory = list(range(2)) + + reduced2 = MagicMock() + reduced2.trajectory = list(range(2)) + uops = MagicMock() + uops.select_atoms.return_value = reduced + uops.select_frames.return_value = reduced2 + run_manager = MagicMock() wf = EntropyWorkflow( run_manager, args, universe, MagicMock(), MagicMock(), MagicMock(), uops @@ -311,9 +325,10 @@ def test_build_reduced_universe_all_returns_original_universe(): out = wf._build_reduced_universe() - assert out is universe + assert out is reduced2 uops.select_atoms.assert_not_called() - run_manager.write_universe.assert_not_called() + uops.select_frames.assert_called_once() + run_manager.write_universe.assert_called_once() def test_split_water_groups_partitions_correctly(): diff --git a/tests/unit/CodeEntropy/levels/nodes/test_conformations_node.py b/tests/unit/CodeEntropy/levels/nodes/test_conformations_node.py index 85f145f7..7e17f075 100644 --- a/tests/unit/CodeEntropy/levels/nodes/test_conformations_node.py +++ b/tests/unit/CodeEntropy/levels/nodes/test_conformations_node.py @@ -19,6 +19,7 @@ def test_compute_conformational_states_node_runs_and_writes_shared_data(): "start": 0, "end": 10, "step": 1, + "n_frames": 10, "args": SimpleNamespace(bin_width=10), } diff --git a/tests/unit/CodeEntropy/levels/nodes/test_find_neighbors.py b/tests/unit/CodeEntropy/levels/nodes/test_find_neighbors.py index 3cfda97e..93185021 100644 --- a/tests/unit/CodeEntropy/levels/nodes/test_find_neighbors.py +++ b/tests/unit/CodeEntropy/levels/nodes/test_find_neighbors.py @@ -18,6 +18,7 @@ def test_compute_find_neighbors_node_runs_and_writes_shared_data(): "start": 0, "end": 10, "step": 1, + "n_frames": 10, "args": SimpleNamespace(search_type="RAD"), } diff --git a/tests/unit/CodeEntropy/levels/test_dihedrals.py b/tests/unit/CodeEntropy/levels/test_dihedrals.py index 6590ecf7..cc3104e6 100644 --- a/tests/unit/CodeEntropy/levels/test_dihedrals.py +++ b/tests/unit/CodeEntropy/levels/test_dihedrals.py @@ -135,9 +135,6 @@ def test_collect_peaks_for_group_sets_empty_outputs_when_no_dihedrals(): dihedrals_ua=dihedrals_ua, dihedrals_res=dihedrals_res, bin_width=30.0, - start=0, - end=10, - step=1, level_list=["united_atom", "residue"], ) @@ -172,9 +169,6 @@ def run(self): molecules=[0], dihedrals=[MagicMock()], bin_width=180.0, - start=0, - end=2, - step=1, ) assert out == [[15.0]] @@ -214,9 +208,6 @@ def run(self): molecules=[0, 1], dihedrals=["D0"], peaks=peaks, - start=0, - end=2, - step=1, ) assert states == ["0", "1", "0", "1"] @@ -240,9 +231,6 @@ def test_assign_states_for_group_sets_empty_lists_and_delegates_for_nonempty(): peaks_ua=[[], [["p"]]], dihedrals_res=[], peaks_res=[], - start=0, - end=2, - step=1, level_list=["united_atom", "residue"], states_ua=states_ua, states_res=states_res, @@ -275,9 +263,6 @@ def test_build_conformational_states_runs_group_and_skips_empty_group(monkeypatc data_container=MagicMock(), levels=levels, groups=groups, - start=0, - end=1, - step=1, bin_width=30.0, ) @@ -321,9 +306,6 @@ def run(self): molecules=[0], dihedrals=["D0", "D1"], bin_width=180.0, - start=0, - end=2, - step=1, ) assert len(out) == 2 @@ -351,9 +333,6 @@ def run(self): molecules=[0], dihedrals=[], peaks=[], - start=0, - end=3, - step=1, ) assert out_state == [] @@ -386,9 +365,6 @@ def run(self): molecules=[0, 1], dihedrals=["D0"], bin_width=90.0, - start=0, - end=2, - step=1, ) assert len(peaks) == 1 @@ -417,9 +393,6 @@ def run(self): molecules=[0], dihedrals=["D0"], bin_width=90.0, - start=0, - end=2, - step=1, ) assert isinstance(peaks, list) @@ -442,9 +415,6 @@ def test_assign_states_for_group_residue_nonempty_calls_assign_states(): peaks_ua=[[]], dihedrals_res=["D"], peaks_res=[["p"]], - start=0, - end=1, - step=1, level_list=["residue"], states_ua=states_ua, states_res=states_res, @@ -457,41 +427,6 @@ def test_assign_states_for_group_residue_nonempty_calls_assign_states(): spy.assert_called_once() -def test_assign_states_first_empty_then_extend(): - uops = MagicMock() - dt = ConformationStateBuilder(universe_operations=uops) - - mol0 = MagicMock() - mol0.trajectory = [] - mol1 = MagicMock() - mol1.trajectory = [0] - - uops.extract_fragment.side_effect = [mol0, mol1] - - angles = np.array([[10.0]], dtype=float) - - class _FakeDihedral: - def __init__(self, _): - pass - - def run(self): - return SimpleNamespace(results=SimpleNamespace(angles=angles)) - - with patch("CodeEntropy.levels.dihedrals.Dihedral", _FakeDihedral): - states, num_flex = dt._assign_states( - data_container=MagicMock(), - molecules=[0, 1], - dihedrals=["D0"], - peaks=[[10.0]], - start=0, - end=1, - step=1, - ) - - assert states == ["0"] - assert num_flex == 0 - - def test_collect_peaks_for_group_calls_identify_peaks_for_ua_and_residue(): dt = ConformationStateBuilder(universe_operations=MagicMock()) @@ -509,9 +444,6 @@ def test_collect_peaks_for_group_calls_identify_peaks_for_ua_and_residue(): dihedrals_ua=dihedrals_ua, dihedrals_res=dihedrals_res, bin_width=30.0, - start=0, - end=10, - step=1, level_list=["united_atom", "residue"], ) @@ -544,9 +476,6 @@ def run(self): molecules=[0], dihedrals=["D0"], peaks=peaks, - start=0, - end=2, - step=1, ) assert states == ["1", "0"] @@ -564,9 +493,6 @@ def test_build_conformational_states_with_progress_handles_no_groups(): data_container=MagicMock(), levels={}, groups={}, # empty - start=0, - end=1, - step=1, bin_width=30.0, progress=progress, ) @@ -592,9 +518,6 @@ def test_build_conformational_states_with_progress_skips_empty_molecule_group(): data_container=MagicMock(), levels=levels, groups=groups, - start=0, - end=1, - step=1, bin_width=30.0, progress=progress, ) @@ -627,9 +550,6 @@ def test_build_conformational_states_with_progress_updates_title_per_group(monke data_container=MagicMock(), levels=levels, groups=groups, - start=0, - end=1, - step=1, bin_width=30.0, progress=progress, ) diff --git a/tests/unit/CodeEntropy/levels/test_level_dag_orchestration.py b/tests/unit/CodeEntropy/levels/test_level_dag_orchestration.py index 17a5a93a..1895cd08 100644 --- a/tests/unit/CodeEntropy/levels/test_level_dag_orchestration.py +++ b/tests/unit/CodeEntropy/levels/test_level_dag_orchestration.py @@ -29,6 +29,7 @@ def test_execute_sets_default_axes_manager_once(): "start": 0, "end": 0, "step": 1, + "n_frames": 1, } dag._run_static_stage = MagicMock() @@ -64,7 +65,7 @@ def test_run_frame_stage_iterates_selected_frames_and_reduces_each(): u = MagicMock() u.trajectory = [ts0, ts1] - shared = {"reduced_universe": u, "start": 0, "end": 2, "step": 1} + shared = {"reduced_universe": u, "start": 0, "end": 2, "step": 1, "n_frames": 2} dag._frame_dag = MagicMock() dag._frame_dag.execute_frame.side_effect = [ @@ -79,8 +80,6 @@ def test_run_frame_stage_iterates_selected_frames_and_reduces_each(): assert dag._frame_dag.execute_frame.call_count == 2 assert dag._reduce_one_frame.call_count == 2 - dag._frame_dag.execute_frame.assert_any_call(shared, 10) - dag._frame_dag.execute_frame.assert_any_call(shared, 11) def test_incremental_mean_handles_non_copyable_values(): @@ -295,7 +294,7 @@ def test_run_frame_stage_with_progress_creates_task_and_updates_titles(): u = MagicMock() u.trajectory = [ts0, ts1] - shared = {"reduced_universe": u, "start": 0, "end": 2, "step": 1} + shared = {"reduced_universe": u, "start": 0, "end": 2, "step": 1, "n_frames": 2} dag._frame_dag = MagicMock() dag._frame_dag.execute_frame.return_value = { @@ -310,8 +309,6 @@ def test_run_frame_stage_with_progress_creates_task_and_updates_titles(): dag._run_frame_stage(shared, progress=progress) progress.add_task.assert_called_once() - progress.update.assert_any_call(77, title="Frame 10") - progress.update.assert_any_call(77, title="Frame 11") assert progress.advance.call_count == 2 @@ -324,9 +321,7 @@ def test_run_frame_stage_with_negative_end_computes_total_frames(): shared = { "reduced_universe": u, - "start": 0, - "end": -1, - "step": 1, + "n_frames": 10, } dag._frame_dag = MagicMock() @@ -343,39 +338,6 @@ def test_run_frame_stage_with_negative_end_computes_total_frames(): progress.add_task.assert_called_once() _, kwargs = progress.add_task.call_args - assert kwargs["total"] == 9 - - assert progress.advance.call_count == 9 - - -def test_run_frame_stage_progress_total_frames_falls_back_to_none_on_error(): - - dag = LevelDAG() - - class BadTrajectory: - def __len__(self): - raise RuntimeError("boom") - - def __getitem__(self, item): - return [] - - u = type("U", (), {})() - u.trajectory = BadTrajectory() - - shared = { - "reduced_universe": u, - "start": 0, - "end": 10, - "step": 1, - } - - dag._frame_dag = MagicMock() - dag._reduce_one_frame = MagicMock() - - progress = MagicMock() - progress.add_task.return_value = 99 + assert kwargs["total"] == 10 - dag._run_frame_stage(shared, progress=progress) - - _, kwargs = progress.add_task.call_args - assert kwargs["total"] is None + assert progress.advance.call_count == 10 diff --git a/tests/unit/CodeEntropy/levels/test_level_dag_reduction.py b/tests/unit/CodeEntropy/levels/test_level_dag_reduction.py index 5c8c4716..5b00f401 100644 --- a/tests/unit/CodeEntropy/levels/test_level_dag_reduction.py +++ b/tests/unit/CodeEntropy/levels/test_level_dag_reduction.py @@ -75,7 +75,7 @@ def test_run_frame_stage_calls_execute_frame_for_each_ts(simple_ts_list): u = MagicMock() u.trajectory = simple_ts_list - shared = {"reduced_universe": u, "start": 0, "end": 3, "step": 1} + shared = {"reduced_universe": u, "start": 0, "end": 3, "step": 1, "n_frames": 3} dag._frame_dag = MagicMock() dag._frame_dag.execute_frame.side_effect = lambda shared_data, frame_index: { diff --git a/tests/unit/CodeEntropy/levels/test_neighbors.py b/tests/unit/CodeEntropy/levels/test_neighbors.py index a9f997d2..c7211d5e 100644 --- a/tests/unit/CodeEntropy/levels/test_neighbors.py +++ b/tests/unit/CodeEntropy/levels/test_neighbors.py @@ -33,10 +33,11 @@ def test_raises_error_unknown_search_type(): universe.trajectory.__len__.return_value = 2 levels = {0: ["united_atom"]} groups = {0: [0]} + n_frames = 2 search_type = "weird" with pytest.raises(ValueError): - neighbors.get_neighbors(universe, levels, groups, search_type) + neighbors.get_neighbors(universe, levels, groups, n_frames, search_type) def test_average_number_neighbors_RAD(): @@ -46,11 +47,12 @@ def test_average_number_neighbors_RAD(): universe.trajectory.__len__.return_value = 2 levels = {0: ["united_atom"]} groups = {0: [0]} + n_frames = 2 search_type = "RAD" neighbors._search.get_RAD_neighbors = MagicMock(side_effect=[[1, 2, 3], [1, 3]]) - result = neighbors.get_neighbors(universe, levels, groups, search_type) + result = neighbors.get_neighbors(universe, levels, groups, n_frames, search_type) assert result == {0: np.float64(2.5)} @@ -62,11 +64,12 @@ def test_average_number_neighbors_grid(): universe.trajectory.__len__.return_value = 2 levels = {0: ["united_atom"]} groups = {0: [0]} + n_frames = 2 search_type = "grid" neighbors._search.get_grid_neighbors = MagicMock(side_effect=[[1, 2, 3], [1, 3]]) - result = neighbors.get_neighbors(universe, levels, groups, search_type) + result = neighbors.get_neighbors(universe, levels, groups, n_frames, search_type) assert result == {0: np.float64(2.5)} @@ -78,13 +81,14 @@ def test_average_number_neighbors_RAD_multiple(): universe.trajectory.__len__.return_value = 2 levels = {0: ["united_atom"]} groups = {0: [0, 1]} + n_frames = 2 search_type = "RAD" neighbors._search.get_RAD_neighbors = MagicMock( side_effect=[[1, 2, 3, 5], [1, 3], [2, 3, 4, 5], [3, 5]] ) - result = neighbors.get_neighbors(universe, levels, groups, search_type) + result = neighbors.get_neighbors(universe, levels, groups, n_frames, search_type) assert result == {0: np.float64(3.0)} diff --git a/tests/unit/CodeEntropy/levels/test_search.py b/tests/unit/CodeEntropy/levels/test_search.py index 51b15e0c..987978f8 100644 --- a/tests/unit/CodeEntropy/levels/test_search.py +++ b/tests/unit/CodeEntropy/levels/test_search.py @@ -67,7 +67,7 @@ def test_get_RAD_neighbors(tmp_path: Path): universe_operations = UniverseOperations() universe = CodeEntropyRunner._build_universe(args, universe_operations) - neighbors = search.get_RAD_neighbors(universe=universe, mol_id=0) + neighbors = search.get_RAD_neighbors(universe=universe, mol_id=0, timestep=0) assert neighbors == [151, 3, 75, 219, 229, 488, 460, 118, 230, 326] @@ -119,7 +119,7 @@ def test_get_grid_neighbors(tmp_path: Path): universe = CodeEntropyRunner._build_universe(args, universe_operations) neighbors = search.get_grid_neighbors( - universe=universe, mol_id=0, highest_level="united_atom" + universe=universe, mol_id=0, highest_level="united_atom", timestep=0 ) assert (neighbors == [151, 3, 75, 219]).all @@ -184,6 +184,7 @@ def test_get_RAD_indices_breaks_when_angle_is_nan(): sorted_distances=sorted_distances, system=system, number_molecules=number_molecules, + timestep=0, ) assert result == [1, 2] @@ -218,9 +219,7 @@ def test_get_grid_neighbors_uses_residue_search_for_non_united_atom(): mock_ans.search.return_value = search_result result = search.get_grid_neighbors( - universe=universe, - mol_id=0, - highest_level="residue", + universe=universe, mol_id=0, highest_level="residue", timestep=0 ) universe.select_atoms.assert_called_once_with("index 4:6") @@ -264,6 +263,7 @@ def test_get_grid_neighbors_uses_atom_search_for_united_atom(): universe=universe, mol_id=0, highest_level="united_atom", + timestep=0, ) universe.select_atoms.assert_called_once_with("index 10:11") From 53648e0e70f43c0135c1cd6a745ae719c18784a1 Mon Sep 17 00:00:00 2001 From: skfegan Date: Thu, 9 Apr 2026 13:39:41 +0100 Subject: [PATCH 2/5] Ensuring dihedral analysis loops over molecules correctly. --- CodeEntropy/levels/dihedrals.py | 419 +++++++++++++++++--------------- 1 file changed, 220 insertions(+), 199 deletions(-) diff --git a/CodeEntropy/levels/dihedrals.py b/CodeEntropy/levels/dihedrals.py index 03fd2dbb..f52e387a 100644 --- a/CodeEntropy/levels/dihedrals.py +++ b/CodeEntropy/levels/dihedrals.py @@ -109,33 +109,20 @@ def build_conformational_states( if progress is not None and task is not None: progress.update(task, title=f"Group {group_id}") - mol = self._universe_operations.extract_fragment( - data_container, molecules[0] - ) - - dihedrals_ua, dihedrals_res = self._collect_dihedrals_for_group( - mol=mol, - level_list=levels[molecules[0]], - ) - - peaks_ua, peaks_res = self._collect_peaks_for_group( + peaks_ua, peaks_res = self._identify_peaks( data_container=data_container, molecules=molecules, - dihedrals_ua=dihedrals_ua, - dihedrals_res=dihedrals_res, bin_width=bin_width, level_list=levels[molecules[0]], ) - self._assign_states_for_group( + self._assign_states( data_container=data_container, group_id=group_id, molecules=molecules, - dihedrals_ua=dihedrals_ua, + level_list=levels[molecules[0]], peaks_ua=peaks_ua, - dihedrals_res=dihedrals_res, peaks_res=peaks_res, - level_list=levels[molecules[0]], states_ua=states_ua, states_res=states_res, flexible_ua=flexible_ua, @@ -147,35 +134,6 @@ def build_conformational_states( return states_ua, states_res, flexible_ua, flexible_res - def _collect_dihedrals_for_group( - self, mol: Any, level_list: list[str] - ) -> tuple[list[list[Any]], list[Any]]: - """Collect UA and residue dihedral AtomGroups for a group. - - Args: - mol: Representative molecule AtomGroup. - level_list: List of enabled hierarchy levels. - - Returns: - Tuple: - dihedrals_ua: List of per-residue dihedral AtomGroups. - dihedrals_res: List of residue-level dihedral AtomGroups. - """ - num_residues = len(mol.residues) - dihedrals_ua: list[list[Any]] = [[] for _ in range(num_residues)] - dihedrals_res: list[Any] = [] - - for level in level_list: - if level == "united_atom": - for res_id in range(num_residues): - heavy_res = self._select_heavy_residue(mol, res_id) - dihedrals_ua[res_id] = self._get_dihedrals(heavy_res, level) - - elif level == "residue": - dihedrals_res = self._get_dihedrals(mol, level) - - return dihedrals_ua, dihedrals_res - def _select_heavy_residue(self, mol: Any, res_id: int) -> Any: """Select heavy atoms in a residue by residue index. @@ -232,60 +190,12 @@ def _get_dihedrals(self, data_container: Any, level: str) -> list[Any]: logger.debug(f"Level: {level}, Dihedrals: {atom_groups}") return atom_groups - def _collect_peaks_for_group( - self, - data_container: Any, - molecules: list[Any], - dihedrals_ua: list[list[Any]], - dihedrals_res: list[Any], - bin_width: float, - level_list: list[str], - ) -> tuple[list[list[Any]], list[Any]]: - """Compute histogram peaks for UA and residue dihedral sets. - - Returns: - Tuple: - peaks_ua: list of peaks per residue - (each item is list-of-peaks per dihedral) - peaks_res: list-of-peaks per dihedral for residue level (or []) - """ - peaks_ua: list[list[Any]] = [[] for _ in range(len(dihedrals_ua))] - peaks_res: list[Any] = [] - - for level in level_list: - if level == "united_atom": - for res_id in range(len(dihedrals_ua)): - if len(dihedrals_ua[res_id]) == 0: - # No dihedrals means no peaks - peaks_ua[res_id] = [] - else: - peaks_ua[res_id] = self._identify_peaks( - data_container=data_container, - molecules=molecules, - dihedrals=dihedrals_ua[res_id], - bin_width=bin_width, - ) - - elif level == "residue": - if len(dihedrals_res) == 0: - # No dihedrals means no peaks - peaks_res = [] - else: - peaks_res = self._identify_peaks( - data_container=data_container, - molecules=molecules, - dihedrals=dihedrals_res, - bin_width=bin_width, - ) - - return peaks_ua, peaks_res - def _identify_peaks( self, data_container: Any, molecules: list[Any], - dihedrals: list[Any], bin_width: float, + level_list: list[Any], ) -> list[list[float]]: """Identify histogram peaks ("convex turning points") for each dihedral. @@ -297,31 +207,122 @@ def _identify_peaks( Args: data_container: MDAnalysis universe. molecules: Molecule ids in the group. - dihedrals: Dihedral AtomGroups. + levels: Molecule levels. bin_width: Histogram bin width (degrees). Returns: List of peaks per dihedral (peak_values[dihedral_index] -> list of peaks). """ - peak_values: list[list[float]] = [] + rep_mol = self._universe_operations.extract_fragment(data_container, 0) + number_frames = len(rep_mol.trajectory) + num_residues = len(rep_mol.residues) - for dihedral_index in range(len(dihedrals)): - phi: list[float] = [] + peaks_ua: list[list[Any]] = [[] for _ in range(num_residues)] + peaks_res: list[Any] = [] + phi_ua: list[list[Any]] = [[] for _ in range(num_residues)] + phi_res: list[Any] = [] - for molecule in molecules: - mol = self._universe_operations.extract_fragment( - data_container, molecule + for molecule in molecules: + mol = self._universe_operations.extract_fragment(data_container, molecule) + + for level in level_list: + if level == "united_atom": + for res_id in range(num_residues): + heavy_res = self._select_heavy_residue(mol, res_id) + dihedrals = self._get_dihedrals(heavy_res, level) + num_dihedrals_ua = len(dihedrals) + if num_dihedrals_ua == 0: + # No dihedrals, no peaks + phi_ua[res_id] = [] + + else: + dihedral_results = Dihedral(dihedrals).run() + phis = self._process_dihedral_phi( + dihedral_results, + num_dihedrals_ua, + number_frames, + ) + phi_ua[res_id].append(phis) + + elif level == "residue": + dihedrals = self._get_dihedrals(mol, level) + num_dihedrals_res = len(dihedrals) + if num_dihedrals_res == 0: + # No dihedrals, no peaks + phi_res = [] + + else: + dihedral_results = Dihedral(dihedrals).run() + phis = self._process_dihedral_phi( + dihedral_results, + num_dihedrals_res, + number_frames, + ) + phi_res.append(phis) + + for level in level_list: + if level == "united_atom": + for res_id in range(num_residues): + peaks_ua[res_id] = self._process_histogram( + num_dihedrals_ua, phi_ua[res_id], bin_width + ) + + elif level == "residue": + peaks_res = self._process_histogram( + num_dihedrals_res, phi_res, bin_width ) - number_frames = len(mol.trajectory) - dihedral_results = Dihedral(dihedrals).run() + return peaks_ua, peaks_res + + def _process_dihedral_phi( + self, + dihedral_results, + num_dihedrals, + number_frames, + ): + """ + Find peaks from array of dihedral angle values. + + Args: + dihedral_results: the result of MDAnalysis Dihedrals.run. + num_dihedrals: the number of dihedrals in the molecule or residue. + + Returns: + peaks + """ + phi_values = [[] for _ in range(num_dihedrals)] + for dihedral_index in range(num_dihedrals): + phi: list[float] = [] + + for timestep in range(number_frames): + value = dihedral_results.results.angles[timestep][dihedral_index] + if value < 0: + value += 360 + phi.append(float(value)) + + phi_values[dihedral_index].append(phi) - for timestep in range(number_frames): - value = dihedral_results.results.angles[timestep][dihedral_index] - if value < 0: - value += 360 - phi.append(float(value)) + return phi_values + def _process_histogram( + self, + num_dihedrals, + phi_values, + bin_width, + ): + """ + Find peaks from array of dihedral angle values. + + Args: + dihedral_results: the result of MDAnalysis Dihedrals.run. + num_dihedrals: the number of dihedrals in the molecule or residue. + + Returns: + peaks + """ + peak_values = [] + for dihedral_index in range(num_dihedrals): + phi = phi_values[dihedral_index] number_bins = int(360 / bin_width) popul, bin_edges = np.histogram(a=phi, bins=number_bins, range=(0, 360)) bin_value = [ @@ -331,9 +332,7 @@ def _identify_peaks( peaks = self._find_histogram_peaks(popul=popul, bin_value=bin_value) peak_values.append(peaks) - logger.debug( - f"Dihedral: {dihedral_index}Peak Values: {peak_values[dihedral_index]}" - ) + logger.debug(f"Dihedral: {dihedral_index} Peaks: {peaks}") return peak_values @@ -369,55 +368,18 @@ def _find_histogram_peaks( return peaks - def _assign_states_for_group( + def _assign_states( self, data_container: Any, group_id: int, molecules: list[Any], - dihedrals_ua: list[list[Any]], + level_list: list[Any], peaks_ua: list[list[Any]], - dihedrals_res: list[Any], peaks_res: list[Any], - level_list: list[str], - states_ua: dict[UAKey, list[str]], - states_res: list[list[str]], - flexible_ua: dict[UAKey, list[int]], - flexible_res: list[int], - ) -> None: - """Assign UA and residue states for a group into output containers.""" - for level in level_list: - if level == "united_atom": - for res_id in range(len(dihedrals_ua)): - key = (group_id, res_id) - if len(dihedrals_ua[res_id]) == 0: - states_ua[key] = [] - flexible_ua[key] = 0 - else: - states_ua[key], flexible_ua[key] = self._assign_states( - data_container=data_container, - molecules=molecules, - dihedrals=dihedrals_ua[res_id], - peaks=peaks_ua[res_id], - ) - - elif level == "residue": - if len(dihedrals_res) == 0: - states_res[group_id] = [] - flexible_res[group_id] = 0 - else: - states_res[group_id], flexible_res[group_id] = self._assign_states( - data_container=data_container, - molecules=molecules, - dihedrals=dihedrals_res, - peaks=peaks_res, - ) - - def _assign_states( - self, - data_container: Any, - molecules: list[Any], - dihedrals: list[Any], - peaks: list[list[Any]], + states_ua: Any, + states_res: Any, + flexible_ua: Any, + flexible_res: Any, ) -> list[str]: """Assign discrete state labels for the provided dihedrals. @@ -435,55 +397,114 @@ def _assign_states( Returns: List of state labels (strings). """ - states: list[str] = [] - num_flexible = 0 + rep_mol = self._universe_operations.extract_fragment(data_container, 0) + number_frames = len(rep_mol.trajectory) + num_residues = len(rep_mol.residues) for molecule in molecules: - conformations: list[list[Any]] = [] mol = self._universe_operations.extract_fragment(data_container, molecule) - number_frames = len(mol.trajectory) - - dihedral_results = Dihedral(dihedrals).run() - - for dihedral_index in range(len(dihedrals)): - conformation: list[Any] = [] - - # Check for flexible dihedrals - if len(peaks[dihedral_index]) > 1 and molecule == 0: - num_flexible += 1 - - # Get conformations - for timestep in range(number_frames): - value = dihedral_results.results.angles[timestep][dihedral_index] - # We want postive values in range 0 to 360 to make - # the peak assignment. - # works using the fact that dihedrals have circular symmetry - # (i.e. -15 degrees = +345 degrees) - if value < 0: - value += 360 - - # Find the peak closest to the dihedral value - distances = [abs(value - peak) for peak in peaks[dihedral_index]] - conformation.append(np.argmin(distances)) - - conformations.append(conformation) - - # Concatenate all the dihedrals in the molecule into the state - # for the frame. - mol_states = [ - state - for state in ( - "".join( - str(int(conformations[d][f])) for d in range(len(dihedrals)) - ) - for f in range(number_frames) - ) - if state - ] - states.extend(mol_states) + for level in level_list: + if level == "united_atom": + for res_id in range(num_residues): + key = (group_id, res_id) + heavy_res = self._select_heavy_residue(mol, res_id) + dihedrals = self._get_dihedrals(heavy_res, level) + num_dihedrals = len(dihedrals) + if num_dihedrals == 0: + # No dihedrals, no conformations + states_ua[key] = [] + flexible_ua[key] = 0 + else: + dihedral_results = Dihedral(dihedrals).run() + states, flexible_ua[key] = self._process_conformations( + peaks_ua[res_id], + dihedral_results, + num_dihedrals, + number_frames, + ) + if key not in states_ua: + states_ua[key] = states + else: + states_ua[key].extend(states) + + logger.debug(f"States UA {key}: {states_ua[key]}") + logger.debug( + f"Number of flexible dihedrals UA {key}: {flexible_ua[key]}" + ) + + if level == "residue": + dihedrals = self._get_dihedrals(mol, level) + num_dihedrals = len(dihedrals) + if num_dihedrals == 0: + # No dihedrals, no conformations + states_res[group_id] = [] + flexible_res[group_id] = 0 + else: + dihedral_results = Dihedral(dihedrals).run() + states, flexible_res[group_id] = self._process_conformations( + peaks_res, + dihedral_results, + num_dihedrals, + number_frames, + molecule, + ) + states_res[group_id].extend(states) + + logger.debug(f"States Res {group_id}: {states_res[group_id]}") + logger.debug( + f"Number of flexible dihedrals Res {group_id}: {flexible_res[group_id]}" + ) + + def _process_conformations( + self, peaks, dihedral_results, num_dihedrals, number_frames + ): + """ + Find conformations + + Args: + peaks: Histogram peaks. + num_dihedrals: Number of dihedral angles in the molecule or residue. + Returns: + conformations + """ + states: list[list[Any]] = [] + conformations: list[list[Any]] = [] + num_flexible = 0 + for dihedral_index in range(num_dihedrals): + conformation: list[Any] = [] + + # Check for flexible dihedrals + if len(peaks[dihedral_index]) > 1: + num_flexible += 1 + + # Get conformations + for timestep in range(number_frames): + value = dihedral_results.results.angles[timestep][dihedral_index] + # We want postive values in range 0 to 360 to make + # the peak assignment. + # works using the fact that dihedrals have circular symmetry + # (i.e. -15 degrees = +345 degrees) + if value < 0: + value += 360 + + # Find the peak closest to the dihedral value + distances = [abs(value - peak) for peak in peaks[dihedral_index]] + conformation.append(np.argmin(distances)) + + conformations.append(conformation) + + # Concatenate all the dihedrals in the molecule into the state + # for the frame. + mol_states = [ + state + for state in ( + "".join(str(int(conformations[d][f])) for d in range(num_dihedrals)) + for f in range(number_frames) + ) + if state + ] - logger.debug(f"States: {states}") - logger.debug(f"Number of flexible dihedrals: {num_flexible}") + states.extend(mol_states) return states, num_flexible From ac1f2ac999409433f391e45cffd116cdecc46096 Mon Sep 17 00:00:00 2001 From: skfegan Date: Tue, 14 Apr 2026 16:47:12 +0100 Subject: [PATCH 3/5] updating counting flexible dihedrals and tests --- CodeEntropy/entropy/workflow.py | 6 +- CodeEntropy/levels/dihedrals.py | 96 +++--- .../unit/CodeEntropy/entropy/test_workflow.py | 2 +- .../CodeEntropy/levels/.test_dihedrals.py.swp | Bin 0 -> 24576 bytes .../unit/CodeEntropy/levels/test_dihedrals.py | 296 ++++++------------ tests/unit/CodeEntropy/levels/test_search.py | 7 +- 6 files changed, 171 insertions(+), 236 deletions(-) create mode 100644 tests/unit/CodeEntropy/levels/.test_dihedrals.py.swp diff --git a/CodeEntropy/entropy/workflow.py b/CodeEntropy/entropy/workflow.py index e31ce2b4..7e52cff4 100644 --- a/CodeEntropy/entropy/workflow.py +++ b/CodeEntropy/entropy/workflow.py @@ -239,9 +239,9 @@ def _build_reduced_universe(self) -> Any: MDAnalysis Universe (reduced according to user selections). """ selection = self._args.selection_string - start = self._args.start - end = self._args.end - step = self._args.step + start = self._args.start or 0 + end = len(self._universe.trajectory) if self._args.end == -1 else self._args.end + step = self._args.step or 1 if selection == "all": reduced_atoms = self._universe else: diff --git a/CodeEntropy/levels/dihedrals.py b/CodeEntropy/levels/dihedrals.py index f52e387a..0c5073ae 100644 --- a/CodeEntropy/levels/dihedrals.py +++ b/CodeEntropy/levels/dihedrals.py @@ -79,9 +79,10 @@ def build_conformational_states( """ number_groups = len(groups) states_ua: dict[UAKey, list[str]] = {} + # states_res: list[list[str]] = [[]] states_res: list[list[str]] = [[] for _ in range(number_groups)] flexible_ua: dict[UAKey, int] = {} - flexible_res: list[int] = [0] * number_groups + flexible_res: list[int] = [] task: TaskID | None = None if progress is not None: @@ -132,6 +133,11 @@ def build_conformational_states( if progress is not None and task is not None: progress.advance(task) + logger.debug(f"States UA: {states_ua}") + logger.debug(f"Number of flexible dihedrals UA: {flexible_ua}") + logger.debug(f"States Res: {states_res}") + logger.debug(f"Number of flexible dihedrals Res: {flexible_res}") + return states_ua, states_res, flexible_ua, flexible_res def _select_heavy_residue(self, mol: Any, res_id: int) -> Any: @@ -217,10 +223,11 @@ def _identify_peaks( number_frames = len(rep_mol.trajectory) num_residues = len(rep_mol.residues) + num_dihedrals_ua: list[Any] = [0 for _ in range(num_residues)] + phi_ua = {} + phi_res: dict[list, list[float]] = {} peaks_ua: list[list[Any]] = [[] for _ in range(num_residues)] peaks_res: list[Any] = [] - phi_ua: list[list[Any]] = [[] for _ in range(num_residues)] - phi_res: list[Any] = [] for molecule in molecules: mol = self._universe_operations.extract_fragment(data_container, molecule) @@ -230,19 +237,21 @@ def _identify_peaks( for res_id in range(num_residues): heavy_res = self._select_heavy_residue(mol, res_id) dihedrals = self._get_dihedrals(heavy_res, level) - num_dihedrals_ua = len(dihedrals) - if num_dihedrals_ua == 0: + num_dihedrals_ua[res_id] = len(dihedrals) + if num_dihedrals_ua[res_id] == 0: # No dihedrals, no peaks phi_ua[res_id] = [] else: + if res_id not in phi_ua: + phi_ua[res_id] = {} dihedral_results = Dihedral(dihedrals).run() - phis = self._process_dihedral_phi( + phi_ua[res_id] = self._process_dihedral_phi( dihedral_results, - num_dihedrals_ua, + num_dihedrals_ua[res_id], number_frames, + phi_ua[res_id], ) - phi_ua[res_id].append(phis) elif level == "residue": dihedrals = self._get_dihedrals(mol, level) @@ -253,24 +262,33 @@ def _identify_peaks( else: dihedral_results = Dihedral(dihedrals).run() - phis = self._process_dihedral_phi( + phi_res = self._process_dihedral_phi( dihedral_results, num_dihedrals_res, number_frames, + phi_res, ) - phi_res.append(phis) + + logger.debug(f"phi_ua {phi_ua}") + logger.debug(f"phi_res {phi_res}") for level in level_list: if level == "united_atom": for res_id in range(num_residues): - peaks_ua[res_id] = self._process_histogram( - num_dihedrals_ua, phi_ua[res_id], bin_width - ) + if phi_ua[res_id] is None: + peaks_ua[res_id] = [] + else: + peaks_ua[res_id] = self._process_histogram( + num_dihedrals_ua[res_id], phi_ua[res_id], bin_width + ) elif level == "residue": - peaks_res = self._process_histogram( - num_dihedrals_res, phi_res, bin_width - ) + if phi_res is None: + peaks_res = [] + else: + peaks_res = self._process_histogram( + num_dihedrals_res, phi_res, bin_width + ) return peaks_ua, peaks_res @@ -279,9 +297,10 @@ def _process_dihedral_phi( dihedral_results, num_dihedrals, number_frames, + phi_values, ): """ - Find peaks from array of dihedral angle values. + Find array of dihedral angle values. Args: dihedral_results: the result of MDAnalysis Dihedrals.run. @@ -290,7 +309,6 @@ def _process_dihedral_phi( Returns: peaks """ - phi_values = [[] for _ in range(num_dihedrals)] for dihedral_index in range(num_dihedrals): phi: list[float] = [] @@ -300,7 +318,10 @@ def _process_dihedral_phi( value += 360 phi.append(float(value)) - phi_values[dihedral_index].append(phi) + if dihedral_index not in phi_values: + phi_values[dihedral_index] = phi + else: + phi_values[dihedral_index].extend(phi) return phi_values @@ -325,6 +346,9 @@ def _process_histogram( phi = phi_values[dihedral_index] number_bins = int(360 / bin_width) popul, bin_edges = np.histogram(a=phi, bins=number_bins, range=(0, 360)) + + logger.debug(f"Histogram: {popul}") + bin_value = [ 0.5 * (bin_edges[i] + bin_edges[i + 1]) for i in range(0, len(popul)) ] @@ -401,6 +425,8 @@ def _assign_states( number_frames = len(rep_mol.trajectory) num_residues = len(rep_mol.residues) + state_res = [] + flex_res = 0 for molecule in molecules: mol = self._universe_operations.extract_fragment(data_container, molecule) @@ -417,7 +443,7 @@ def _assign_states( flexible_ua[key] = 0 else: dihedral_results = Dihedral(dihedrals).run() - states, flexible_ua[key] = self._process_conformations( + states, flexible = self._process_conformations( peaks_ua[res_id], dihedral_results, num_dihedrals, @@ -425,36 +451,30 @@ def _assign_states( ) if key not in states_ua: states_ua[key] = states + flexible_ua[key] = flexible else: states_ua[key].extend(states) - - logger.debug(f"States UA {key}: {states_ua[key]}") - logger.debug( - f"Number of flexible dihedrals UA {key}: {flexible_ua[key]}" - ) + flexible_ua[key] = max(flexible_ua[key], flexible) if level == "residue": dihedrals = self._get_dihedrals(mol, level) num_dihedrals = len(dihedrals) if num_dihedrals == 0: # No dihedrals, no conformations - states_res[group_id] = [] - flexible_res[group_id] = 0 + state_res = [] else: dihedral_results = Dihedral(dihedrals).run() - states, flexible_res[group_id] = self._process_conformations( + states, flexible = self._process_conformations( peaks_res, dihedral_results, num_dihedrals, number_frames, - molecule, ) - states_res[group_id].extend(states) + state_res.extend(states) + flex_res = max(flex_res, flexible) - logger.debug(f"States Res {group_id}: {states_res[group_id]}") - logger.debug( - f"Number of flexible dihedrals Res {group_id}: {flexible_res[group_id]}" - ) + states_res.append(state_res) + flexible_res.append(flex_res) def _process_conformations( self, peaks, dihedral_results, num_dihedrals, number_frames @@ -475,8 +495,8 @@ def _process_conformations( conformation: list[Any] = [] # Check for flexible dihedrals - if len(peaks[dihedral_index]) > 1: - num_flexible += 1 + # if len(peaks[dihedral_index]) > 1: + # num_flexible += 1 # Get conformations for timestep in range(number_frames): @@ -492,6 +512,10 @@ def _process_conformations( distances = [abs(value - peak) for peak in peaks[dihedral_index]] conformation.append(np.argmin(distances)) + unique = np.unique(conformation) + if len(unique) > 1: + num_flexible += 1 + conformations.append(conformation) # Concatenate all the dihedrals in the molecule into the state diff --git a/tests/unit/CodeEntropy/entropy/test_workflow.py b/tests/unit/CodeEntropy/entropy/test_workflow.py index 8e7e27bc..9271ac7a 100644 --- a/tests/unit/CodeEntropy/entropy/test_workflow.py +++ b/tests/unit/CodeEntropy/entropy/test_workflow.py @@ -235,7 +235,7 @@ def test_build_reduced_universe_non_all_selects_and_writes_universe(): assert out is reduced2 uops.select_atoms.assert_called_once_with(universe, "protein") - uops.select_frames.assert_called_once_with(reduced, 0, -1, 1) + uops.select_frames.assert_called_once_with(reduced, 0, 3, 1) def test_compute_water_entropy_updates_selection_string_and_calls_internal_method(): diff --git a/tests/unit/CodeEntropy/levels/.test_dihedrals.py.swp b/tests/unit/CodeEntropy/levels/.test_dihedrals.py.swp new file mode 100644 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zKMD`Qop1+S1GDf_c!K!;VUU>rZulTb?0*>M;BwdmCD;gGC$4`C?u0ww7oiE4z%Dok z)`9Hxf1J2p_W3^u_rcw87x=Id{*`fl2EGLM!|iYz9D$uMas00|Q1n0-X4us>%>tU-sLX)R&c!u3fu!|!8Kcn~M#6?Z~`Jp~( zCYjyikBYzQB#Uk$bfz+SEn~=folftY@+6-;e6eHHM5A-=Cu%J^xrpq7#&ImlO{5!X ze3<5FzKdmRwakZZXIHPEEB9o~a->7fFVssR>dl?(V%_LfXQKo|qMg;2O0ugYJekQ( zaZ$b0aL8ZT&eKH@9Glb<^i<22O5&HyQURUZQBa(YK?j8P`zfMGuoCsB@b$%vnb>j_ZX3Nju_6GA(N0AJVQ8ME-$sP5Y=SkLpQ!hYVxYR63Z^ Date: Wed, 15 Apr 2026 14:20:47 +0100 Subject: [PATCH 4/5] updating regression test baselines --- CodeEntropy/entropy/workflow.py | 4 +- CodeEntropy/levels/level_dag.py | 6 +- .../baselines/benzaldehyde/axes_off.json | 20 +++--- .../combined_forcetorque_false.json | 20 +++--- .../baselines/benzaldehyde/default.json | 22 +++--- .../baselines/benzaldehyde/frame_window.json | 28 ++++---- .../baselines/benzaldehyde/grouping_each.json | 36 +++++----- .../baselines/benzaldehyde/rad.json | 22 +++--- .../benzaldehyde/selection_subset.json | 20 +++--- .../baselines/benzene/axes_off.json | 20 +++--- .../benzene/combined_forcetorque_off.json | 20 +++--- .../regression/baselines/benzene/default.json | 20 +++--- .../baselines/benzene/frame_window.json | 28 ++++---- .../baselines/benzene/grouping_each.json | 40 +++++------ tests/regression/baselines/benzene/rad.json | 20 +++--- .../baselines/benzene/selection_subset.json | 20 +++--- .../baselines/cyclohexane/axes_off.json | 16 ++--- .../cyclohexane/combined_forcetorque_off.json | 16 ++--- .../baselines/cyclohexane/default.json | 22 +++--- .../baselines/cyclohexane/frame_window.json | 26 +++---- .../baselines/cyclohexane/grouping_each.json | 16 ++--- .../regression/baselines/cyclohexane/rad.json | 22 +++--- .../cyclohexane/selection_subset.json | 16 ++--- tests/regression/baselines/dna/axes_off.json | 36 +++++----- .../dna/combined_forcetorque_off.json | 24 +++---- tests/regression/baselines/dna/default.json | 24 +++---- .../baselines/dna/frame_window.json | 36 +++++----- .../baselines/dna/grouping_each.json | 24 +++---- .../baselines/dna/selection_subset.json | 24 +++---- .../baselines/ethyl-acetate/axes_off.json | 24 +++---- .../combined_forcetorque_off.json | 24 +++---- .../baselines/ethyl-acetate/default.json | 24 +++---- .../baselines/ethyl-acetate/frame_window.json | 30 ++++---- .../ethyl-acetate/grouping_each.json | 66 +++++++++--------- .../baselines/ethyl-acetate/rad.json | 24 +++---- .../ethyl-acetate/selection_subset.json | 24 +++---- .../baselines/methane/axes_off.json | 16 ++--- .../methane/combined_forcetorque_off.json | 16 ++--- .../regression/baselines/methane/default.json | 20 +++--- .../baselines/methane/frame_window.json | 22 +++--- .../baselines/methane/grouping_each.json | 16 ++--- tests/regression/baselines/methane/rad.json | 20 +++--- .../baselines/methane/selection_subset.json | 16 ++--- .../baselines/methanol/axes_off.json | 16 ++--- .../methanol/combined_forcetorque_off.json | 16 ++--- .../baselines/methanol/default.json | 20 +++--- .../baselines/methanol/frame_window.json | 24 +++---- .../baselines/methanol/grouping_each.json | 24 +++---- tests/regression/baselines/methanol/rad.json | 20 +++--- .../baselines/methanol/selection_subset.json | 16 ++--- .../baselines/octonol/axes_off.json | 24 +++---- .../octonol/combined_forcetorque_off.json | 24 +++---- .../regression/baselines/octonol/default.json | 24 +++---- .../baselines/octonol/frame_window.json | 30 ++++---- .../baselines/octonol/grouping_each.json | 62 ++++++++-------- tests/regression/baselines/octonol/rad.json | 24 +++---- .../baselines/octonol/selection_subset.json | 24 +++---- .../regression/baselines/water/axes_off.json | 16 ++--- .../water/combined_forcetorque_off.json | 16 ++--- tests/regression/baselines/water/default.json | 20 +++--- .../baselines/water/frame_window.json | 22 +++--- .../baselines/water/grouping_each.json | 16 ++--- tests/regression/baselines/water/rad.json | 20 +++--- .../baselines/water/selection_subset.json | 16 ++--- .../regression/baselines/water/water_off.json | 16 ++--- .../CodeEntropy/levels/.test_dihedrals.py.swp | Bin 24576 -> 0 bytes 66 files changed, 740 insertions(+), 740 deletions(-) delete mode 100644 tests/unit/CodeEntropy/levels/.test_dihedrals.py.swp diff --git a/CodeEntropy/entropy/workflow.py b/CodeEntropy/entropy/workflow.py index 7e52cff4..75115cd7 100644 --- a/CodeEntropy/entropy/workflow.py +++ b/CodeEntropy/entropy/workflow.py @@ -239,9 +239,9 @@ def _build_reduced_universe(self) -> Any: MDAnalysis Universe (reduced according to user selections). """ selection = self._args.selection_string - start = self._args.start or 0 + start = self._args.start end = len(self._universe.trajectory) if self._args.end == -1 else self._args.end - step = self._args.step or 1 + step = self._args.step if selection == "all": reduced_atoms = self._universe else: diff --git a/CodeEntropy/levels/level_dag.py b/CodeEntropy/levels/level_dag.py index 7b1388ed..72e07197 100644 --- a/CodeEntropy/levels/level_dag.py +++ b/CodeEntropy/levels/level_dag.py @@ -196,11 +196,11 @@ def _run_frame_stage( title="Initializing", ) - for ts in range(n_frames): + for frame_index in range(n_frames): if progress is not None and task is not None: - progress.update(task, title=f"Frame {ts}") + progress.update(task, title=f"Frame {frame_index}") - frame_out = self._frame_dag.execute_frame(shared_data, ts) + frame_out = self._frame_dag.execute_frame(shared_data, frame_index) self._reduce_one_frame(shared_data, frame_out) if progress is not None and task is not None: diff --git a/tests/regression/baselines/benzaldehyde/axes_off.json b/tests/regression/baselines/benzaldehyde/axes_off.json index 4437a2f5..19438eb1 100644 --- a/tests/regression/baselines/benzaldehyde/axes_off.json +++ b/tests/regression/baselines/benzaldehyde/axes_off.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzaldehyde/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzaldehyde/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/benzaldehyde/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/benzaldehyde/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzaldehyde/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/benzaldehyde/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "resid 1:10", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-53/test_regression_matches_baseli0/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw0/test_regression_matches_baseli0/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,10 +23,10 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { @@ -37,9 +37,9 @@ "residue:FTmat-Rovibrational": 61.61036267672132, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, - "residue:Orientational": 7.791711490122748 + "residue:Orientational": 20.481571492615355 }, - "total": 190.41925181422317 + "total": 203.1091118167158 } } } diff --git a/tests/regression/baselines/benzaldehyde/combined_forcetorque_false.json b/tests/regression/baselines/benzaldehyde/combined_forcetorque_false.json index 33fecafd..3b7be298 100644 --- a/tests/regression/baselines/benzaldehyde/combined_forcetorque_false.json +++ b/tests/regression/baselines/benzaldehyde/combined_forcetorque_false.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzaldehyde/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzaldehyde/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/benzaldehyde/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/benzaldehyde/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzaldehyde/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/benzaldehyde/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "resid 1:10", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-53/test_regression_matches_baseli1/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw0/test_regression_matches_baseli1/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,10 +23,10 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { @@ -37,9 +37,9 @@ "residue:Rovibrational": 68.46147102540942, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, - "residue:Orientational": 7.791711490122748 + "residue:Orientational": 20.481571492615355 }, - "total": 195.49800254632487 + "total": 208.1878625488175 } } } diff --git a/tests/regression/baselines/benzaldehyde/default.json b/tests/regression/baselines/benzaldehyde/default.json index b1d70cff..1c89052d 100644 --- a/tests/regression/baselines/benzaldehyde/default.json +++ b/tests/regression/baselines/benzaldehyde/default.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzaldehyde/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzaldehyde/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/benzaldehyde/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/benzaldehyde/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzaldehyde/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/benzaldehyde/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "all", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-53/test_regression_matches_baseli2/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw1/test_regression_matches_baseli0/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,10 +23,10 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { @@ -35,11 +35,11 @@ "united_atom:Rovibrational": 27.950376507672583, "residue:FTmat-Transvibrational": 71.03412922724692, "residue:FTmat-Rovibrational": 59.44169664956799, - "united_atom:Conformational": 0.0, + "united_atom:Conformational": 7.522643899702263, "residue:Conformational": 0.0, - "residue:Orientational": 59.5156759876787 + "residue:Orientational": 59.43920971558428 }, - "total": 242.82706070457093 + "total": 250.27323833217878 } } } diff --git a/tests/regression/baselines/benzaldehyde/frame_window.json b/tests/regression/baselines/benzaldehyde/frame_window.json index a9f6aa56..1453f918 100644 --- a/tests/regression/baselines/benzaldehyde/frame_window.json +++ b/tests/regression/baselines/benzaldehyde/frame_window.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzaldehyde/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzaldehyde/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/benzaldehyde/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/benzaldehyde/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzaldehyde/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/benzaldehyde/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "resid 1:10", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-53/test_regression_matches_baseli3/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw1/test_regression_matches_baseli1/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,23 +23,23 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { "components": { - "united_atom:Transvibrational": 40.30267601961045, - "united_atom:Rovibrational": 38.21906858443615, - "residue:FTmat-Transvibrational": 73.41098578352612, - "residue:FTmat-Rovibrational": 57.881504393660364, + "united_atom:Transvibrational": 0.06976323861519099, + "united_atom:Rovibrational": 43.1148685234083, + "residue:FTmat-Transvibrational": 81.88770108142911, + "residue:FTmat-Rovibrational": 54.95209390854072, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, - "residue:Orientational": 7.791711490122748 + "residue:Orientational": 20.481571492615355 }, - "total": 217.60594627135583 + "total": 200.50599824460866 } } } diff --git a/tests/regression/baselines/benzaldehyde/grouping_each.json b/tests/regression/baselines/benzaldehyde/grouping_each.json index 58b08b2d..77d8cc66 100644 --- a/tests/regression/baselines/benzaldehyde/grouping_each.json +++ b/tests/regression/baselines/benzaldehyde/grouping_each.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzaldehyde/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzaldehyde/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/benzaldehyde/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/benzaldehyde/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzaldehyde/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/benzaldehyde/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "resid 1:10", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-53/test_regression_matches_baseli4/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw2/test_regression_matches_baseli0/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "each", @@ -23,10 +23,10 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { @@ -37,9 +37,9 @@ "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, - "residue:Orientational": 9.587915463990273 + "residue:Orientational": 31.909265242174982 }, - "total": 26.488985268171085 + "total": 48.81033504635579 }, "1": { "components": { @@ -61,9 +61,9 @@ "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, - "residue:Orientational": 13.250255095331166 + "residue:Orientational": 31.909265242174982 }, - "total": 30.70184213788489 + "total": 49.36085228472871 }, "3": { "components": { @@ -97,9 +97,9 @@ "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, - "residue:Orientational": 23.16437388578126 + "residue:Orientational": 31.909265242174982 }, - "total": 34.22999650128771 + "total": 42.97488785768143 }, "6": { "components": { @@ -109,9 +109,9 @@ "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, - "residue:Orientational": 18.044518549147842 + "residue:Orientational": 0.0 }, - "total": 37.76863350196386 + "total": 19.72411495281602 }, "7": { "components": { @@ -133,9 +133,9 @@ "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, - "residue:Orientational": 10.453350878685521 + "residue:Orientational": 31.909265242174982 }, - "total": 26.605755727773698 + "total": 48.06167009126315 }, "9": { "components": { diff --git a/tests/regression/baselines/benzaldehyde/rad.json b/tests/regression/baselines/benzaldehyde/rad.json index 8b8dea12..eedb2d84 100644 --- a/tests/regression/baselines/benzaldehyde/rad.json +++ b/tests/regression/baselines/benzaldehyde/rad.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzaldehyde/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzaldehyde/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/benzaldehyde/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/benzaldehyde/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzaldehyde/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/benzaldehyde/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "all", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-53/test_regression_matches_baseli5/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw2/test_regression_matches_baseli1/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,10 +23,10 @@ "search_type": "RAD" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "4d39e9aeeed72fc3993f4a4eb6485da40524ebc5" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { @@ -35,11 +35,11 @@ "united_atom:Rovibrational": 27.950376507672583, "residue:FTmat-Transvibrational": 71.03412922724692, "residue:FTmat-Rovibrational": 59.44169664956799, - "united_atom:Conformational": 0.0, + "united_atom:Conformational": 7.522643899702263, "residue:Conformational": 0.0, - "residue:Orientational": 25.3107189764825 + "residue:Orientational": 25.502722133228936 }, - "total": 208.62210369337473 + "total": 216.33675074982344 } } } diff --git a/tests/regression/baselines/benzaldehyde/selection_subset.json b/tests/regression/baselines/benzaldehyde/selection_subset.json index ee4b3fa5..d92576ae 100644 --- a/tests/regression/baselines/benzaldehyde/selection_subset.json +++ b/tests/regression/baselines/benzaldehyde/selection_subset.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzaldehyde/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzaldehyde/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/benzaldehyde/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/benzaldehyde/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzaldehyde/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/benzaldehyde/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "resid 1:10", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-53/test_regression_matches_baseli6/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw3/test_regression_matches_baseli0/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,10 +23,10 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "4d39e9aeeed72fc3993f4a4eb6485da40524ebc5" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { @@ -37,9 +37,9 @@ "residue:FTmat-Rovibrational": 61.67126452972779, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, - "residue:Orientational": 7.791711490122748 + "residue:Orientational": 20.481571492615355 }, - "total": 206.65613994967572 + "total": 219.34599995216834 } } } diff --git a/tests/regression/baselines/benzene/axes_off.json b/tests/regression/baselines/benzene/axes_off.json index a70a4cca..3230a15b 100644 --- a/tests/regression/baselines/benzene/axes_off.json +++ b/tests/regression/baselines/benzene/axes_off.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzene/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzene/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/benzene/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/benzene/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzene/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/benzene/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "resid 1:10", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-50/test_regression_matches_baseli0/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw3/test_regression_matches_baseli1/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,10 +23,10 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { @@ -37,9 +37,9 @@ "residue:FTmat-Rovibrational": 47.171663134129304, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, - "residue:Orientational": 1.1255349480631325 + "residue:Orientational": 0.0 }, - "total": 162.42256458945369 + "total": 161.29702964139057 } } } diff --git a/tests/regression/baselines/benzene/combined_forcetorque_off.json b/tests/regression/baselines/benzene/combined_forcetorque_off.json index 5b264d2c..2c3650f6 100644 --- a/tests/regression/baselines/benzene/combined_forcetorque_off.json +++ b/tests/regression/baselines/benzene/combined_forcetorque_off.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzene/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzene/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/benzene/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/benzene/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzene/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/benzene/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "resid 1:10", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-50/test_regression_matches_baseli1/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw4/test_regression_matches_baseli0/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,10 +23,10 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { @@ -37,9 +37,9 @@ "residue:Rovibrational": 52.85496348419672, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, - "residue:Orientational": 1.1255349480631325 + "residue:Orientational": 0.0 }, - "total": 152.43617664580827 + "total": 151.31064169774515 } } } diff --git a/tests/regression/baselines/benzene/default.json b/tests/regression/baselines/benzene/default.json index 68b17b2a..d8a5c706 100644 --- a/tests/regression/baselines/benzene/default.json +++ b/tests/regression/baselines/benzene/default.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzene/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzene/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/benzene/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/benzene/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzene/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/benzene/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "all", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-50/test_regression_matches_baseli2/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw4/test_regression_matches_baseli1/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,10 +23,10 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { @@ -37,9 +37,9 @@ "residue:FTmat-Rovibrational": 59.93761874375924, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, - "residue:Orientational": 41.237966715197246 + "residue:Orientational": 41.58427729275938 }, - "total": 210.45393701689989 + "total": 210.800247594462 } } } diff --git a/tests/regression/baselines/benzene/frame_window.json b/tests/regression/baselines/benzene/frame_window.json index 191bd676..57941a15 100644 --- a/tests/regression/baselines/benzene/frame_window.json +++ b/tests/regression/baselines/benzene/frame_window.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzene/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzene/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/benzene/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/benzene/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzene/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/benzene/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "resid 1:10", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-50/test_regression_matches_baseli3/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw6/test_regression_matches_baseli0/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,23 +23,23 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { "components": { - "united_atom:Transvibrational": 11.46552036084548, - "united_atom:Rovibrational": 34.98492056748493, - "residue:FTmat-Transvibrational": 71.83491878606151, - "residue:FTmat-Rovibrational": 55.6098400281744, + "united_atom:Transvibrational": 0.19795850062580336, + "united_atom:Rovibrational": 37.022046871408385, + "residue:FTmat-Transvibrational": 89.61712603903918, + "residue:FTmat-Rovibrational": 59.882255851985164, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, - "residue:Orientational": 1.1255349480631325 + "residue:Orientational": 0.0 }, - "total": 175.02073469062944 + "total": 186.71938726305854 } } } diff --git a/tests/regression/baselines/benzene/grouping_each.json b/tests/regression/baselines/benzene/grouping_each.json index 3c5a91f8..f88998d8 100644 --- a/tests/regression/baselines/benzene/grouping_each.json +++ b/tests/regression/baselines/benzene/grouping_each.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzene/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzene/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/benzene/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/benzene/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzene/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/benzene/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "resid 1:10", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-0/test_regression_matches_baseli0/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw6/test_regression_matches_baseli1/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "each", @@ -23,10 +23,10 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "40e8a36db44df29720dfc6783865ec87de6ee120" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { @@ -49,9 +49,9 @@ "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, - "residue:Orientational": 9.716642731179457 + "residue:Orientational": 15.089233620075317 }, - "total": 25.00225165968083 + "total": 30.374842548576687 }, "2": { "components": { @@ -61,9 +61,9 @@ "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, - "residue:Orientational": 0.0 + "residue:Orientational": 15.089233620075317 }, - "total": 20.40290447179586 + "total": 35.492138091871176 }, "3": { "components": { @@ -85,9 +85,9 @@ "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, - "residue:Orientational": 5.804802962268455 + "residue:Orientational": 0.0 }, - "total": 13.037954242118563 + "total": 7.233151279850108 }, "5": { "components": { @@ -97,9 +97,9 @@ "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, - "residue:Orientational": 6.519123559451743 + "residue:Orientational": 0.0 }, - "total": 15.060497602422519 + "total": 8.541374042970777 }, "6": { "components": { @@ -109,9 +109,9 @@ "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, - "residue:Orientational": 1.1102416417044547 + "residue:Orientational": 0.0 }, - "total": 16.582772624429612 + "total": 15.472530982725159 }, "7": { "components": { @@ -133,9 +133,9 @@ "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, - "residue:Orientational": 4.476183988092513 + "residue:Orientational": 0.0 }, - "total": 27.162341494172075 + "total": 22.686157506079564 }, "9": { "components": { diff --git a/tests/regression/baselines/benzene/rad.json b/tests/regression/baselines/benzene/rad.json index 521ebc10..cabb1626 100644 --- a/tests/regression/baselines/benzene/rad.json +++ b/tests/regression/baselines/benzene/rad.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzene/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzene/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/benzene/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/benzene/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzene/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/benzene/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "all", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-50/test_regression_matches_baseli5/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw5/test_regression_matches_baseli0/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,10 +23,10 @@ "search_type": "RAD" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "4d39e9aeeed72fc3993f4a4eb6485da40524ebc5" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { @@ -37,9 +37,9 @@ "residue:FTmat-Rovibrational": 59.93761874375924, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, - "residue:Orientational": 12.282076945243183 + "residue:Orientational": 12.386543820026672 }, - "total": 181.49804724694582 + "total": 181.6025141217293 } } } diff --git a/tests/regression/baselines/benzene/selection_subset.json b/tests/regression/baselines/benzene/selection_subset.json index 81cce2f5..3d08939d 100644 --- a/tests/regression/baselines/benzene/selection_subset.json +++ b/tests/regression/baselines/benzene/selection_subset.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzene/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzene/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/benzene/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/benzene/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzene/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/benzene/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "resid 1:10", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-50/test_regression_matches_baseli6/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw5/test_regression_matches_baseli1/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,10 +23,10 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "4d39e9aeeed72fc3993f4a4eb6485da40524ebc5" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { @@ -37,9 +37,9 @@ "residue:FTmat-Rovibrational": 47.26253953880574, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, - "residue:Orientational": 1.1255349480631325 + "residue:Orientational": 0.0 }, - "total": 160.40471136929105 + "total": 159.27917642122793 } } } diff --git a/tests/regression/baselines/cyclohexane/axes_off.json b/tests/regression/baselines/cyclohexane/axes_off.json index ffa61e5d..688b2489 100644 --- a/tests/regression/baselines/cyclohexane/axes_off.json +++ b/tests/regression/baselines/cyclohexane/axes_off.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/cyclohexane/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/cyclohexane/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/cyclohexane/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/cyclohexane/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/cyclohexane/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/cyclohexane/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "resid 1:10", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-45/test_regression_matches_baseli0/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw7/test_regression_matches_baseli0/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,10 +23,10 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { diff --git a/tests/regression/baselines/cyclohexane/combined_forcetorque_off.json b/tests/regression/baselines/cyclohexane/combined_forcetorque_off.json index 41706214..27aa7261 100644 --- a/tests/regression/baselines/cyclohexane/combined_forcetorque_off.json +++ b/tests/regression/baselines/cyclohexane/combined_forcetorque_off.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/cyclohexane/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/cyclohexane/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/cyclohexane/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/cyclohexane/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/cyclohexane/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/cyclohexane/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "resid 1:10", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-45/test_regression_matches_baseli1/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw7/test_regression_matches_baseli1/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,10 +23,10 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { diff --git a/tests/regression/baselines/cyclohexane/default.json b/tests/regression/baselines/cyclohexane/default.json index 6580e9b2..7cc76505 100644 --- a/tests/regression/baselines/cyclohexane/default.json +++ b/tests/regression/baselines/cyclohexane/default.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/cyclohexane/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/cyclohexane/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/cyclohexane/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/cyclohexane/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/cyclohexane/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/cyclohexane/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "all", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-45/test_regression_matches_baseli2/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw8/test_regression_matches_baseli0/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,10 +23,10 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { @@ -35,11 +35,11 @@ "united_atom:Rovibrational": 47.71088602161552, "residue:FTmat-Transvibrational": 70.3922327806972, "residue:FTmat-Rovibrational": 63.44920824648768, - "united_atom:Conformational": 0.0, + "united_atom:Conformational": 1.288879206695518, "residue:Conformational": 0.0, - "residue:Orientational": 47.30759597445523 + "residue:Orientational": 47.54362774624537 }, - "total": 240.58639488195587 + "total": 242.11130586044152 } } } diff --git a/tests/regression/baselines/cyclohexane/frame_window.json b/tests/regression/baselines/cyclohexane/frame_window.json index 819082e4..03639897 100644 --- a/tests/regression/baselines/cyclohexane/frame_window.json +++ b/tests/regression/baselines/cyclohexane/frame_window.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/cyclohexane/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/cyclohexane/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/cyclohexane/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/cyclohexane/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/cyclohexane/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/cyclohexane/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "resid 1:10", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-45/test_regression_matches_baseli3/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw8/test_regression_matches_baseli1/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,23 +23,23 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { "components": { - "united_atom:Transvibrational": 17.398382397359153, - "united_atom:Rovibrational": 73.96792995794405, - "residue:FTmat-Transvibrational": 76.4267996157354, - "residue:FTmat-Rovibrational": 63.30469126284744, + "united_atom:Transvibrational": 0.9922566704968832, + "united_atom:Rovibrational": 25.157330630108138, + "residue:FTmat-Transvibrational": 88.28792477558463, + "residue:FTmat-Rovibrational": 65.39813357771244, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 0.0 }, - "total": 231.09780323388605 + "total": 179.83564565390208 } } } diff --git a/tests/regression/baselines/cyclohexane/grouping_each.json b/tests/regression/baselines/cyclohexane/grouping_each.json index 46acbee8..53bc9b59 100644 --- a/tests/regression/baselines/cyclohexane/grouping_each.json +++ b/tests/regression/baselines/cyclohexane/grouping_each.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/cyclohexane/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/cyclohexane/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/cyclohexane/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/cyclohexane/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/cyclohexane/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/cyclohexane/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "resid 1:10", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-45/test_regression_matches_baseli4/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw10/test_regression_matches_baseli0/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "each", @@ -23,10 +23,10 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { diff --git a/tests/regression/baselines/cyclohexane/rad.json b/tests/regression/baselines/cyclohexane/rad.json index 4ee61d76..64340bc2 100644 --- a/tests/regression/baselines/cyclohexane/rad.json +++ b/tests/regression/baselines/cyclohexane/rad.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/cyclohexane/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/cyclohexane/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/cyclohexane/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/cyclohexane/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/cyclohexane/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/cyclohexane/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "all", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-45/test_regression_matches_baseli5/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw10/test_regression_matches_baseli1/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,10 +23,10 @@ "search_type": "RAD" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "4d39e9aeeed72fc3993f4a4eb6485da40524ebc5" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { @@ -35,11 +35,11 @@ "united_atom:Rovibrational": 47.71088602161552, "residue:FTmat-Transvibrational": 70.3922327806972, "residue:FTmat-Rovibrational": 63.44920824648768, - "united_atom:Conformational": 0.0, + "united_atom:Conformational": 1.288879206695518, "residue:Conformational": 0.0, - "residue:Orientational": 13.963860657362106 + "residue:Orientational": 14.049324060636614 }, - "total": 207.24265956486275 + "total": 208.61700217483278 } } } diff --git a/tests/regression/baselines/cyclohexane/selection_subset.json b/tests/regression/baselines/cyclohexane/selection_subset.json index 86332b26..491c4d84 100644 --- a/tests/regression/baselines/cyclohexane/selection_subset.json +++ b/tests/regression/baselines/cyclohexane/selection_subset.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/cyclohexane/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/cyclohexane/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/cyclohexane/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/cyclohexane/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/cyclohexane/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/cyclohexane/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "resid 1:10", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-45/test_regression_matches_baseli6/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw9/test_regression_matches_baseli0/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,10 +23,10 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "4d39e9aeeed72fc3993f4a4eb6485da40524ebc5" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { diff --git a/tests/regression/baselines/dna/axes_off.json b/tests/regression/baselines/dna/axes_off.json index e130d0ed..da7dccfe 100644 --- a/tests/regression/baselines/dna/axes_off.json +++ b/tests/regression/baselines/dna/axes_off.json @@ -1,8 +1,8 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/dna/md_A4_dna.tpr", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/dna/md_A4_dna_xf.trr" + "/home/ogo12949/CodeEntropy/.testdata/dna/md_A4_dna.tpr", + "/home/ogo12949/CodeEntropy/.testdata/dna/md_A4_dna_xf.trr" ], "force_file": null, "file_format": null, @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-44/test_regression_matches_baseli0/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw9/test_regression_matches_baseli1/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,39 +23,39 @@ "search_type": "RAD" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { "components": { "united_atom:Transvibrational": 0.0, - "united_atom:Rovibrational": 1.2269044878385265, + "united_atom:Rovibrational": 138.6554635683915, "residue:Transvibrational": 0.0, - "residue:Rovibrational": 27.45710747332319, - "polymer:FTmat-Transvibrational": 48.62026970762269, + "residue:Rovibrational": 3.7744745512812843, + "polymer:FTmat-Transvibrational": 13.548865634429543, "polymer:FTmat-Rovibrational": 0.0, - "united_atom:Conformational": 7.0411434528236345, + "united_atom:Conformational": 10.584542990557836, "residue:Conformational": 0.0, "polymer:Orientational": 4.758905336627712 }, - "total": 89.10433045823575 + "total": 171.3222520812879 }, "1": { "components": { "united_atom:Transvibrational": 0.0, - "united_atom:Rovibrational": 1.7972774672527945, + "united_atom:Rovibrational": 0.018570889591209457, "residue:Transvibrational": 0.0, - "residue:Rovibrational": 25.287669468441067, - "polymer:FTmat-Transvibrational": 60.47397935339153, + "residue:Rovibrational": 6.178603242071742, + "polymer:FTmat-Transvibrational": 14.075720078226187, "polymer:FTmat-Rovibrational": 0.0, - "united_atom:Conformational": 6.410455987098191, - "residue:Conformational": 0.46183561256411515, + "united_atom:Conformational": 5.292271495278918, + "residue:Conformational": 0.0, "polymer:Orientational": 4.758905336627712 }, - "total": 99.1901232253754 + "total": 30.32407104179577 } } } diff --git a/tests/regression/baselines/dna/combined_forcetorque_off.json b/tests/regression/baselines/dna/combined_forcetorque_off.json index aa5253da..f8556755 100644 --- a/tests/regression/baselines/dna/combined_forcetorque_off.json +++ b/tests/regression/baselines/dna/combined_forcetorque_off.json @@ -1,8 +1,8 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/dna/md_A4_dna.tpr", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/dna/md_A4_dna_xf.trr" + "/home/ogo12949/CodeEntropy/.testdata/dna/md_A4_dna.tpr", + "/home/ogo12949/CodeEntropy/.testdata/dna/md_A4_dna_xf.trr" ], "force_file": null, "file_format": null, @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-44/test_regression_matches_baseli1/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw11/test_regression_matches_baseli0/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,10 +23,10 @@ "search_type": "RAD" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { @@ -37,11 +37,11 @@ "residue:Rovibrational": 3.376800684085249, "polymer:Transvibrational": 21.18266215491188, "polymer:Rovibrational": 12.837576042626923, - "united_atom:Conformational": 7.0411434528236345, + "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "polymer:Orientational": 4.758905336627712 }, - "total": 49.19924835008753 + "total": 42.1581048972639 }, "1": { "components": { @@ -51,11 +51,11 @@ "residue:Rovibrational": 2.3863201082544565, "polymer:Transvibrational": 16.607667396609116, "polymer:Rovibrational": 12.304363914795593, - "united_atom:Conformational": 6.410455987098191, - "residue:Conformational": 0.46183561256411515, + "united_atom:Conformational": 0.0, + "residue:Conformational": 0.0, "polymer:Orientational": 4.758905336627712 }, - "total": 42.94801263360868 + "total": 36.07572103394637 } } } diff --git a/tests/regression/baselines/dna/default.json b/tests/regression/baselines/dna/default.json index 4f1cf692..77163490 100644 --- a/tests/regression/baselines/dna/default.json +++ b/tests/regression/baselines/dna/default.json @@ -1,8 +1,8 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/dna/md_A4_dna.tpr", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/dna/md_A4_dna_xf.trr" + "/home/ogo12949/CodeEntropy/.testdata/dna/md_A4_dna.tpr", + "/home/ogo12949/CodeEntropy/.testdata/dna/md_A4_dna_xf.trr" ], "force_file": null, "file_format": null, @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-44/test_regression_matches_baseli2/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw11/test_regression_matches_baseli1/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,10 +23,10 @@ "search_type": "RAD" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { @@ -37,11 +37,11 @@ "residue:Rovibrational": 3.376800684085249, "polymer:FTmat-Transvibrational": 12.341104347192612, "polymer:FTmat-Rovibrational": 0.0, - "united_atom:Conformational": 7.0411434528236345, + "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "polymer:Orientational": 4.758905336627712 }, - "total": 27.52011449974134 + "total": 20.478971046917703 }, "1": { "components": { @@ -51,11 +51,11 @@ "residue:Rovibrational": 2.3863201082544565, "polymer:FTmat-Transvibrational": 11.11037253388596, "polymer:FTmat-Rovibrational": 0.0, - "united_atom:Conformational": 6.410455987098191, - "residue:Conformational": 0.46183561256411515, + "united_atom:Conformational": 0.0, + "residue:Conformational": 0.0, "polymer:Orientational": 4.758905336627712 }, - "total": 25.14635385608993 + "total": 18.274062256427623 } } } diff --git a/tests/regression/baselines/dna/frame_window.json b/tests/regression/baselines/dna/frame_window.json index d9782bc9..2a76ec5b 100644 --- a/tests/regression/baselines/dna/frame_window.json +++ b/tests/regression/baselines/dna/frame_window.json @@ -1,8 +1,8 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/dna/md_A4_dna.tpr", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/dna/md_A4_dna_xf.trr" + "/home/ogo12949/CodeEntropy/.testdata/dna/md_A4_dna.tpr", + "/home/ogo12949/CodeEntropy/.testdata/dna/md_A4_dna_xf.trr" ], "force_file": null, "file_format": null, @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-44/test_regression_matches_baseli3/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw12/test_regression_matches_baseli0/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,39 +23,39 @@ "search_type": "RAD" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { "components": { "united_atom:Transvibrational": 0.0, - 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"united_atom:Conformational": 6.410455987098191, - "residue:Conformational": 0.46183561256411515, + "united_atom:Conformational": 5.292271495278918, + "residue:Conformational": 0.0, "polymer:Orientational": 4.758905336627712 }, - "total": 99.43967060084383 + "total": 30.259644290140763 } } } diff --git a/tests/regression/baselines/dna/grouping_each.json b/tests/regression/baselines/dna/grouping_each.json index 15551c86..7e2fd86b 100644 --- a/tests/regression/baselines/dna/grouping_each.json +++ b/tests/regression/baselines/dna/grouping_each.json @@ -1,8 +1,8 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/dna/md_A4_dna.tpr", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/dna/md_A4_dna_xf.trr" + "/home/ogo12949/CodeEntropy/.testdata/dna/md_A4_dna.tpr", + "/home/ogo12949/CodeEntropy/.testdata/dna/md_A4_dna_xf.trr" ], "force_file": null, "file_format": null, @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-44/test_regression_matches_baseli4/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw12/test_regression_matches_baseli1/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "each", @@ -23,10 +23,10 @@ "search_type": "RAD" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { @@ -37,11 +37,11 @@ "residue:Rovibrational": 3.376800684085249, "polymer:FTmat-Transvibrational": 12.341104347192612, "polymer:FTmat-Rovibrational": 0.0, - "united_atom:Conformational": 7.0411434528236345, + "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "polymer:Orientational": 4.758905336627712 }, - "total": 27.52011449974134 + "total": 20.478971046917703 }, "1": { "components": { @@ -51,11 +51,11 @@ "residue:Rovibrational": 2.3863201082544565, "polymer:FTmat-Transvibrational": 11.11037253388596, "polymer:FTmat-Rovibrational": 0.0, - "united_atom:Conformational": 6.410455987098191, - "residue:Conformational": 0.46183561256411515, + "united_atom:Conformational": 0.0, + "residue:Conformational": 0.0, "polymer:Orientational": 4.758905336627712 }, - "total": 25.14635385608993 + "total": 18.274062256427623 } } } diff --git a/tests/regression/baselines/dna/selection_subset.json b/tests/regression/baselines/dna/selection_subset.json index a29436b7..32816e03 100644 --- a/tests/regression/baselines/dna/selection_subset.json +++ b/tests/regression/baselines/dna/selection_subset.json @@ -1,8 +1,8 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/dna/md_A4_dna.tpr", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/dna/md_A4_dna_xf.trr" + "/home/ogo12949/CodeEntropy/.testdata/dna/md_A4_dna.tpr", + "/home/ogo12949/CodeEntropy/.testdata/dna/md_A4_dna_xf.trr" ], "force_file": null, "file_format": null, @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-44/test_regression_matches_baseli5/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw13/test_regression_matches_baseli0/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,10 +23,10 @@ "search_type": "RAD" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { @@ -37,11 +37,11 @@ "residue:Rovibrational": 3.376800684085249, "polymer:FTmat-Transvibrational": 12.341104347192612, "polymer:FTmat-Rovibrational": 0.0, - "united_atom:Conformational": 7.0411434528236345, + "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "polymer:Orientational": 4.758905336627712 }, - "total": 27.52011449974134 + "total": 20.478971046917703 }, "1": { "components": { @@ -51,11 +51,11 @@ "residue:Rovibrational": 2.3863201082544565, "polymer:FTmat-Transvibrational": 11.11037253388596, "polymer:FTmat-Rovibrational": 0.0, - "united_atom:Conformational": 6.410455987098191, - "residue:Conformational": 0.46183561256411515, + "united_atom:Conformational": 0.0, + "residue:Conformational": 0.0, "polymer:Orientational": 4.758905336627712 }, - "total": 25.14635385608993 + "total": 18.274062256427623 } } } diff --git a/tests/regression/baselines/ethyl-acetate/axes_off.json b/tests/regression/baselines/ethyl-acetate/axes_off.json index ada5c385..0d455db5 100644 --- a/tests/regression/baselines/ethyl-acetate/axes_off.json +++ b/tests/regression/baselines/ethyl-acetate/axes_off.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/ethyl-acetate/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/ethyl-acetate/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/ethyl-acetate/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/ethyl-acetate/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/ethyl-acetate/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/ethyl-acetate/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "resid 1:10", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-1/popen-gw0/test_regression_matches_baseli0/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw13/test_regression_matches_baseli1/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,23 +23,23 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-20-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "35b54c7d4ea40dac345db7fe8f6a0285bf6852e8" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { "components": { - 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"/home/harry-swift/BioSim/software/CodeEntropy/.testdata/ethyl-acetate/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/ethyl-acetate/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/ethyl-acetate/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/ethyl-acetate/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/ethyl-acetate/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "resid 1:10", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-47/test_regression_matches_baseli1/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw14/test_regression_matches_baseli0/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,23 +23,23 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { "components": { - "united_atom:Transvibrational": 1.5315510444158251, + "united_atom:Transvibrational": 1.196367074472673, "united_atom:Rovibrational": 82.36455154278131, "residue:Transvibrational": 64.68750154134017, "residue:Rovibrational": 58.903938937880085, - "united_atom:Conformational": 8.140778318198597, + "united_atom:Conformational": 7.90098624365273, "residue:Conformational": 0.0, - "residue:Orientational": 3.2718547817092687 + "residue:Orientational": 0.0 }, - "total": 218.90017616632525 + "total": 215.05334534012698 } } } diff --git a/tests/regression/baselines/ethyl-acetate/default.json b/tests/regression/baselines/ethyl-acetate/default.json index 99dd1a11..0f20cb27 100644 --- a/tests/regression/baselines/ethyl-acetate/default.json +++ b/tests/regression/baselines/ethyl-acetate/default.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/ethyl-acetate/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/ethyl-acetate/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/ethyl-acetate/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/ethyl-acetate/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/ethyl-acetate/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/ethyl-acetate/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "all", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-47/test_regression_matches_baseli2/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw14/test_regression_matches_baseli1/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,23 +23,23 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { "components": { - "united_atom:Transvibrational": 20.24374894231227, + "united_atom:Transvibrational": 19.703248485425714, "united_atom:Rovibrational": 49.35007067210558, "residue:FTmat-Transvibrational": 67.91350627765567, "residue:FTmat-Rovibrational": 60.042233035077246, - "united_atom:Conformational": 8.140778318198597, + "united_atom:Conformational": 8.175537881068413, "residue:Conformational": 0.0, - "residue:Orientational": 65.3684992300889 + "residue:Orientational": 65.33877737416202 }, - "total": 271.0588364754383 + "total": 270.52337372549465 } } } diff --git a/tests/regression/baselines/ethyl-acetate/frame_window.json b/tests/regression/baselines/ethyl-acetate/frame_window.json index 13f69fde..5243dcfa 100644 --- a/tests/regression/baselines/ethyl-acetate/frame_window.json +++ b/tests/regression/baselines/ethyl-acetate/frame_window.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/ethyl-acetate/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/ethyl-acetate/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/ethyl-acetate/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/ethyl-acetate/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/ethyl-acetate/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/ethyl-acetate/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "resid 1:10", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-47/test_regression_matches_baseli3/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw15/test_regression_matches_baseli0/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,23 +23,23 @@ "search_type": "grid" }, "provenance": { - 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"output_file": "/tmp/pytest-of-harry-swift/pytest-47/test_regression_matches_baseli4/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw15/test_regression_matches_baseli1/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "each", @@ -23,10 +23,10 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { @@ -35,11 +35,11 @@ "united_atom:Rovibrational": 0.041680247513564334, "residue:FTmat-Transvibrational": 13.339420001372439, "residue:FTmat-Rovibrational": 0.0, - "united_atom:Conformational": 8.140778318198597, + "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 0.0 }, - 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"/home/harry-swift/BioSim/software/CodeEntropy/.testdata/ethyl-acetate/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/ethyl-acetate/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/ethyl-acetate/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/ethyl-acetate/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/ethyl-acetate/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/ethyl-acetate/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "all", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-47/test_regression_matches_baseli5/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw11/test_regression_matches_baseli2/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,23 +23,23 @@ "search_type": "RAD" }, "provenance": { - 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"/home/harry-swift/BioSim/software/CodeEntropy/.testdata/ethyl-acetate/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/ethyl-acetate/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/ethyl-acetate/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/ethyl-acetate/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/ethyl-acetate/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/ethyl-acetate/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "resid 1:10", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-47/test_regression_matches_baseli6/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw13/test_regression_matches_baseli2/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,23 +23,23 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "4d39e9aeeed72fc3993f4a4eb6485da40524ebc5" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { "components": { - "united_atom:Transvibrational": 1.5315510444158251, + "united_atom:Transvibrational": 1.196367074472673, "united_atom:Rovibrational": 82.36455154278131, "residue:FTmat-Transvibrational": 74.5939232239247, "residue:FTmat-Rovibrational": 55.42964192531005, - "united_atom:Conformational": 8.140778318198597, + "united_atom:Conformational": 7.90098624365273, "residue:Conformational": 0.0, - "residue:Orientational": 3.2718547817092687 + "residue:Orientational": 0.0 }, - "total": 225.33230083633973 + "total": 221.48547001014148 } } } diff --git a/tests/regression/baselines/methane/axes_off.json b/tests/regression/baselines/methane/axes_off.json index 15e8583a..be31bc27 100644 --- a/tests/regression/baselines/methane/axes_off.json +++ b/tests/regression/baselines/methane/axes_off.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methane/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methane/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/methane/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/methane/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methane/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/methane/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "resid 1:10", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 112.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-51/test_regression_matches_baseli0/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw12/test_regression_matches_baseli2/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,10 +23,10 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { diff --git a/tests/regression/baselines/methane/combined_forcetorque_off.json b/tests/regression/baselines/methane/combined_forcetorque_off.json index 6d52a3db..baf41a2e 100644 --- a/tests/regression/baselines/methane/combined_forcetorque_off.json +++ b/tests/regression/baselines/methane/combined_forcetorque_off.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methane/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methane/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/methane/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/methane/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methane/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/methane/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "resid 1:10", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 112.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-51/test_regression_matches_baseli1/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw11/test_regression_matches_baseli3/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,10 +23,10 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { diff --git a/tests/regression/baselines/methane/default.json b/tests/regression/baselines/methane/default.json index 82657644..f95f6b9a 100644 --- a/tests/regression/baselines/methane/default.json +++ b/tests/regression/baselines/methane/default.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methane/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methane/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/methane/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/methane/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methane/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/methane/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "all", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 112.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-51/test_regression_matches_baseli2/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw2/test_regression_matches_baseli2/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,10 +23,10 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { @@ -34,9 +34,9 @@ "united_atom:Transvibrational": 40.3239711717637, "united_atom:Rovibrational": 33.60582165153992, "united_atom:Conformational": 0.0, - "united_atom:Orientational": 3.6608703176607116 + "united_atom:Orientational": 3.596676624528629 }, - "total": 77.59066314096432 + "total": 77.52646944783224 } } } diff --git a/tests/regression/baselines/methane/frame_window.json b/tests/regression/baselines/methane/frame_window.json index 473cf6b6..315c8a65 100644 --- a/tests/regression/baselines/methane/frame_window.json +++ b/tests/regression/baselines/methane/frame_window.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methane/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methane/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/methane/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/methane/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methane/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/methane/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "resid 1:10", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 112.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-51/test_regression_matches_baseli3/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw12/test_regression_matches_baseli3/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,20 +23,20 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { "components": { - "united_atom:Transvibrational": 40.70376001258969, - "united_atom:Rovibrational": 33.778792396823484, + "united_atom:Transvibrational": 42.1495717236188, + "united_atom:Rovibrational": 39.226038972684975, "united_atom:Conformational": 0.0, "united_atom:Orientational": 0.0 }, - "total": 74.48255240941317 + "total": 81.37561069630377 } } } diff --git a/tests/regression/baselines/methane/grouping_each.json b/tests/regression/baselines/methane/grouping_each.json index 22524ede..143d4d26 100644 --- a/tests/regression/baselines/methane/grouping_each.json +++ b/tests/regression/baselines/methane/grouping_each.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methane/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methane/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/methane/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/methane/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methane/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/methane/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "resid 1:10", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 112.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-51/test_regression_matches_baseli4/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw10/test_regression_matches_baseli2/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "each", @@ -23,10 +23,10 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { diff --git a/tests/regression/baselines/methane/rad.json b/tests/regression/baselines/methane/rad.json index d8385fb2..70d9aefa 100644 --- a/tests/regression/baselines/methane/rad.json +++ b/tests/regression/baselines/methane/rad.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methane/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methane/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/methane/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/methane/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methane/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/methane/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "all", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 112.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-51/test_regression_matches_baseli5/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw6/test_regression_matches_baseli2/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,10 +23,10 @@ "search_type": "RAD" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { @@ -34,9 +34,9 @@ "united_atom:Transvibrational": 40.3239711717637, "united_atom:Rovibrational": 33.60582165153992, "united_atom:Conformational": 0.0, - "united_atom:Orientational": 6.742734054179628 + "united_atom:Orientational": 6.667209510980459 }, - "total": 80.67252687748325 + "total": 80.59700233428407 } } } diff --git a/tests/regression/baselines/methane/selection_subset.json b/tests/regression/baselines/methane/selection_subset.json index 3cc5fcc8..afdd234f 100644 --- a/tests/regression/baselines/methane/selection_subset.json +++ b/tests/regression/baselines/methane/selection_subset.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methane/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methane/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/methane/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/methane/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methane/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/methane/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "resid 1:10", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 112.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-51/test_regression_matches_baseli6/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw4/test_regression_matches_baseli2/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,10 +23,10 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { diff --git a/tests/regression/baselines/methanol/axes_off.json b/tests/regression/baselines/methanol/axes_off.json index 3f772aa3..a4b5de8a 100644 --- a/tests/regression/baselines/methanol/axes_off.json +++ b/tests/regression/baselines/methanol/axes_off.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methanol/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methanol/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/methanol/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/methanol/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methanol/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/methanol/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "resid 1:10", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-46/test_regression_matches_baseli0/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw0/test_regression_matches_baseli2/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,10 +23,10 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { diff --git a/tests/regression/baselines/methanol/combined_forcetorque_off.json b/tests/regression/baselines/methanol/combined_forcetorque_off.json index 4e1a044e..7a70b9bc 100644 --- a/tests/regression/baselines/methanol/combined_forcetorque_off.json +++ b/tests/regression/baselines/methanol/combined_forcetorque_off.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methanol/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methanol/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/methanol/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/methanol/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methanol/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/methanol/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "resid 1:10", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-46/test_regression_matches_baseli1/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw15/test_regression_matches_baseli2/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,10 +23,10 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { diff --git a/tests/regression/baselines/methanol/default.json b/tests/regression/baselines/methanol/default.json index a3958278..e85e15ac 100644 --- a/tests/regression/baselines/methanol/default.json +++ b/tests/regression/baselines/methanol/default.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methanol/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methanol/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/methanol/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/methanol/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methanol/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/methanol/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "all", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-46/test_regression_matches_baseli2/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw3/test_regression_matches_baseli2/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,10 +23,10 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { @@ -37,9 +37,9 @@ "residue:FTmat-Rovibrational": 32.05829756161347, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, - "residue:Orientational": 31.476329452223162 + "residue:Orientational": 31.66363493251588 }, - "total": 153.2188991677791 + "total": 153.40620464807185 } } } diff --git a/tests/regression/baselines/methanol/frame_window.json b/tests/regression/baselines/methanol/frame_window.json index cbbecb9d..3c853174 100644 --- a/tests/regression/baselines/methanol/frame_window.json +++ b/tests/regression/baselines/methanol/frame_window.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methanol/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methanol/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/methanol/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/methanol/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methanol/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/methanol/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "resid 1:10", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-46/test_regression_matches_baseli3/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw14/test_regression_matches_baseli2/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,23 +23,23 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { "components": { "united_atom:Transvibrational": 0.0, - "united_atom:Rovibrational": 34.6755419354061, - "residue:FTmat-Transvibrational": 61.225853411706915, - "residue:FTmat-Rovibrational": 29.74713345439499, + "united_atom:Rovibrational": 43.01626564417083, + "residue:FTmat-Transvibrational": 74.91032652381023, + "residue:FTmat-Rovibrational": 32.84395719280311, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 0.0 }, - "total": 125.64852880150801 + "total": 150.77054936078417 } } } diff --git a/tests/regression/baselines/methanol/grouping_each.json b/tests/regression/baselines/methanol/grouping_each.json index 4df0bc9d..149c5c8e 100644 --- a/tests/regression/baselines/methanol/grouping_each.json +++ b/tests/regression/baselines/methanol/grouping_each.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methanol/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methanol/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/methanol/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/methanol/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methanol/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/methanol/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "resid 1:10", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-46/test_regression_matches_baseli4/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw12/test_regression_matches_baseli4/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "each", @@ -23,10 +23,10 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { @@ -97,9 +97,9 @@ "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, - "residue:Orientational": 0.2618944025459311 + "residue:Orientational": 0.0 }, - "total": 7.393907187868461 + "total": 7.132012785322529 }, "6": { "components": { @@ -133,9 +133,9 @@ "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, - "residue:Orientational": 0.9125191517246148 + "residue:Orientational": 0.0 }, - "total": 9.395203932274601 + "total": 8.482684780549986 }, "9": { "components": { diff --git a/tests/regression/baselines/methanol/rad.json b/tests/regression/baselines/methanol/rad.json index 6928ee36..eb41eb0e 100644 --- a/tests/regression/baselines/methanol/rad.json +++ b/tests/regression/baselines/methanol/rad.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methanol/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methanol/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/methanol/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/methanol/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methanol/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/methanol/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "all", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-46/test_regression_matches_baseli5/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw9/test_regression_matches_baseli2/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,10 +23,10 @@ "search_type": "RAD" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { @@ -37,9 +37,9 @@ "residue:FTmat-Rovibrational": 32.05829756161347, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, - "residue:Orientational": 17.099561921032407 + "residue:Orientational": 17.021167486252484 }, - "total": 138.84213163658836 + "total": 138.76373720180845 } } } diff --git a/tests/regression/baselines/methanol/selection_subset.json b/tests/regression/baselines/methanol/selection_subset.json index cb017f32..f8ad84f5 100644 --- a/tests/regression/baselines/methanol/selection_subset.json +++ b/tests/regression/baselines/methanol/selection_subset.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methanol/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methanol/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/methanol/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/methanol/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/methanol/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/methanol/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "resid 1:10", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-46/test_regression_matches_baseli6/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw7/test_regression_matches_baseli2/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,10 +23,10 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { diff --git a/tests/regression/baselines/octonol/axes_off.json b/tests/regression/baselines/octonol/axes_off.json index d4c364b4..8cc88689 100644 --- a/tests/regression/baselines/octonol/axes_off.json +++ b/tests/regression/baselines/octonol/axes_off.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/octonol/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/octonol/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/octonol/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/octonol/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/octonol/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/octonol/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "resid 1:10", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-48/test_regression_matches_baseli0/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw13/test_regression_matches_baseli3/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,23 +23,23 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { "components": { - "united_atom:Transvibrational": 4.018871224957591, + "united_atom:Transvibrational": 0.2907129992470817, "united_atom:Rovibrational": 16.39249280495534, "residue:FTmat-Transvibrational": 83.57043751308888, "residue:FTmat-Rovibrational": 58.87291960143169, - 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"output_file": "/tmp/pytest-of-harry-swift/pytest-48/test_regression_matches_baseli1/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw9/test_regression_matches_baseli3/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,23 +23,23 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { "components": { - "united_atom:Transvibrational": 3.6406563361703705, + "united_atom:Transvibrational": 0.34382967782781193, "united_atom:Rovibrational": 19.154228264604278, "residue:Transvibrational": 74.72816183790984, "residue:Rovibrational": 60.84390144550801, - 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"output_file": "/tmp/pytest-of-harry-swift/pytest-48/test_regression_matches_baseli2/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw12/test_regression_matches_baseli5/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,23 +23,23 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { "components": { - "united_atom:Transvibrational": 50.77228933028987, + "united_atom:Transvibrational": 37.860034170693694, "united_atom:Rovibrational": 84.2608785308744, "residue:FTmat-Transvibrational": 66.13571365167344, "residue:FTmat-Rovibrational": 57.090651827515686, - 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"output_file": "/tmp/pytest-of-harry-swift/pytest-48/test_regression_matches_baseli3/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw6/test_regression_matches_baseli3/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,23 +23,23 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { "components": { - "united_atom:Transvibrational": 75.76011510628999, - "united_atom:Rovibrational": 162.26463085986236, - "residue:FTmat-Transvibrational": 74.84326467422125, - "residue:FTmat-Rovibrational": 60.95710412746361, - "united_atom:Conformational": 20.4159084259166, + "united_atom:Transvibrational": 0.5593770868041172, + "united_atom:Rovibrational": 13.488941026792721, + "residue:FTmat-Transvibrational": 79.60741090497159, + "residue:FTmat-Rovibrational": 60.864478264811964, + "united_atom:Conformational": 16.651144380045313, "residue:Conformational": 0.0, - 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"output_file": "/tmp/pytest-of-harry-swift/pytest-48/test_regression_matches_baseli4/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw15/test_regression_matches_baseli3/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "each", @@ -23,10 +23,10 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { @@ -35,11 +35,11 @@ "united_atom:Rovibrational": 6.942013165337579e-05, "residue:FTmat-Transvibrational": 18.33494873681406, "residue:FTmat-Rovibrational": 0.0, - "united_atom:Conformational": 20.4159084259166, + "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, - "residue:Orientational": 31.535415760973137 + "residue:Orientational": 0.0 }, - "total": 70.28634234383546 + "total": 18.33501815694571 }, "1": { "components": { @@ -47,11 +47,11 @@ "united_atom:Rovibrational": 0.00013794104464519378, "residue:FTmat-Transvibrational": 14.571797812433102, "residue:FTmat-Rovibrational": 0.0, - "united_atom:Conformational": 25.283804882769058, + "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, - "residue:Orientational": 29.347813215860114 + "residue:Orientational": 45.863560270951176 }, - "total": 69.20355385210692 + "total": 60.43549602442892 }, "2": { "components": { @@ -59,11 +59,11 @@ "united_atom:Rovibrational": 0.0007753303955700146, "residue:FTmat-Transvibrational": 11.64466865126831, "residue:FTmat-Rovibrational": 0.0, - "united_atom:Conformational": 22.83087746936638, + "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 0.0 }, - "total": 34.47632145103026 + "total": 11.64544398166388 }, "3": { "components": { @@ -71,11 +71,11 @@ "united_atom:Rovibrational": 0.0031285818933102145, "residue:FTmat-Transvibrational": 21.24135891910478, "residue:FTmat-Rovibrational": 0.0, - "united_atom:Conformational": 22.633172290252627, + "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 0.0 }, - "total": 43.87765979125072 + "total": 21.24448750099809 }, "4": { "components": { @@ -83,11 +83,11 @@ "united_atom:Rovibrational": 0.0015070029381425056, "residue:FTmat-Transvibrational": 12.221662826352398, "residue:FTmat-Rovibrational": 0.0, - "united_atom:Conformational": 20.33932047774727, + "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 0.0 }, - "total": 32.562490307037805 + "total": 12.22316982929054 }, "5": { "components": { @@ -95,11 +95,11 @@ "united_atom:Rovibrational": 0.005775850934008876, "residue:FTmat-Transvibrational": 7.615636453348747, "residue:FTmat-Rovibrational": 0.0, - "united_atom:Conformational": 21.436442667442684, + "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 0.0 }, - "total": 29.05785497172544 + "total": 7.621412304282756 }, "6": { "components": { @@ -107,11 +107,11 @@ "united_atom:Rovibrational": 0.00028812747686091, "residue:FTmat-Transvibrational": 16.555914111511576, "residue:FTmat-Rovibrational": 0.0, - "united_atom:Conformational": 24.290085876338953, + "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 0.0 }, - "total": 40.84628811532739 + "total": 16.556202238988437 }, "7": { "components": { @@ -119,11 +119,11 @@ "united_atom:Rovibrational": 0.0013568745282136598, "residue:FTmat-Transvibrational": 15.71067757186967, "residue:FTmat-Rovibrational": 0.0, - "united_atom:Conformational": 16.445839353700418, + "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 0.0 }, - "total": 32.1578738000983 + "total": 15.712034446397883 }, "8": { "components": { @@ -131,11 +131,11 @@ "united_atom:Rovibrational": 8.389568220414916e-05, "residue:FTmat-Transvibrational": 13.516454082542095, "residue:FTmat-Rovibrational": 0.0, - "united_atom:Conformational": 16.20911564736676, + "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 0.0 }, - "total": 29.72565362559106 + "total": 13.5165379782243 }, "9": { "components": { @@ -143,11 +143,11 @@ "united_atom:Rovibrational": 0.00015446787843376823, "residue:FTmat-Transvibrational": 20.97761266375896, "residue:FTmat-Rovibrational": 0.0, - "united_atom:Conformational": 23.903613021846652, + "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, - "residue:Orientational": 39.134234408387165 + "residue:Orientational": 45.863560270951176 }, - "total": 84.01561456187122 + "total": 66.84132740258858 } } } diff --git a/tests/regression/baselines/octonol/rad.json b/tests/regression/baselines/octonol/rad.json index 2209df1e..90121a69 100644 --- a/tests/regression/baselines/octonol/rad.json +++ b/tests/regression/baselines/octonol/rad.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/octonol/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/octonol/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/octonol/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/octonol/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/octonol/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/octonol/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "all", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-48/test_regression_matches_baseli5/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw0/test_regression_matches_baseli3/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,23 +23,23 @@ "search_type": "RAD" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "4d39e9aeeed72fc3993f4a4eb6485da40524ebc5" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { "components": { - "united_atom:Transvibrational": 50.77228933028987, + "united_atom:Transvibrational": 37.860034170693694, "united_atom:Rovibrational": 84.2608785308744, "residue:FTmat-Transvibrational": 66.13571365167344, "residue:FTmat-Rovibrational": 57.090651827515686, - "united_atom:Conformational": 20.4159084259166, + "united_atom:Conformational": 34.22940197506605, "residue:Conformational": 0.0, - "residue:Orientational": 28.13775462144063 + "residue:Orientational": 28.084239413273323 }, - "total": 306.8131963877106 + "total": 307.66091956909656 } } } diff --git a/tests/regression/baselines/octonol/selection_subset.json b/tests/regression/baselines/octonol/selection_subset.json index ffcd7b9b..ef07f7b2 100644 --- a/tests/regression/baselines/octonol/selection_subset.json +++ b/tests/regression/baselines/octonol/selection_subset.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/octonol/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/octonol/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/octonol/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/octonol/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/octonol/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/octonol/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "resid 1:10", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-48/test_regression_matches_baseli6/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw3/test_regression_matches_baseli3/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,23 +23,23 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "4d39e9aeeed72fc3993f4a4eb6485da40524ebc5" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { "components": { - "united_atom:Transvibrational": 3.6406563361703705, + "united_atom:Transvibrational": 0.34382967782781193, "united_atom:Rovibrational": 19.154228264604278, "residue:FTmat-Transvibrational": 83.17889385114952, "residue:FTmat-Rovibrational": 57.480841206687685, - "united_atom:Conformational": 20.4159084259166, + "united_atom:Conformational": 16.83949354267619, "residue:Conformational": 0.0, - "residue:Orientational": 19.06182405604338 + "residue:Orientational": 25.79114991860739 }, - "total": 202.93235214057185 + "total": 202.78843646155286 } } } diff --git a/tests/regression/baselines/water/axes_off.json b/tests/regression/baselines/water/axes_off.json index a071e454..172edc92 100644 --- a/tests/regression/baselines/water/axes_off.json +++ b/tests/regression/baselines/water/axes_off.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/water/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/water/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/water/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/water/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/water/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/water/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "resid 1:10", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-49/test_regression_matches_baseli0/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw12/test_regression_matches_baseli6/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,10 +23,10 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { diff --git a/tests/regression/baselines/water/combined_forcetorque_off.json b/tests/regression/baselines/water/combined_forcetorque_off.json index c52e1149..c1e6c67e 100644 --- a/tests/regression/baselines/water/combined_forcetorque_off.json +++ b/tests/regression/baselines/water/combined_forcetorque_off.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/water/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/water/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/water/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/water/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/water/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/water/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "resid 1:10", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-49/test_regression_matches_baseli1/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw13/test_regression_matches_baseli4/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,10 +23,10 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { diff --git a/tests/regression/baselines/water/default.json b/tests/regression/baselines/water/default.json index 9dc3b266..f05b6965 100644 --- a/tests/regression/baselines/water/default.json +++ b/tests/regression/baselines/water/default.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/water/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/water/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/water/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/water/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/water/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/water/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "all", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-49/test_regression_matches_baseli2/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw15/test_regression_matches_baseli4/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,10 +23,10 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { @@ -34,9 +34,9 @@ "united_atom:Transvibrational": 43.725393337304425, "united_atom:Rovibrational": 17.28911070147887, "united_atom:Conformational": 0.0, - "united_atom:Orientational": 32.00715225476484 + "united_atom:Orientational": 32.193445593362114 }, - "total": 93.02165629354813 + "total": 93.20794963214541 } } } diff --git a/tests/regression/baselines/water/frame_window.json b/tests/regression/baselines/water/frame_window.json index 5061a109..6f4fc5f8 100644 --- a/tests/regression/baselines/water/frame_window.json +++ b/tests/regression/baselines/water/frame_window.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/water/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/water/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/water/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/water/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/water/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/water/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "resid 1:10", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-49/test_regression_matches_baseli3/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw0/test_regression_matches_baseli4/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,20 +23,20 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { "components": { - "united_atom:Transvibrational": 46.684099714230925, - "united_atom:Rovibrational": 17.694014405444744, + "united_atom:Transvibrational": 48.25352455371683, + "united_atom:Rovibrational": 23.131550866115766, "united_atom:Conformational": 0.0, "united_atom:Orientational": 0.0 }, - "total": 64.37811411967567 + "total": 71.38507541983259 } } } diff --git a/tests/regression/baselines/water/grouping_each.json b/tests/regression/baselines/water/grouping_each.json index df4b8a9b..7ad50620 100644 --- a/tests/regression/baselines/water/grouping_each.json +++ b/tests/regression/baselines/water/grouping_each.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/water/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/water/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/water/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/water/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/water/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/water/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "resid 1:10", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-49/test_regression_matches_baseli4/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw7/test_regression_matches_baseli3/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "each", @@ -23,10 +23,10 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { diff --git a/tests/regression/baselines/water/rad.json b/tests/regression/baselines/water/rad.json index 89962d0e..57abf9fd 100644 --- a/tests/regression/baselines/water/rad.json +++ b/tests/regression/baselines/water/rad.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/water/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/water/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/water/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/water/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/water/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/water/forces.frc", "file_format": "MDCRD", "kcal_force_units": false, "selection_string": "all", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-49/test_regression_matches_baseli5/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw5/test_regression_matches_baseli2/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,10 +23,10 @@ "search_type": "RAD" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { @@ -34,9 +34,9 @@ "united_atom:Transvibrational": 79.20298312418278, "united_atom:Rovibrational": 50.90260688502127, "united_atom:Conformational": 0.0, - "united_atom:Orientational": 22.599402683404527 + "united_atom:Orientational": 22.760377489372107 }, - "total": 152.70499269260856 + "total": 152.86596749857614 } } } diff --git a/tests/regression/baselines/water/selection_subset.json b/tests/regression/baselines/water/selection_subset.json index 5d188214..3fc34fe6 100644 --- a/tests/regression/baselines/water/selection_subset.json +++ b/tests/regression/baselines/water/selection_subset.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/water/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/water/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/water/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/water/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/water/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/water/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "resid 1:10", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-49/test_regression_matches_baseli6/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw9/test_regression_matches_baseli4/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -23,10 +23,10 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { diff --git a/tests/regression/baselines/water/water_off.json b/tests/regression/baselines/water/water_off.json index 55472326..85614af9 100644 --- a/tests/regression/baselines/water/water_off.json +++ b/tests/regression/baselines/water/water_off.json @@ -1,10 +1,10 @@ { "args": { "top_traj_file": [ - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/water/molecules.top", - "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/water/trajectory.crd" + "/home/ogo12949/CodeEntropy/.testdata/water/molecules.top", + "/home/ogo12949/CodeEntropy/.testdata/water/trajectory.crd" ], - "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/water/forces.frc", + "force_file": "/home/ogo12949/CodeEntropy/.testdata/water/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, "selection_string": "resid 1:10", @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-49/test_regression_matches_baseli7/job001/output_file.json", + "output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw6/test_regression_matches_baseli4/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": false, "grouping": "molecules", @@ -23,10 +23,10 @@ "search_type": "grid" }, "provenance": { - "python": "3.14.3", - "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", - "codeentropy_version": "2.1.0", - "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" + "python": "3.13.5", + "platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.1", + "git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096" }, "groups": { "0": { diff --git a/tests/unit/CodeEntropy/levels/.test_dihedrals.py.swp b/tests/unit/CodeEntropy/levels/.test_dihedrals.py.swp deleted file mode 100644 index c6bb916bc99e0072ce82bf21003991d97f24464e..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 24576 zcmeI43$P?tS%7=pkeEeC3_c>Fc4l2OH#<8!b9XnJU6>@B4OxPfB}HHhbGd2y-syX9 zbLaLVAV&Vf-K+x|$ z=k#NqcfxKe8|%OhH_})*RnwzHjU+H;41DTmrcSatY)T$R&_VAeTTcfm{N)1ab-F638WxOW-+> zfLph$tLQhB1OV&*as2=E8J6`Ia0mP*ycgaBuZ7FuHE=$>48HkN%lZcVF}wqAgu}1` zZ-9&8BKRTr-`J_z2t&F1!UC_+dEu{qzGL zhZ|rP-VE#Eo2MZI_;2_qG$DXD!I|*%sg`vN{t#}1>)9w+JY0DKH?0uT1W`EVMn0So?-{0rChN_m5wY>&1OsXj5MF+ zM?LDcyxKye=|)qkRlE^|(_P^%`tw&b=a-99mMZHsTVdHd7`5H`$XRH+iz{9bmD^s_ zX$Q`Jx6$!vwbE>;%6ylp`BrZ}YPP!+%v4Htbv7;=)_*3oiirmP% zq~ka0Uc1QtmHl2j^qgkPYpde0CRe1dTYmNRS@#xf+4|!6b*|H2=sGRWT@IZCZMPLV zfwxE}`#ndCm#?}r?=~8tv*7b{$q%FEV%uHOjfzt{85^6A8-`vxvUOK&85eF%-&Rji z$2BFYmA*)6uXf!y4Z5$*6l711S9jc~xl$ke zb()>1)#0xLOJ3jv&2;0_zzB;1haOUn)cAyD(GFzW2~g9Ty;Tj78FD}LgD`S~d9TO` zWJGLdSH14eHN0JW^w^u44KI)?Q_=-H!eof~6U~(|SoEUI1#tl-tuD1hGt85is*~0{ z=|(>3Ns9${YhfzYmx0nPV@s#UmR7T+sI2FB3kwLUHe<t#OqwRi=Jfl(in9dXX|WULETy zLNod?p&DduOaCc)#H~A*D$iQp&!dR-oDx5?>RH9qg-*2O2F@@skCa|w3zJ7FYjf3O zI8)eF5$n6FTA0;OWYVY{PlrlN>&#$vGleBp`lPMKvR*BVNtZ^_t2x$JQwF_W$yBVE zij}^Ky7{x78z)iej4ZHh4Ka41wsy?#&6QNYn{zUeXY^Y60zKx@D7G7Pm0}mgW~Eb+ z2)M;=RC|Sb_Jww}j1f_Hwt7!!FRhuCy@PhOva^bDQZ3D(4|dRNsi(7*m9b@5mOOVq zvq8}47W%EQxhq}6JT*mi4RS|*y;jNkLp?Ic*g^(zW>5r~(;8jNKAKD%S|7^XtUur9 z^i{=ys={>QxcPx`+p@jLnKOfbf*)g%b~tdZmw#9F5{k)j#b4><7%d5-HF_Axj1Rl%h+R` zp4f4`gMQ>Vrnz@;-VukqWb>p!NavDo6Mfd9C04Lo_*-kr*+UboXPL$k*m?YwZWMg|-?_kduX@8~F#5vzRB8IRm zQz7WAw7N{WgjA+mv4j#VlvfCNY*Q_Hig1_RXnsjwfs9ZXSGkI+4R0@39=6xm_QjhIv7|9E}=7;*hWa3@>`9!Si8E}Q~?M=bvU+z%gypNBWY3|tLo!MBLp zAB0c9UGO&OLJfWlPK76k-H*b@;CJD7;MbuGdtn_MBZmJQkQo061TYO%_z`%9`2A^k z1U?6!g)Y1iE`)R84EP!`yu|qb0utwc6mEs<;Z^X1a3-7qzfVm68!!)Zum^1TDL5UT zB&L4??uC2cFkAzBpaN&Zw~^_8!GFRhKxBL~nsZpExiT z-WNn!Ci~4$1B(Yk8GjR%vX?jzV zaOR%%h2iNO+P+gq06L|2ttE2McO#`$O1IBmt4|zDg~8DNWPet5hiV;H>+`x**>jaV z9V0cRB&l1jwSypCbb+*K+fjE*=oBn_UFATDKihLB9#%vtk^}B?TbBF z6DTe;yn~XWG078#BhI?05}mOSbV{M+0RJ;52xq?1Vtj^n%oK9|a4wrqF33S$&@LFZtjYdzZ#!V8! z+LBhMw@jkVJq;42-rF>G!vtip+)`_ywbdjP$!d^?)~7RSoR0mV?k6fDMQHyCQ{h9` zmTY^ytt6;AwfPwHO<8hiHPfA3U{;4QffFh0psaKZoUB(dGU`g=iYKRSCGS}$11c*P zdJ0K1%o*e6v)&*NIJ1!qrcP4~sDLS*DO4pXr&6Ehmq|&9vRO&@BvtDz5ng3>&NT;ujKc+a2EUzYx&=TKY@qfUbr3tSb=@; zVps>CWXxsU9k>Q&VFz3QtA0cs_0>T{}&48ugzOd9m==-JjG z?Z;0+Tz!{^)Hceme)dgkXgz)r3sGV6tT?SDzqgjQE2Hees9gN;o(pN$ z+GtsFS@Ox+uubo;_HL&FAyhb>J@^jITCOS`(ER?_1zWNBB* zgUoJ6Q`^a~B-5j|m8EUD)HuW*vafB`j)vGiOU7}yrRrOc<;lV%CI7ONuiA2;I?i%c zd&H~dD4mRJbAlG}CtGdp+u*js4C=Eg<#3UDlNdn(xvpeS+kov$W}`HCFuM!&Zntz| zii3w2V5ra^4#ZaSxZ{Kq5G05S%je|wzGh}~&rAO|Y2w|OM_{<+$r@oQ^CVg_zI+d{ z8YO#LyKofu*&5aAxytSKx=9OugS`Z7Z0kfO?WG=jf{wNyEKagzGP}8PI-O_7xJQ`{ zNRo^g5tOIiQtu{MBhg_SVWnsiS1H|m*=t0LO7O~KI4;j)r&|BtK(HrqpTz(1`~9CG z*1rkf4NcesvfqCj{3JX~e18-^12;e!&V?7jqr~%{gnQsH9E1b#CfEjBVGBG(T>miK z2R{ct3pLmd=fgI5lDPh_;TCv5yd6Ba0Jeh-PZ7_{9{&g7L-0Ph0j`Hv!=MWjehDsvjj$G;B(DEU_$~Mq2;udx8P>s9iR&MMV<2n)?*fVWk3bb(4v!Jr zKMD`Qop1+S1GDf_c!K!;VUU>rZulTb?0*>M;BwdmCD;gGC$4`C?u0ww7oiE4z%Dok z)`9Hxf1J2p_W3^u_rcw87x=Id{*`fl2EGLM!|iYz9D$uMas00|Q1n0-X4us>%>tU-sLX)R&c!u3fu!|!8Kcn~M#6?Z~`Jp~( zCYjyikBYzQB#Uk$bfz+SEn~=folftY@+6-;e6eHHM5A-=Cu%J^xrpq7#&ImlO{5!X ze3<5FzKdmRwakZZXIHPEEB9o~a->7fFVssR>dl?(V%_LfXQKo|qMg;2O0ugYJekQ( zaZ$b0aL8ZT&eKH@9Glb<^i<22O5&HyQURUZQBa(YK?j8P`zfMGuoCsB@b$%vnb>j_ZX3Nju_6GA(N0AJVQ8ME-$sP5Y=SkLpQ!hYVxYR63Z^ Date: Fri, 17 Apr 2026 13:44:59 +0100 Subject: [PATCH 5/5] more tests --- CodeEntropy/levels/mda.py | 24 ----- .../unit/CodeEntropy/levels/test_dihedrals.py | 102 ++++++++++++++---- 2 files changed, 83 insertions(+), 43 deletions(-) diff --git a/CodeEntropy/levels/mda.py b/CodeEntropy/levels/mda.py index b28cb3cb..f8cdec40 100644 --- a/CodeEntropy/levels/mda.py +++ b/CodeEntropy/levels/mda.py @@ -121,30 +121,6 @@ def extract_fragment( selection_string = f"index {frag.indices[0]}:{frag.indices[-1]}" return self.select_atoms(universe, selection_string) - def extract_fragments( - self, universe: mda.Universe, molecule_ids: list[int] - ) -> mda.Universe: - """Extract a single molecule (fragment) as a standalone reduced universe. - - Args: - universe: The source universe. - molecule_id: Fragment index in `universe.atoms.fragments`. - - Returns: - A reduced universe containing only the atoms of the selected fragment. - """ - group_indices = [] - for mol_id in molecule_ids: - frag = universe.atoms.fragments[mol_id] - group_indices.extend(frag.indices) - - selection_string = "index " - for i in group_indices: - group_indices[i] = int(group_indices[i]) - selection_string += f"{group_indices[i]} " - - return self.select_atoms(universe, selection_string) - def merge_forces( self, tprfile: str, diff --git a/tests/unit/CodeEntropy/levels/test_dihedrals.py b/tests/unit/CodeEntropy/levels/test_dihedrals.py index ee6bfe73..1bbdbe95 100644 --- a/tests/unit/CodeEntropy/levels/test_dihedrals.py +++ b/tests/unit/CodeEntropy/levels/test_dihedrals.py @@ -123,11 +123,14 @@ def test_identify_peaks_wraps_negative_angles_and_calls_find_histogram_peaks(): mol = MagicMock() mol.trajectory = [0, 1] + mol.residues = [MagicMock()] + mol.residues[0].atoms.indices = np.array([0, 1, 2, 3], dtype=int) uops.extract_fragment.return_value = mol dihedral = MagicMock() angles = np.array([[-10.0], [10.0]], dtype=float) + dt._select_heavy_residue = MagicMock(return_value=mol) dt._get_dihedrals = MagicMock(return_value=dihedral) dt._process_dihedral_phi = MagicMock(return_value=angles) @@ -142,15 +145,16 @@ def run(self): patch("CodeEntropy.levels.dihedrals.Dihedral", _FakeDihedral), patch.object(dt, "_process_histogram", return_value=[15.0]) as peaks_spy, ): - out = dt._identify_peaks( + out_ua, out_res = dt._identify_peaks( data_container=MagicMock(), molecules=[0], bin_width=10.0, - level_list=["residue"], + level_list=["united_atom", "residue"], ) - assert out == ([], [15.0]) - peaks_spy.assert_called_once() + assert out_ua[0] == [15.0] + assert out_res == [15.0] + assert peaks_spy.call_count == 2 def test_find_histogram_peaks_hits_interior_and_wraparound_last_bin(): @@ -168,16 +172,19 @@ def test_assign_states_initialises_then_extends_for_multiple_molecules(): mol = MagicMock() mol.trajectory = [0, 1] + mol.residues = [MagicMock()] + mol.residues[0].atoms.indices = np.array([0, 1, 2, 3], dtype=int) uops.extract_fragment.return_value = mol dihedrals = ["D0"] angles = np.array([[5.0], [15.0]], dtype=float) peaks = [[5.0, 15.0]] - states_ua = [] + states_ua = {} states_res = [] - flexible_ua = [] + flexible_ua = {} flexible_res = [] + dt._select_heavy_residue = MagicMock(return_value=mol) dt._get_dihedrals = MagicMock(return_value=dihedrals) class _FakeDihedral: @@ -192,8 +199,8 @@ def run(self): data_container=MagicMock(), group_id=0, molecules=[0, 1], - level_list=["residue"], - peaks_ua=[], + level_list=["united_atom", "residue"], + peaks_ua=[peaks], peaks_res=peaks, states_ua=states_ua, states_res=states_res, @@ -201,6 +208,8 @@ def run(self): flexible_res=flexible_res, ) + assert states_ua[(0, 0)] == ["0", "1", "0", "1"] + assert flexible_ua[(0, 0)] == 1 assert states_res[0] == ["0", "1", "0", "1"] assert flexible_res[0] == 1 @@ -233,6 +242,8 @@ def test_identify_peaks_handles_multiple_dihedrals(): mol = MagicMock() mol.trajectory = [0, 1] + mol.residues = [MagicMock()] + mol.residues[0].atoms.indices = np.array([0, 1, 2, 3], dtype=int) uops.extract_fragment.return_value = mol dihedrals = (["D0", "D1"],) @@ -244,6 +255,7 @@ def test_identify_peaks_handles_multiple_dihedrals(): dtype=float, ) + dt._select_heavy_residue = MagicMock(return_value=mol) dt._get_dihedrals = MagicMock(return_value=dihedrals) dt._process_dihedral_phi = MagicMock(return_value=angles) dt._process_histogram = MagicMock(return_value=[1, 2]) @@ -256,14 +268,15 @@ def run(self): return SimpleNamespace(results=SimpleNamespace(angles=angles)) with patch("CodeEntropy.levels.dihedrals.Dihedral", _FakeDihedral): - out = dt._identify_peaks( + out_ua, out_res = dt._identify_peaks( data_container=MagicMock(), molecules=[0], bin_width=30.0, level_list=["united_atom", "residue"], ) - assert len(out) == 2 + assert len(out_ua[0]) == 2 + assert len(out_res) == 2 def test_assign_states_filters_out_empty_state_strings_when_no_dihedrals(): @@ -272,14 +285,17 @@ def test_assign_states_filters_out_empty_state_strings_when_no_dihedrals(): mol = MagicMock() mol.trajectory = [0, 1, 2] + mol.residues = [MagicMock()] + mol.residues[0].atoms.indices = np.array([0, 1, 2, 3], dtype=int) uops.extract_fragment.return_value = mol dihedrals = [] - states_ua = [] + states_ua = {} states_res = [] - flexible_ua = [] + flexible_ua = {} flexible_res = [] + dt._select_heavy_residue = MagicMock(return_value=mol) dt._get_dihedrals = MagicMock(return_value=dihedrals) class _FakeDihedral: @@ -294,7 +310,7 @@ def run(self): data_container=MagicMock(), group_id=0, molecules=[0], - level_list=["residue"], + level_list=["united_atom", "residue"], peaks_ua=[], peaks_res=[], states_ua=states_ua, @@ -303,6 +319,8 @@ def run(self): flexible_res=flexible_res, ) + assert states_ua[(0, 0)] == [] + assert flexible_ua[(0, 0)] == 0 assert states_res[0] == [] assert flexible_res[0] == 0 @@ -313,8 +331,12 @@ def test_identify_peaks_multiple_molecules_real_histogram(): mol0 = MagicMock() mol0.trajectory = [0, 1] + mol0.residues = [MagicMock()] + mol0.residues[0].atoms.indices = np.array([0, 1, 2, 3], dtype=int) mol1 = MagicMock() mol1.trajectory = [0, 1] + mol1.residues = [MagicMock()] + mol1.residues[0].atoms.indices = np.array([0, 1, 2, 3], dtype=int) uops.extract_fragment.side_effect = [mol0, mol0, mol1] @@ -323,6 +345,7 @@ def test_identify_peaks_multiple_molecules_real_histogram(): phi_values = {} phi_values[0] = np.array([[10.0], [20.0]], dtype=float) + dt._select_heavy_residue = MagicMock(return_value=mol0) dt._get_dihedrals = MagicMock(return_value=dihedrals) dt._process_dihedral_phi = MagicMock(return_value=phi_values) @@ -344,10 +367,10 @@ def run(self): data_container=MagicMock(), molecules=[0, 1], bin_width=90.0, - level_list=["residue"], + level_list=["united_atom", "residue"], ) - assert len(peaks_ua) == 0 + assert len(peaks_ua) == 1 assert len(peaks_res) == 1 @@ -357,16 +380,19 @@ def test_assign_states_wraps_negative_angles(): mol = MagicMock() mol.trajectory = [0, 1] + mol.residues = [MagicMock()] + mol.residues[0].atoms.indices = np.array([0, 1, 2, 3], dtype=int) uops.extract_fragment.return_value = mol angles = np.array([[-10.0], [10.0]], dtype=float) peaks = [[10.0, 350.0]] dihedrals = ["D0"] - states_ua = [] + states_ua = {} states_res = [] - flexible_ua = [] + flexible_ua = {} flexible_res = [] + dt._select_heavy_residue = MagicMock(return_value=mol) dt._get_dihedrals = MagicMock(return_value=dihedrals) class _FakeDihedral: @@ -381,8 +407,8 @@ def run(self): data_container=MagicMock(), group_id=0, molecules=[0, 1], - level_list=["residue"], - peaks_ua=[], + level_list=["united_atom", "residue"], + peaks_ua=[peaks], peaks_res=peaks, states_ua=states_ua, states_res=states_res, @@ -390,6 +416,8 @@ def run(self): flexible_res=flexible_res, ) + assert states_ua[(0, 0)] == ["1", "0", "1", "0"] + assert flexible_ua[(0, 0)] == 1 assert states_res[0] == ["1", "0", "1", "0"] assert flexible_res[0] == 1 @@ -464,3 +492,39 @@ def test_build_conformational_states_with_progress_updates_title_per_group(monke progress.update.assert_any_call(9, title="Group 1") progress.advance.assert_called_with(9) + + +def test_process_dihedral_phi(): + uops = MagicMock() + dt = ConformationStateBuilder(universe_operations=uops) + + dihedral_results = MagicMock() + dihedral_results.results.angles = [[0, 1, 2], [3, 4, 5]] + num_dihedrals = 3 + number_frames = 2 + phi_values = {} + + phi_values = dt._process_dihedral_phi( + dihedral_results, num_dihedrals, number_frames, phi_values + ) + + assert len(phi_values) == 3 + assert phi_values[0] == [0, 3] + + +def test_process_dihedral_phi_negative(): + uops = MagicMock() + dt = ConformationStateBuilder(universe_operations=uops) + + dihedral_results = MagicMock() + dihedral_results.results.angles = [[0, 1, 2], [-3, 4, 5]] + num_dihedrals = 3 + number_frames = 2 + phi_values = {} + + phi_values = dt._process_dihedral_phi( + dihedral_results, num_dihedrals, number_frames, phi_values + ) + + assert len(phi_values) == 3 + assert phi_values[0] == [0, 357]