diff --git a/CodeEntropy/levels/axes.py b/CodeEntropy/levels/axes.py index e2cbfa5a..2dee616d 100644 --- a/CodeEntropy/levels/axes.py +++ b/CodeEntropy/levels/axes.py @@ -82,15 +82,13 @@ def get_residue_axes( * Translational axes are principal axes of data_container. * Find edge heavy atom (i.e. heavy atoms bonded to neighbour residue). Compute rotation centre and axes as in get_terminal_axes. - Compute custom MOI, using heavy atom positions and - heavy atom + hydrogen masses. + Compute custom MOI using all atom positions and masses. - If bonded to at least two other residues: * Translational axes are principal axes of data_container. * Find edge heavy atoms (i.e. heavy atoms bonded to neighbour residues). Compute rotation centre and axes as in get_non_terminal_axes. - Compute a custom MOI, using heavy atom positions and - heavy atom + hydrogen masses. + Compute custom MOI using all atom positions and masses. Args: data_container (MDAnalysis.Universe or AtomGroup): @@ -134,17 +132,8 @@ def get_residue_axes( f"resindex {index_next})" ) - uas = residue.select_atoms("mass 2 to 999") - ua_masses = self.get_UA_masses(residue) - if len(edge_atom_set) == 0: - moi_tensor = self.get_moment_of_inertia_tensor( - center_of_mass=np.array(residue.center_of_mass()), - positions=uas.positions, - masses=ua_masses, - dimensions=data_container.dimensions[:3], - ) - rot_axes, moment_of_inertia = self.get_custom_principal_axes(moi_tensor) + rot_axes, moment_of_inertia = self.get_vanilla_axes(residue) trans_axes = rot_axes # per original convention rot_center = np.array(residue.center_of_mass()) else: @@ -165,8 +154,8 @@ def get_residue_axes( ) moment_of_inertia = self.get_custom_residue_moment_of_inertia( center_of_mass=rot_center, - positions=uas.positions, - masses=ua_masses, + positions=residue.atoms.positions, + masses=residue.atoms.masses, custom_rot_axes=rot_axes, dimensions=data_container.dimensions[:3], ) @@ -202,24 +191,10 @@ def get_residue_axes_from_topology( - center: Residue centre, shape ``(3,)``. - moment_of_inertia: Principal moments, shape ``(3,)``. """ - dimensions = ( - np.asarray(box, dtype=float) - if box is not None - else np.asarray(u.dimensions[:3], dtype=float) - ) center = residue_atoms.center_of_mass(unwrap=True) if not topology.has_neighbor_bonds: - heavy_atoms = u.atoms[topology.residue_heavy_indices] - moment_of_inertia_tensor = self.get_moment_of_inertia_tensor( - center_of_mass=center, - positions=heavy_atoms.positions, - masses=topology.residue_ua_masses, - dimensions=dimensions, - ) - rot_axes, moment_of_inertia = self.get_custom_principal_axes( - moment_of_inertia_tensor - ) + rot_axes, moment_of_inertia = self.get_vanilla_axes(residue_atoms) trans_axes = rot_axes else: make_whole(mol.atoms) @@ -275,7 +250,7 @@ def get_UA_axes(self, data_container, index: int, res_position): index = int(index) # UA bead index heavy_atoms = data_container.select_atoms("mass 2 to 999") - # use the same customPI trans axes as the residue level + # use the same trans axes as the residue level if len(heavy_atoms) > 1: if len(data_container.residues) == 1: # only the one residue => use principal axes @@ -925,8 +900,8 @@ def get_custom_residue_moment_of_inertia( Args: center_of_mass: (3, ) COM for bead - positions: (N,3) positions of the UAs in the bead - masses: (N,) masses of the UAs in the bead + positions: (N,3) positions of the atoms in the bead + masses: (N,) masses of the atoms in the bead custom_rot_axes: (3,3) array of residue rotation axes dimensions: (3,) simulation_box_dimensions diff --git a/tests/regression/baselines/benzaldehyde/axes_off.json b/tests/regression/baselines/benzaldehyde/axes_off.json index 5bddd538..e58815e0 100644 --- a/tests/regression/baselines/benzaldehyde/axes_off.json +++ b/tests/regression/baselines/benzaldehyde/axes_off.json @@ -2,15 +2,15 @@ "groups": { "0": { "components": { - "united_atom:Transvibrational": 0.08982962903796131, - "united_atom:Rovibrational": 32.16018134884085, - "residue:FTmat-Transvibrational": 88.7671666695003, + "united_atom:Transvibrational": 0.08982962903796153, + "united_atom:Rovibrational": 32.160181348840844, + "residue:FTmat-Transvibrational": 88.76716666950027, "residue:FTmat-Rovibrational": 61.61036267672132, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 20.481571492615355 }, - "total": 203.1091118167158 + "total": 203.10911181671574 } } } diff --git a/tests/regression/baselines/benzaldehyde/combined_forcetorque_false.json b/tests/regression/baselines/benzaldehyde/combined_forcetorque_false.json index a5d1af0e..05ac9f28 100644 --- a/tests/regression/baselines/benzaldehyde/combined_forcetorque_false.json +++ b/tests/regression/baselines/benzaldehyde/combined_forcetorque_false.json @@ -2,15 +2,15 @@ "groups": { "0": { "components": { - "united_atom:Transvibrational": 0.07119323721997475, - "united_atom:Rovibrational": 49.68669738152346, - "residue:Transvibrational": 69.48692941204929, - "residue:Rovibrational": 68.46147102540942, + "united_atom:Transvibrational": 0.07119323721997481, + "united_atom:Rovibrational": 49.686697381523466, + "residue:Transvibrational": 69.80330954121192, + "residue:Rovibrational": 73.59711177182774, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 20.481571492615355 }, - "total": 208.1878625488175 + "total": 213.63988342439845 } } } diff --git a/tests/regression/baselines/benzaldehyde/frame_window.json b/tests/regression/baselines/benzaldehyde/frame_window.json index 70bb2766..e6f04f70 100644 --- a/tests/regression/baselines/benzaldehyde/frame_window.json +++ b/tests/regression/baselines/benzaldehyde/frame_window.json @@ -2,15 +2,15 @@ "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": 40.30267601961048, + "united_atom:Rovibrational": 38.219068584436165, + "residue:FTmat-Transvibrational": 74.59522673101434, + "residue:FTmat-Rovibrational": 58.48870270355095, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 20.481571492615355 }, - "total": 230.29580627384846 + "total": 232.0872455312273 } } } diff --git a/tests/regression/baselines/benzaldehyde/grouping_each.json b/tests/regression/baselines/benzaldehyde/grouping_each.json index deacf42c..c148ba43 100644 --- a/tests/regression/baselines/benzaldehyde/grouping_each.json +++ b/tests/regression/baselines/benzaldehyde/grouping_each.json @@ -4,121 +4,121 @@ "components": { "united_atom:Transvibrational": 0.0, "united_atom:Rovibrational": 0.062499436482478535, - "residue:FTmat-Transvibrational": 16.83857036769833, + "residue:FTmat-Transvibrational": 16.92340904741005, "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 31.909265242174982 }, - "total": 48.81033504635579 + "total": 48.89517372606751 }, "1": { "components": { "united_atom:Transvibrational": 0.0, "united_atom:Rovibrational": 0.04214874235319735, - "residue:FTmat-Transvibrational": 9.439228173427328, + "residue:FTmat-Transvibrational": 9.50856420599859, "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 0.0 }, - "total": 9.481376915780524 + "total": 9.550712948351787 }, "2": { "components": { "united_atom:Transvibrational": 0.0, "united_atom:Rovibrational": 0.0022147884278620493, - "residue:FTmat-Transvibrational": 17.449372254125855, + "residue:FTmat-Transvibrational": 17.765096867249817, "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 31.909265242174982 }, - "total": 49.3608522847287 + "total": 49.67657689785266 }, "3": { "components": { "united_atom:Transvibrational": 0.0, "united_atom:Rovibrational": 0.001983835543157824, - "residue:FTmat-Transvibrational": 15.803976930845373, + "residue:FTmat-Transvibrational": 15.979343677823543, "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 0.0 }, - "total": 15.80596076638853 + "total": 15.9813275133667 }, "4": { "components": { "united_atom:Transvibrational": 0.0, "united_atom:Rovibrational": 0.003874883925216773, - "residue:FTmat-Transvibrational": 23.899916844406114, + "residue:FTmat-Transvibrational": 24.03232930250616, "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 0.0 }, - "total": 23.90379172833133 + "total": 24.036204186431377 }, "5": { "components": { "united_atom:Transvibrational": 0.0, "united_atom:Rovibrational": 0.010824819910336868, - 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"total": 18.910802763391942 + "total": 19.070712470907033 }, "8": { "components": { "united_atom:Transvibrational": 0.0, "united_atom:Rovibrational": 0.020362757918507036, - "residue:FTmat-Transvibrational": 16.13204209116967, + "residue:FTmat-Transvibrational": 16.57161042803149, "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 31.909265242174982 }, - "total": 48.06167009126315 + "total": 48.50123842812498 }, "9": { "components": { "united_atom:Transvibrational": 0.0, "united_atom:Rovibrational": 0.00023139743934636996, - "residue:FTmat-Transvibrational": 21.42548529236268, + "residue:FTmat-Transvibrational": 21.777605911862764, "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 0.0 }, - "total": 21.425716689802027 + "total": 21.77783730930211 } } } diff --git a/tests/regression/baselines/benzaldehyde/selection_subset.json b/tests/regression/baselines/benzaldehyde/selection_subset.json index 6d50b1a7..1975b15c 100644 --- a/tests/regression/baselines/benzaldehyde/selection_subset.json +++ b/tests/regression/baselines/benzaldehyde/selection_subset.json @@ -2,15 +2,15 @@ "groups": { "0": { "components": { - "united_atom:Transvibrational": 0.07119323721997475, - "united_atom:Rovibrational": 49.68669738152346, - "residue:FTmat-Transvibrational": 87.43527331108173, - "residue:FTmat-Rovibrational": 61.67126452972779, + "united_atom:Transvibrational": 0.07119323721997481, + "united_atom:Rovibrational": 49.686697381523466, + "residue:FTmat-Transvibrational": 88.76716666950027, + "residue:FTmat-Rovibrational": 61.61036267672132, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 20.481571492615355 }, - "total": 219.34599995216834 + "total": 220.61699145758038 } } } diff --git a/tests/regression/baselines/benzene/axes_off.json b/tests/regression/baselines/benzene/axes_off.json index 6177e0d0..9f57ef48 100644 --- a/tests/regression/baselines/benzene/axes_off.json +++ b/tests/regression/baselines/benzene/axes_off.json @@ -2,9 +2,9 @@ "groups": { "0": { "components": { - "united_atom:Transvibrational": 0.17824017761231503, - "united_atom:Rovibrational": 37.12706256545503, - "residue:FTmat-Transvibrational": 76.8200637641939, + "united_atom:Transvibrational": 0.17824017761231412, + "united_atom:Rovibrational": 37.12706256545502, + "residue:FTmat-Transvibrational": 76.82006376419392, "residue:FTmat-Rovibrational": 47.171663134129304, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, diff --git a/tests/regression/baselines/benzene/combined_forcetorque_off.json b/tests/regression/baselines/benzene/combined_forcetorque_off.json index 16b5e375..e1585d07 100644 --- a/tests/regression/baselines/benzene/combined_forcetorque_off.json +++ b/tests/regression/baselines/benzene/combined_forcetorque_off.json @@ -2,15 +2,15 @@ "groups": { "0": { "components": { - "united_atom:Transvibrational": 0.16311383522946216, - "united_atom:Rovibrational": 40.695812407899396, - "residue:Transvibrational": 57.59675197041957, - "residue:Rovibrational": 52.85496348419672, + "united_atom:Transvibrational": 0.16311383522946185, + "united_atom:Rovibrational": 40.69581240789943, + "residue:Transvibrational": 58.30403178667887, + "residue:Rovibrational": 53.84947651174329, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 0.0 }, - "total": 151.31064169774515 + "total": 153.01243454155104 } } } diff --git a/tests/regression/baselines/benzene/frame_window.json b/tests/regression/baselines/benzene/frame_window.json index c1ffd000..49f08445 100644 --- a/tests/regression/baselines/benzene/frame_window.json +++ b/tests/regression/baselines/benzene/frame_window.json @@ -2,15 +2,15 @@ "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": 11.465520360845467, + "united_atom:Rovibrational": 34.98492056748487, + "residue:FTmat-Transvibrational": 74.31826351535895, + "residue:FTmat-Rovibrational": 55.98936607558771, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 0.0 }, - "total": 173.89519974256632 + "total": 176.758070519277 } } } diff --git a/tests/regression/baselines/benzene/grouping_each.json b/tests/regression/baselines/benzene/grouping_each.json index 36535d8f..6f18b18e 100644 --- a/tests/regression/baselines/benzene/grouping_each.json +++ b/tests/regression/baselines/benzene/grouping_each.json @@ -4,121 +4,121 @@ "components": { "united_atom:Transvibrational": 0.0, "united_atom:Rovibrational": 0.001760679467943202, - "residue:FTmat-Transvibrational": 19.14539159233644, + "residue:FTmat-Transvibrational": 19.578679589524242, "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 0.0 }, - "total": 19.147152271804384 + "total": 19.580440268992184 }, "1": { "components": { "united_atom:Transvibrational": 0.0, - "united_atom:Rovibrational": 0.010093246924291187, - "residue:FTmat-Transvibrational": 15.27551568157708, + "united_atom:Rovibrational": 0.010093246924291217, + "residue:FTmat-Transvibrational": 15.715354239834078, "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 15.089233620075317 }, - "total": 30.374842548576687 + "total": 30.81468110683369 }, "2": { "components": { "united_atom:Transvibrational": 0.0, "united_atom:Rovibrational": 0.07511923174012403, - "residue:FTmat-Transvibrational": 20.327785240055736, + "residue:FTmat-Transvibrational": 20.399982464339494, "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 15.089233620075317 }, - 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"total": 151.94722026765817 + "total": 163.41945964917272 } } } diff --git a/tests/regression/baselines/octonol/axes_off.json b/tests/regression/baselines/octonol/axes_off.json index bc391e6f..3bd2a567 100644 --- a/tests/regression/baselines/octonol/axes_off.json +++ b/tests/regression/baselines/octonol/axes_off.json @@ -2,9 +2,9 @@ "groups": { "0": { "components": { - "united_atom:Transvibrational": 0.2907129992470817, - "united_atom:Rovibrational": 16.39249280495534, - "residue:FTmat-Transvibrational": 83.57043751308888, + "united_atom:Transvibrational": 0.29071299924708216, + "united_atom:Rovibrational": 16.392492804955346, + "residue:FTmat-Transvibrational": 83.57043751308886, "residue:FTmat-Rovibrational": 58.87291960143169, "united_atom:Conformational": 16.83949354267619, "residue:Conformational": 0.0, diff --git a/tests/regression/baselines/octonol/combined_forcetorque_off.json b/tests/regression/baselines/octonol/combined_forcetorque_off.json index 920589a7..38468676 100644 --- a/tests/regression/baselines/octonol/combined_forcetorque_off.json +++ b/tests/regression/baselines/octonol/combined_forcetorque_off.json @@ -2,15 +2,15 @@ "groups": { "0": { "components": { - "united_atom:Transvibrational": 0.34382967782781193, - "united_atom:Rovibrational": 19.154228264604278, - "residue:Transvibrational": 74.72816183790984, - "residue:Rovibrational": 60.84390144550801, + "united_atom:Transvibrational": 0.3438296778278115, + "united_atom:Rovibrational": 19.154228264604267, + "residue:Transvibrational": 72.53825217841872, + "residue:Rovibrational": 63.76876798105059, "united_atom:Conformational": 16.83949354267619, "residue:Conformational": 0.0, "residue:Orientational": 25.79114991860739 }, - "total": 197.70076468713353 + "total": 198.43572156318498 } } } diff --git a/tests/regression/baselines/octonol/frame_window.json b/tests/regression/baselines/octonol/frame_window.json index 5c07dcc2..25866017 100644 --- a/tests/regression/baselines/octonol/frame_window.json +++ b/tests/regression/baselines/octonol/frame_window.json @@ -2,15 +2,15 @@ "groups": { "0": { "components": { - "united_atom:Transvibrational": 65.86600728016141, - "united_atom:Rovibrational": 162.26463085986236, - "residue:FTmat-Transvibrational": 74.84326467422125, - "residue:FTmat-Rovibrational": 60.95710412746361, + "united_atom:Transvibrational": 65.86600728016144, + "united_atom:Rovibrational": 162.26463085986254, + "residue:FTmat-Transvibrational": 76.00604043328042, + "residue:FTmat-Rovibrational": 62.15737287426515, "united_atom:Conformational": 16.651144380045313, "residue:Conformational": 0.0, "residue:Orientational": 25.79114991860739 }, - "total": 406.37330124036134 + "total": 408.73634574622224 } } } diff --git a/tests/regression/baselines/octonol/grouping_each.json b/tests/regression/baselines/octonol/grouping_each.json index b4801742..2f8059fa 100644 --- a/tests/regression/baselines/octonol/grouping_each.json +++ b/tests/regression/baselines/octonol/grouping_each.json @@ -3,122 +3,122 @@ "0": { "components": { "united_atom:Transvibrational": 0.0, - "united_atom:Rovibrational": 6.942013165337579e-05, - "residue:FTmat-Transvibrational": 18.33494873681406, + "united_atom:Rovibrational": 6.942013165337589e-05, + "residue:FTmat-Transvibrational": 19.071330421089645, "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 0.0 }, - "total": 18.33501815694571 + "total": 19.071399841221297 }, "1": { "components": { "united_atom:Transvibrational": 0.0, "united_atom:Rovibrational": 0.00013794104464519378, - "residue:FTmat-Transvibrational": 14.571797812433102, + "residue:FTmat-Transvibrational": 14.64706046020792, "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 45.863560270951176 }, - "total": 60.43549602442892 + "total": 60.51075867220374 }, "2": { "components": { "united_atom:Transvibrational": 0.0, - "united_atom:Rovibrational": 0.0007753303955700146, - "residue:FTmat-Transvibrational": 11.64466865126831, + "united_atom:Rovibrational": 0.000775330395570017, + "residue:FTmat-Transvibrational": 12.849039746264522, "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 0.0 }, - "total": 11.64544398166388 + "total": 12.849815076660091 }, "3": { "components": { "united_atom:Transvibrational": 0.0, - "united_atom:Rovibrational": 0.0031285818933102145, - "residue:FTmat-Transvibrational": 21.24135891910478, + "united_atom:Rovibrational": 0.0031285818933102097, + "residue:FTmat-Transvibrational": 21.84720949192935, "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 0.0 }, - "total": 21.24448750099809 + "total": 21.85033807382266 }, "4": { "components": { "united_atom:Transvibrational": 0.0, "united_atom:Rovibrational": 0.0015070029381425056, - "residue:FTmat-Transvibrational": 12.221662826352398, + "residue:FTmat-Transvibrational": 12.367134537261949, "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 0.0 }, - "total": 12.22316982929054 + "total": 12.368641540200091 }, "5": { "components": { "united_atom:Transvibrational": 0.0, "united_atom:Rovibrational": 0.005775850934008876, - "residue:FTmat-Transvibrational": 7.615636453348747, + "residue:FTmat-Transvibrational": 8.75079593507118, "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 0.0 }, - "total": 7.621412304282756 + "total": 8.756571786005189 }, "6": { "components": { "united_atom:Transvibrational": 0.0, "united_atom:Rovibrational": 0.00028812747686091, - "residue:FTmat-Transvibrational": 16.555914111511576, + "residue:FTmat-Transvibrational": 16.651398255680196, "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 0.0 }, - "total": 16.556202238988437 + "total": 16.651686383157056 }, "7": { "components": { "united_atom:Transvibrational": 0.0, "united_atom:Rovibrational": 0.0013568745282136598, - "residue:FTmat-Transvibrational": 15.71067757186967, + "residue:FTmat-Transvibrational": 15.814234753264744, "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 0.0 }, - "total": 15.712034446397883 + "total": 15.815591627792957 }, "8": { "components": { "united_atom:Transvibrational": 0.0, "united_atom:Rovibrational": 8.389568220414916e-05, - "residue:FTmat-Transvibrational": 13.516454082542095, + "residue:FTmat-Transvibrational": 14.1766367513517, "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 0.0 }, - "total": 13.5165379782243 + "total": 14.176720647033903 }, "9": { "components": { "united_atom:Transvibrational": 0.0, "united_atom:Rovibrational": 0.00015446787843376823, - "residue:FTmat-Transvibrational": 20.97761266375896, + "residue:FTmat-Transvibrational": 21.032421082499322, "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 45.863560270951176 }, - "total": 66.84132740258858 + "total": 66.89613582132893 } } } diff --git a/tests/regression/baselines/octonol/selection_subset.json b/tests/regression/baselines/octonol/selection_subset.json index 5f9d18f1..7b0b849e 100644 --- a/tests/regression/baselines/octonol/selection_subset.json +++ b/tests/regression/baselines/octonol/selection_subset.json @@ -2,15 +2,15 @@ "groups": { "0": { "components": { - "united_atom:Transvibrational": 0.34382967782781193, - "united_atom:Rovibrational": 19.154228264604278, - "residue:FTmat-Transvibrational": 83.17889385114952, - "residue:FTmat-Rovibrational": 57.480841206687685, + "united_atom:Transvibrational": 0.3438296778278115, + "united_atom:Rovibrational": 19.154228264604267, + "residue:FTmat-Transvibrational": 83.57043751308886, + "residue:FTmat-Rovibrational": 58.87291960143169, "united_atom:Conformational": 16.83949354267619, "residue:Conformational": 0.0, "residue:Orientational": 25.79114991860739 }, - "total": 202.78843646155286 + "total": 204.5720585182362 } } } diff --git a/tests/regression/baselines/water/axes_off.json b/tests/regression/baselines/water/axes_off.json index 9b798bdc..084d728c 100644 --- a/tests/regression/baselines/water/axes_off.json +++ b/tests/regression/baselines/water/axes_off.json @@ -3,7 +3,7 @@ "0": { "components": { "united_atom:Transvibrational": 51.22145722965398, - "united_atom:Rovibrational": 17.307840626636324, + "united_atom:Rovibrational": 17.307840626636327, "united_atom:Conformational": 0.0, "united_atom:Orientational": 0.0 }, diff --git a/tests/regression/baselines/water/grouping_each.json b/tests/regression/baselines/water/grouping_each.json index acccd86b..80aa22cb 100644 --- a/tests/regression/baselines/water/grouping_each.json +++ b/tests/regression/baselines/water/grouping_each.json @@ -2,7 +2,7 @@ "groups": { "0": { "components": { - "united_atom:Transvibrational": 14.945907953805552, + "united_atom:Transvibrational": 14.94590795380555, "united_atom:Rovibrational": 1.8947243953648254, "united_atom:Conformational": 0.0, "united_atom:Orientational": 0.0 @@ -11,17 +11,17 @@ }, "1": { "components": { - "united_atom:Transvibrational": 8.111522208287779, + "united_atom:Transvibrational": 8.111522208287777, "united_atom:Rovibrational": 0.9607747968334215, "united_atom:Conformational": 0.0, "united_atom:Orientational": 0.0 }, - "total": 9.0722970051212 + "total": 9.072297005121198 }, "2": { "components": { - "united_atom:Transvibrational": 15.79497347968759, - "united_atom:Rovibrational": 4.606072530590255, + "united_atom:Transvibrational": 15.794973479687595, + "united_atom:Rovibrational": 4.606072530590252, "united_atom:Conformational": 0.0, "united_atom:Orientational": 0.0 }, @@ -30,7 +30,7 @@ "3": { "components": { "united_atom:Transvibrational": 9.462487265119448, - "united_atom:Rovibrational": 1.6509513986984767, + "united_atom:Rovibrational": 1.650951398698477, "united_atom:Conformational": 0.0, "united_atom:Orientational": 0.0 }, diff --git a/tests/unit/CodeEntropy/levels/test_axes.py b/tests/unit/CodeEntropy/levels/test_axes.py index 2b856a08..ee152ff4 100644 --- a/tests/unit/CodeEntropy/levels/test_axes.py +++ b/tests/unit/CodeEntropy/levels/test_axes.py @@ -102,14 +102,9 @@ def _select_atoms(q): u.select_atoms.side_effect = _select_atoms - monkeypatch.setattr(ax, "get_UA_masses", lambda mol: [10.0, 12.0]) - monkeypatch.setattr(ax, "get_moment_of_inertia_tensor", lambda **kwargs: np.eye(3)) monkeypatch.setattr( - ax, - "get_custom_principal_axes", - lambda moi: (np.eye(3), np.array([3.0, 2.0, 1.0])), + ax, "get_vanilla_axes", lambda molecule: (np.eye(3), np.array([3.0, 2.0, 1.0])) ) - trans, rot, center, moi = ax.get_residue_axes(u, index=7, relative_index=0) assert np.allclose(trans, np.eye(3)) @@ -128,7 +123,6 @@ def test_get_residue_axes_one_residue_uses_principal_axes(monkeypatch): u = MagicMock() u.dimensions = np.array([10.0, 10.0, 10.0, 90, 90, 90]) - u.atoms.principal_axes.return_value = np.eye(3) # atom_set non-empty => bonded branch def _select_atoms(q): @@ -142,9 +136,7 @@ def _select_atoms(q): monkeypatch.setattr("CodeEntropy.levels.axes.make_whole", lambda _ag: None) monkeypatch.setattr( - ax, - "get_moment_of_inertia_tensor", - lambda **kwargs: np.array([[9.0, 0.0, 0.0], [0.0, 8.0, 0.0], [0.0, 0.0, 7.0]]), + ax, "get_vanilla_axes", lambda molecule: (np.eye(3), np.array([9.0, 8.0, 7.0])) ) trans, rot, center, moi = ax.get_residue_axes(u, index=10, relative_index=0) @@ -493,13 +485,8 @@ def _select_atoms(q): return [] u.select_atoms.side_effect = _select_atoms - - monkeypatch.setattr(ax, "get_UA_masses", lambda mol: [10.0, 12.0]) - monkeypatch.setattr(ax, "get_moment_of_inertia_tensor", lambda **kwargs: np.eye(3)) monkeypatch.setattr( - ax, - "get_custom_principal_axes", - lambda moi: (np.eye(3), np.array([3.0, 2.0, 1.0])), + ax, "get_vanilla_axes", lambda mol: (2 * np.eye(3), np.array([3.0, 2.0, 1.0])) ) trans, rot, center, moi = ax.get_residue_axes(u, index=7, relative_index=0) @@ -515,13 +502,11 @@ def test_get_residue_axes_one_residue_principal_axes_path(monkeypatch): residue = MagicMock() residue.__len__.return_value = 1 - residue.atoms.principal_axes.return_value = np.eye(3) * 2 residue.atoms.center_of_mass.return_value = np.array([1.0, 2.0, 3.0]) residue.center_of_mass.return_value = np.array([1.0, 2.0, 3.0]) u = MagicMock() u.dimensions = np.array([10.0, 10.0, 10.0, 90, 90, 90]) - u.atoms.principal_axes.return_value = np.eye(3) * 2 def _select_atoms(q): if q.startswith("(resindex"): @@ -533,17 +518,14 @@ def _select_atoms(q): u.select_atoms.side_effect = _select_atoms monkeypatch.setattr("CodeEntropy.levels.axes.make_whole", lambda _ag: None) - monkeypatch.setattr( - ax, - "get_moment_of_inertia_tensor", - lambda **kwargs: np.array([[9.0, 0.0, 0.0], [0.0, 8.0, 0.0], [0.0, 0.0, 7.0]]), + ax, "get_vanilla_axes", lambda _ag: (2 * np.eye(3), np.array([9.0, 8.0, 7.0])) ) trans, rot, center, moi = ax.get_residue_axes(u, index=10, relative_index=0) - assert np.allclose(trans, np.eye(3)) - assert np.allclose(rot, np.eye(3)) + assert np.allclose(trans, 2 * np.eye(3)) + assert np.allclose(rot, 2 * np.eye(3)) assert np.allclose(center, np.array([1.0, 2.0, 3.0])) assert np.allclose(moi, np.array([9.0, 8.0, 7.0])) @@ -795,11 +777,9 @@ def test_get_residue_axes_from_topology_no_neighbor_bonds_uses_cached_indices( has_neighbor_bonds=False, ) - get_tensor = MagicMock(return_value=np.eye(3)) get_principal = MagicMock(return_value=(np.eye(3) * 2.0, np.array([3.0, 2.0, 1.0]))) - monkeypatch.setattr(ax, "get_moment_of_inertia_tensor", get_tensor) - monkeypatch.setattr(ax, "get_custom_principal_axes", get_principal) + monkeypatch.setattr(ax, "get_vanilla_axes", get_principal) box = np.array([20.0, 30.0, 40.0]) trans_axes, rot_axes, center, moi = ax.get_residue_axes_from_topology( @@ -815,17 +795,6 @@ def test_get_residue_axes_from_topology_no_neighbor_bonds_uses_cached_indices( np.testing.assert_allclose(center, np.array([9.0, 8.0, 7.0])) np.testing.assert_allclose(moi, np.array([3.0, 2.0, 1.0])) - tensor_kwargs = get_tensor.call_args.kwargs - np.testing.assert_allclose( - tensor_kwargs["center_of_mass"], - np.array([9.0, 8.0, 7.0]), - ) - np.testing.assert_allclose( - tensor_kwargs["positions"], - np.array([[1.0, 2.0, 3.0], [4.0, 5.0, 6.0]]), - ) - np.testing.assert_allclose(tensor_kwargs["masses"], np.array([13.0, 14.0])) - np.testing.assert_allclose(tensor_kwargs["dimensions"], box) get_principal.assert_called_once()