diff --git a/CodeEntropy/levels/axes.py b/CodeEntropy/levels/axes.py index 04c59315..87d8832a 100644 --- a/CodeEntropy/levels/axes.py +++ b/CodeEntropy/levels/axes.py @@ -82,15 +82,14 @@ 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 atoms 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 atoms positions and masses. + Args: data_container (MDAnalysis.Universe or AtomGroup): @@ -134,19 +133,8 @@ 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_principal_axes_from_tensor( - moi_tensor - ) + rot_axes, moment_of_inertia = self.get_molecule_axes(residue) trans_axes = rot_axes # per original convention rot_center = np.array(residue.center_of_mass()) else: @@ -167,8 +155,8 @@ 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], ) @@ -181,7 +169,6 @@ def get_residue_axes_from_topology( mol, residue_atoms, topology, - box: np.ndarray | None, ): """Compute residue axes using cached static topology. @@ -195,7 +182,6 @@ def get_residue_axes_from_topology( mol: Current-frame molecule fragment. residue_atoms: AtomGroup for the residue in the current frame. topology: Cached ``ResidueAxesTopology`` for this residue. - box: Current periodic box lengths. If omitted, ``u.dimensions`` is used. Returns: Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]: @@ -204,24 +190,10 @@ 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_principal_axes_from_tensor( - moment_of_inertia_tensor - ) + rot_axes, moment_of_inertia = self.get_molecule_axes(residue_atoms) trans_axes = rot_axes else: make_whole(mol.atoms) @@ -277,7 +249,7 @@ 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 @@ -411,16 +383,7 @@ def get_UA_axes_from_topology( heavy_atom = u.atoms[int(topology.heavy_atom_index)] if len(heavy_atoms) > 1: - center = residue_atoms.center_of_mass(unwrap=True) - 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, - ) - trans_axes, _moment_of_inertia = self.get_principal_axes_from_tensor( - moment_of_inertia_tensor - ) + trans_axes = self.get_principal_axes_from_group(residue_atoms) else: make_whole(residue_atoms) trans_axes = self.get_principal_axes_from_group(residue_atoms) @@ -921,8 +884,8 @@ 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 @@ -1137,30 +1100,6 @@ def get_principal_axes_from_group(self, group) -> np.ndarray: ) return principal_axes - def get_UA_masses(self, molecule) -> list[float]: - """Return united-atom (UA) masses for a molecule. - - For a given molecule, return a list of masses of UAs (combination of the - heavy atoms + bonded hydrogen atoms). This list is used to get the moment - of inertia tensor for molecules larger than one UA. - - Args: - molecule: MDAnalysis AtomGroup representing the molecule. - - Returns: - list[float]: UA masses for each heavy atom. - """ - ua_masses: list[float] = [] - for atom in molecule: - if atom.mass > 1.1: - ua_mass = float(atom.mass) - bonded_atoms = molecule.select_atoms(f"bonded index {atom.index}") - bonded_h_atoms = bonded_atoms.select_atoms("mass 1 to 1.1") - for h in bonded_h_atoms: - ua_mass += float(h.mass) - ua_masses.append(ua_mass) - return ua_masses - def get_chain(self, residue, first, last): """ For a given MDAnalysis AtomGroup and two given heavy atoms diff --git a/CodeEntropy/levels/nodes/covariance.py b/CodeEntropy/levels/nodes/covariance.py index 63db3140..57a7a922 100644 --- a/CodeEntropy/levels/nodes/covariance.py +++ b/CodeEntropy/levels/nodes/covariance.py @@ -578,7 +578,6 @@ def _build_residue_vectors( relative_res_i=relative_res_i, axes_manager=axes_manager, axes_topology=axes_topology, - box=box, customised_axes=customised_axes, ) @@ -615,7 +614,6 @@ def _get_residue_axes( relative_res_i: int, axes_manager: Any, axes_topology: Any | None, - box: np.ndarray | None, customised_axes: bool, ) -> tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]: """Return axes, centre, and inertia data for a residue bead. @@ -630,7 +628,6 @@ def _get_residue_axes( might differ from residue index of first residue in topology. axes_manager: Axes helper used to select axes, centres, and moments. axes_topology: Optional cached axes topology generated during static setup. - box: Optional periodic box vector. customised_axes: Whether customised residue axes should be used. Returns: @@ -644,11 +641,7 @@ def _get_residue_axes( if residue_topology is not None: return axes_manager.get_residue_axes_from_topology( - u=u, - mol=mol, - residue_atoms=res.atoms, - topology=residue_topology, - box=box, + u=u, mol=mol, residue_atoms=res.atoms, topology=residue_topology ) return axes_manager.get_residue_axes( diff --git a/tests/regression/baselines/benzaldehyde/combined_forcetorque_false.json b/tests/regression/baselines/benzaldehyde/combined_forcetorque_false.json index d79e5335..0a348984 100644 --- a/tests/regression/baselines/benzaldehyde/combined_forcetorque_false.json +++ b/tests/regression/baselines/benzaldehyde/combined_forcetorque_false.json @@ -3,14 +3,14 @@ "0": { "components": { "united_atom:Transvibrational": 0.06817494136874551, - "united_atom:Rovibrational": 49.686697381523516, - "residue:Transvibrational": 69.25273989458984, - "residue:Rovibrational": 68.6481013342223, + "united_atom:Rovibrational": 49.686697381523466, + "residue:Transvibrational": 69.24977659775257, + "residue:Rovibrational": 69.73922011617867, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 20.481571492615355 }, - "total": 208.13728504431975 + "total": 209.22544052943883 } } } diff --git a/tests/regression/baselines/benzaldehyde/default.json b/tests/regression/baselines/benzaldehyde/default.json index 328d1a45..b422b1a0 100644 --- a/tests/regression/baselines/benzaldehyde/default.json +++ b/tests/regression/baselines/benzaldehyde/default.json @@ -2,15 +2,15 @@ "groups": { "0": { "components": { - "united_atom:Transvibrational": 24.92182210331405, - "united_atom:Rovibrational": 27.950376507672583, - "residue:FTmat-Transvibrational": 70.97090266225698, - "residue:FTmat-Rovibrational": 59.588669973122094, + "united_atom:Transvibrational": 24.921822103314035, + "united_atom:Rovibrational": 27.950376507672594, + "residue:FTmat-Transvibrational": 71.231562004914, + "residue:FTmat-Rovibrational": 60.43602521189648, "united_atom:Conformational": 7.522643899702263, "residue:Conformational": 0.0, "residue:Orientational": 59.43920971558428 }, - "total": 250.39362486165226 + "total": 251.50163944308366 } } } diff --git a/tests/regression/baselines/benzaldehyde/frame_window.json b/tests/regression/baselines/benzaldehyde/frame_window.json index e01bcfa4..89afecfa 100644 --- a/tests/regression/baselines/benzaldehyde/frame_window.json +++ b/tests/regression/baselines/benzaldehyde/frame_window.json @@ -3,14 +3,14 @@ "0": { "components": { "united_atom:Transvibrational": 37.90368186636453, - "united_atom:Rovibrational": 38.21906858443616, - "residue:FTmat-Transvibrational": 73.76730786578054, - "residue:FTmat-Rovibrational": 57.689489298548764, + "united_atom:Rovibrational": 38.219068584436165, + "residue:FTmat-Transvibrational": 74.05827280885852, + "residue:FTmat-Rovibrational": 58.53451127009362, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 20.481571492615355 }, - "total": 228.06111910774533 + "total": 229.1971060223682 } } } diff --git a/tests/regression/baselines/benzaldehyde/grouping_each.json b/tests/regression/baselines/benzaldehyde/grouping_each.json index 8a8b842a..ce584d8d 100644 --- a/tests/regression/baselines/benzaldehyde/grouping_each.json +++ b/tests/regression/baselines/benzaldehyde/grouping_each.json @@ -3,122 +3,122 @@ "0": { "components": { "united_atom:Transvibrational": 0.0, - "united_atom:Rovibrational": 0.062499436482478445, - "residue:FTmat-Transvibrational": 16.83857036769834, + "united_atom:Rovibrational": 0.062499436482478535, + "residue:FTmat-Transvibrational": 16.92340904741005, "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 31.909265242174982 }, - "total": 48.8103350463558 + "total": 48.89517372606751 }, "1": { "components": { "united_atom:Transvibrational": 0.0, "united_atom:Rovibrational": 0.04214874235319735, - "residue:FTmat-Transvibrational": 9.439228173427328, + "residue:FTmat-Transvibrational": 9.508564205998585, "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 0.0 }, - "total": 9.481376915780524 + "total": 9.550712948351782 }, "2": { "components": { "united_atom:Transvibrational": 0.0, - "united_atom:Rovibrational": 0.0022147884278620397, - "residue:FTmat-Transvibrational": 17.449372254125855, + "united_atom:Rovibrational": 0.0022147884278620493, + "residue:FTmat-Transvibrational": 17.7650968672498, "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 31.909265242174982 }, - "total": 49.36085228472869 + "total": 49.67657689785264 }, "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": 24.03232930250617, "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 0.0 }, - "total": 23.90379172833133 + "total": 24.036204186431387 }, "5": { "components": { "united_atom:Transvibrational": 0.0, "united_atom:Rovibrational": 0.010824819910336868, - "residue:FTmat-Transvibrational": 11.054797795596103, + "residue:FTmat-Transvibrational": 11.176470961462535, "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 31.909265242174982 }, - "total": 42.97488785768142 + "total": 43.09656102354785 }, "6": { "components": { "united_atom:Transvibrational": 0.0, "united_atom:Rovibrational": 0.00018982532508837537, - "residue:FTmat-Transvibrational": 19.723925127490933, + "residue:FTmat-Transvibrational": 19.83851614381679, "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 0.0 }, - "total": 19.72411495281602 + "total": 19.838705969141877 }, "7": { "components": { "united_atom:Transvibrational": 0.0, "united_atom:Rovibrational": 0.004033941970593011, - "residue:FTmat-Transvibrational": 18.906768821421363, + "residue:FTmat-Transvibrational": 19.06667852893644, "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 0.0 }, - "total": 18.910802763391956 + "total": 19.070712470907033 }, "8": { "components": { "united_atom:Transvibrational": 0.0, - "united_atom:Rovibrational": 0.020362757918507064, - "residue:FTmat-Transvibrational": 16.13204209116967, + "united_atom:Rovibrational": 0.020362757918507036, + "residue:FTmat-Transvibrational": 16.57161042803149, "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 31.909265242174982 }, - "total": 48.06167009126316 + "total": 48.50123842812498 }, "9": { "components": { "united_atom:Transvibrational": 0.0, - "united_atom:Rovibrational": 0.0002313974393463703, - "residue:FTmat-Transvibrational": 21.42548529236267, + "united_atom:Rovibrational": 0.00023139743934636996, + "residue:FTmat-Transvibrational": 21.777605911862775, "residue:FTmat-Rovibrational": 0.0, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 0.0 }, - "total": 21.425716689802016 + "total": 21.77783730930212 } } } diff --git a/tests/regression/baselines/benzaldehyde/rad.json b/tests/regression/baselines/benzaldehyde/rad.json index 8e7f85c5..c90914d9 100644 --- a/tests/regression/baselines/benzaldehyde/rad.json +++ b/tests/regression/baselines/benzaldehyde/rad.json @@ -2,15 +2,15 @@ "groups": { "0": { "components": { - "united_atom:Transvibrational": 24.92182210331405, - "united_atom:Rovibrational": 27.950376507672583, - "residue:FTmat-Transvibrational": 70.97090266225698, - "residue:FTmat-Rovibrational": 59.588669973122094, + "united_atom:Transvibrational": 24.921822103314035, + "united_atom:Rovibrational": 27.950376507672594, + "residue:FTmat-Transvibrational": 71.231562004914, + "residue:FTmat-Rovibrational": 60.43602521189648, "united_atom:Conformational": 7.522643899702263, "residue:Conformational": 0.0, "residue:Orientational": 25.502722133228936 }, - "total": 216.45713727929692 + "total": 217.56515186072832 } } } diff --git a/tests/regression/baselines/benzaldehyde/selection_subset.json b/tests/regression/baselines/benzaldehyde/selection_subset.json index f3647458..e3c767bb 100644 --- a/tests/regression/baselines/benzaldehyde/selection_subset.json +++ b/tests/regression/baselines/benzaldehyde/selection_subset.json @@ -3,14 +3,14 @@ "0": { "components": { "united_atom:Transvibrational": 0.06817494136874551, - "united_atom:Rovibrational": 49.686697381523516, - "residue:FTmat-Transvibrational": 85.94814793508021, - "residue:FTmat-Rovibrational": 61.7256510401677, + "united_atom:Rovibrational": 49.686697381523466, + "residue:FTmat-Transvibrational": 86.6413638447789, + "residue:FTmat-Rovibrational": 62.24303760058523, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 20.481571492615355 }, - "total": 217.91024279075552 + "total": 219.1208452608717 } } } diff --git a/tests/regression/baselines/benzene/combined_forcetorque_off.json b/tests/regression/baselines/benzene/combined_forcetorque_off.json index 00069722..ddfc45b8 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": 0.2005675966254925, - "united_atom:Rovibrational": 40.695812407899396, - "residue:Transvibrational": 60.612932277845054, - "residue:Rovibrational": 52.53948263906845, + "united_atom:Transvibrational": 0.20056759662549248, + "united_atom:Rovibrational": 40.69581240789943, + "residue:Transvibrational": 60.73823316940173, + "residue:Rovibrational": 54.35470538676784, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 0.0 }, - "total": 154.0487949214384 + "total": 155.9893185606945 } } } diff --git a/tests/regression/baselines/benzene/default.json b/tests/regression/baselines/benzene/default.json index e500bba9..19e98c33 100644 --- a/tests/regression/baselines/benzene/default.json +++ b/tests/regression/baselines/benzene/default.json @@ -2,15 +2,15 @@ "groups": { "0": { "components": { - "united_atom:Transvibrational": 9.070682016770117, - "united_atom:Rovibrational": 27.5343801262502, - "residue:FTmat-Transvibrational": 72.694076398699, - "residue:FTmat-Rovibrational": 59.84501427492273, + "united_atom:Transvibrational": 9.070682016770112, + "united_atom:Rovibrational": 27.534380126250213, + "residue:FTmat-Transvibrational": 73.34909170672572, + "residue:FTmat-Rovibrational": 61.127301914885564, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 41.58427729275938 }, - "total": 210.72843010940142 + "total": 212.66573305739098 } } } diff --git a/tests/regression/baselines/benzene/frame_window.json b/tests/regression/baselines/benzene/frame_window.json index c9b3c6c8..698a7e92 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": 13.027950562276953, - "united_atom:Rovibrational": 34.984920567484934, - "residue:FTmat-Transvibrational": 75.50603474425517, - "residue:FTmat-Rovibrational": 54.88466842760242, + "united_atom:Transvibrational": 13.02795056227694, + "united_atom:Rovibrational": 34.98492056748487, + "residue:FTmat-Transvibrational": 76.31666900908246, + "residue:FTmat-Rovibrational": 55.741216775589876, "united_atom:Conformational": 0.0, "residue:Conformational": 0.0, "residue:Orientational": 0.0 }, - "total": 178.40357430161947 + "total": 180.07075691443413 } } } diff --git a/tests/regression/baselines/benzene/grouping_each.json b/tests/regression/baselines/benzene/grouping_each.json index bb58de19..50d772d2 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, - 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"total": 150.9789861100737 + "total": 164.07268174402878 } } } diff --git a/tests/regression/baselines/octonol/combined_forcetorque_off.json b/tests/regression/baselines/octonol/combined_forcetorque_off.json index 40e39c56..136f507d 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": 0.2801426785866466, - "united_atom:Rovibrational": 19.154228264604278, - "residue:Transvibrational": 73.10868503314677, - "residue:Rovibrational": 61.50929695375963, + "united_atom:Transvibrational": 0.2801426785866467, + "united_atom:Rovibrational": 19.154228264604267, + "residue:Transvibrational": 72.99206520550513, + "residue:Rovibrational": 63.35835952854332, "united_atom:Conformational": 16.83949354267619, "residue:Conformational": 0.0, "residue:Orientational": 25.79114991860739 }, - "total": 196.68299639138093 + "total": 198.4154391385229 } } } diff --git a/tests/regression/baselines/octonol/default.json b/tests/regression/baselines/octonol/default.json index 8ac4ed4b..39651d41 100644 --- a/tests/regression/baselines/octonol/default.json +++ b/tests/regression/baselines/octonol/default.json @@ -2,15 +2,15 @@ "groups": { "0": { "components": { - 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"united_atom:Transvibrational": 37.773345787136435, - "united_atom:Rovibrational": 84.26087853087444, - "residue:FTmat-Transvibrational": 66.1742370152873, - "residue:FTmat-Rovibrational": 57.07006496269577, + "united_atom:Transvibrational": 37.773345787136414, + "united_atom:Rovibrational": 84.26087853087442, + "residue:FTmat-Transvibrational": 66.27397939927971, + "residue:FTmat-Rovibrational": 58.77768843093995, "united_atom:Conformational": 34.22940197506605, "residue:Conformational": 0.0, "residue:Orientational": 28.084239413273323 }, - "total": 307.59216768433333 + "total": 309.3995335365699 } } } diff --git a/tests/regression/baselines/octonol/selection_subset.json b/tests/regression/baselines/octonol/selection_subset.json index d6ffcecc..3ea7ff18 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": 0.2801426785866466, - "united_atom:Rovibrational": 19.154228264604278, - "residue:FTmat-Transvibrational": 82.11968297566696, - "residue:FTmat-Rovibrational": 57.710124884782225, + "united_atom:Transvibrational": 0.2801426785866467, + "united_atom:Rovibrational": 19.154228264604267, + "residue:FTmat-Transvibrational": 81.9451817383594, + "residue:FTmat-Rovibrational": 59.553917441172246, "united_atom:Conformational": 16.83949354267619, "residue:Conformational": 0.0, "residue:Orientational": 25.79114991860739 }, - "total": 201.89482226492368 + "total": 203.56411358400612 } } } diff --git a/tests/unit/CodeEntropy/levels/nodes/test_covariance_node.py b/tests/unit/CodeEntropy/levels/nodes/test_covariance_node.py index 38bd6ddd..ff02facd 100644 --- a/tests/unit/CodeEntropy/levels/nodes/test_covariance_node.py +++ b/tests/unit/CodeEntropy/levels/nodes/test_covariance_node.py @@ -573,7 +573,6 @@ def test_get_residue_axes_customised_uses_cached_topology_when_available(): relative_res_i=0, axes_manager=axes_manager, axes_topology=axes_topology, - box=None, customised_axes=True, ) @@ -601,7 +600,6 @@ def test_get_residue_axes_customised_delegates_to_axes_manager(): relative_res_i=0, axes_manager=axes_manager, axes_topology=None, - box=None, customised_axes=True, ) == expected @@ -636,7 +634,6 @@ def test_get_residue_axes_molecule_uses_make_whole_and_molecule_axes(): relative_res_i=0, axes_manager=axes_manager, axes_topology=None, - box=None, customised_axes=False, ) diff --git a/tests/unit/CodeEntropy/levels/test_axes.py b/tests/unit/CodeEntropy/levels/test_axes.py index ba1d6c81..a58b1d49 100644 --- a/tests/unit/CodeEntropy/levels/test_axes.py +++ b/tests/unit/CodeEntropy/levels/test_axes.py @@ -103,12 +103,8 @@ 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_principal_axes_from_tensor", - lambda moi: (np.eye(3), np.array([3.0, 2.0, 1.0])), + ax, "get_molecule_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) @@ -142,9 +138,7 @@ 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_molecule_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) @@ -299,28 +293,6 @@ def test_get_principal_axes_from_tensor_returns_axes_and_moments(): assert vals.shape == (3,) -def test_get_UA_masses_sums_bonded_hydrogens(): - ax = AxesCalculator() - - heavy = _FakeAtom(index=0, mass=12.0, position=[0, 0, 0]) - h1 = _FakeAtom(index=1, mass=1.0, position=[1, 0, 0]) - h2 = _FakeAtom(index=2, mass=1.0, position=[0, 1, 0]) - - bonded_atoms = _FakeAtomGroup( - [h1, h2], select_map={"mass 1 to 1.1": _FakeAtomGroup([h1, h2])} - ) - - mol = _FakeAtomGroup( - [heavy, h1, h2], - select_map={ - "bonded index 0": bonded_atoms, - }, - ) - - masses = ax.get_UA_masses(mol) - assert masses == [14.0] - - def test_get_molecule_axes_sorts_eigenvalues_desc_by_abs(monkeypatch): ax = AxesCalculator() mol = MagicMock() @@ -638,12 +610,10 @@ 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_principal_axes_from_tensor", - lambda moi: (np.eye(3), np.array([3.0, 2.0, 1.0])), + "get_molecule_axes", + lambda molecule: (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) @@ -678,14 +648,14 @@ def _select_atoms(q): 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]]), + "get_molecule_axes", + lambda molecule: (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])) @@ -818,7 +788,6 @@ def _select_atoms(q): "get_bonded_axes", lambda system, atom, dimensions: (np.eye(3), np.array([1.0, 1.0, 1.0])), ) - monkeypatch.setattr(ax, "get_UA_masses", lambda _ag: [12.0, 12.0]) trans_axes, rot_axes, center, moi = ax.get_UA_axes( data_container, index=0, res_position=None @@ -937,19 +906,15 @@ 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_principal_axes_from_tensor", get_principal) + monkeypatch.setattr(ax, "get_molecule_axes", get_principal) - box = np.array([20.0, 30.0, 40.0]) trans_axes, rot_axes, center, moi = ax.get_residue_axes_from_topology( u=universe, mol=mol, residue_atoms=residue_atoms, topology=topology, - box=box, ) np.testing.assert_allclose(trans_axes, np.eye(3) * 2.0) @@ -957,17 +922,6 @@ 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() @@ -998,7 +952,6 @@ def test_get_residue_axes_from_topology_neighbor_bonds_uses_molecule_axes( mol=mol, residue_atoms=residue_atoms, topology=topology, - box=None, ) make_whole.assert_called_once_with(mol.atoms) @@ -1027,12 +980,10 @@ def test_get_UA_axes_from_topology_multiple_heavy_uses_cached_indices_and_box( residue_ua_masses=(13.0, 14.0), ) - 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]))) + get_principal = MagicMock(return_value=(np.eye(3) * 2.0)) get_bonded = MagicMock(return_value=(np.eye(3) * 4.0, np.array([1.0, 1.0, 1.0]))) - monkeypatch.setattr(ax, "get_moment_of_inertia_tensor", get_tensor) - monkeypatch.setattr(ax, "get_principal_axes_from_tensor", get_principal) + monkeypatch.setattr(ax, "get_principal_axes_from_group", get_principal) monkeypatch.setattr(ax, "get_bonded_axes_from_topology", get_bonded) box = np.array([20.0, 30.0, 40.0]) @@ -1048,19 +999,7 @@ def test_get_UA_axes_from_topology_multiple_heavy_uses_cached_indices_and_box( np.testing.assert_allclose(center, heavy_atom.position) np.testing.assert_allclose(moi, np.array([1.0, 1.0, 1.0])) - get_tensor.assert_called_once() - 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() - np.testing.assert_allclose(get_principal.call_args.args[0], np.eye(3)) get_bonded.assert_called_once_with( u=universe, heavy_atom=heavy_atom, @@ -2238,3 +2177,44 @@ def test_get_non_terminal_axes_3points(monkeypatch): assert np.allclose(centre, [1, 0, 0]) assert np.allclose(axes, 3 * np.eye(3)) + + +def test_get_residue_axes_all_atom_MOI(monkeypatch): + ax = AxesCalculator() + u = MagicMock() + u.dimensions = np.array([10.0, 10.0, 10.0, 90, 90, 90]) + residue = u.select_atoms("resindex 1") + residue.__len__.return_value = 5 + monkeypatch.setattr("CodeEntropy.levels.axes.make_whole", lambda _ag: None) + atoms = _FakeAtomGroup( + [ + _atom(index=0, mass=12.0, pos=(1, 0, 0)), + _atom(index=1, mass=12.0, pos=(0, 1, 0)), + _atom(index=2, mass=12.0, pos=(0, 0, 1)), + _atom(index=3, mass=1.0, pos=(0, 0, 0)), + _atom(index=4, mass=1.0, pos=(1, 1, 1)), + ], + positions=np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1], [0, 0, 0], [1, 1, 1]]), + ) + residue.atoms.positions = atoms.positions + residue.atoms.masses = atoms.masses + + def _select_atoms(q): + if q.startswith("resindex"): + return atoms[0:2] + + u.atoms.select_atoms.side_effect = _select_atoms + monkeypatch.setattr(ax, "get_principal_axes_from_group", lambda _ag: 2 * np.eye(3)) + monkeypatch.setattr( + ax, + "get_non_terminal_axes", + lambda residue, edges, dimensions: ([1, 0, 0], np.eye(3)), + ) + trans_axes, rot_axes, rot_center, moi = ax.get_residue_axes( + data_container=u, index=1, relative_index=0, residue=None + ) + + assert np.allclose(trans_axes, 2 * np.eye(3)) + assert np.allclose(rot_axes, np.eye(3)) + assert np.allclose(rot_center, [1, 0, 0]) + assert np.allclose(moi, [26, 38, 38])