CodeEntropy 2.6.0__py3-none-any.whl → 2.7.0__py3-none-any.whl

CodeEntropy/__init__.py

@@ -8,4 +8,4 @@ entropy estimates, supporting a wide range of applications in molecular simulati
 and statistical mechanics.
 """
 
-__version__ = "2.6.0"
+__version__ = "2.7.0"

CodeEntropy/levels/axes.py

@@ -82,15 +82,14 @@ class AxesCalculator:
             * 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 @@ class AxesCalculator:
             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 @@ class AxesCalculator:
                 )
             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 @@ class AxesCalculator:
         mol,
         residue_atoms,
         topology,
-        box: np.ndarray | None,
     ):
         """Compute residue axes using cached static topology.
 
@@ -195,7 +182,6 @@ class AxesCalculator:
             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 @@ class AxesCalculator:
                 - 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 @@ class AxesCalculator:
 
         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 @@ class AxesCalculator:
         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 @@ class AxesCalculator:
 
         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 @@ class AxesCalculator:
         )
         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

CodeEntropy/levels/nodes/covariance.py

@@ -578,7 +578,6 @@ class FrameCovarianceNode:
                 relative_res_i=relative_res_i,
                 axes_manager=axes_manager,
                 axes_topology=axes_topology,
-                box=box,
                 customised_axes=customised_axes,
             )
 
@@ -615,7 +614,6 @@ class FrameCovarianceNode:
         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 @@ class FrameCovarianceNode:
             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 @@ class FrameCovarianceNode:
 
             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(

{codeentropy-2.6.0.dist-info → codeentropy-2.7.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: CodeEntropy
-Version: 2.6.0
+Version: 2.7.0
 Summary: CodeEntropy is a Python package for computing the configurational entropy of macromolecular systems using forces sampled from molecular dynamics (MD) simulations. It implements the multiscale cell correlation method to provide accurate and efficient entropy estimates, supporting a wide range of applications in molecular simulation and statistical mechanics.
 Keywords: entropy,macromolecular systems,MD simulation
 Author-email: Arghya 'Argo' Chakravorty <arghyac@umich.edu>, Donald Chung-HK <donald.chung@stfc.ac.uk>, Sarah Fegan <sarah.fegan@stfc.ac.uk>, James Gebbie-Rayet <james.gebbie@stfc.ac.uk>, Sarah Harris <sarah.harris@sheffield.ac.uk>, Richard Henchman <rhen7213@uni.sydney.edu.au>, Jonathan Higham <j.higham4@lancaster.ac.uk>, Jas Kalayan <jas.kalayan@stfc.ac.uk>, Ioana Papa <iapapa1@sheffield.ac.uk>

{codeentropy-2.6.0.dist-info → codeentropy-2.7.0.dist-info}/RECORD

@@ -1,4 +1,4 @@
-CodeEntropy/__init__.py,sha256=hAmtMNRexWP67gOAWLWAag9bka7HMDFyE3BMl7IRJHw,404
+CodeEntropy/__init__.py,sha256=6RAN3bQeIAMTRqrJvnQxdaIyZdou_JcpKJo8Ve8-NTM,404
 CodeEntropy/__main__.py,sha256=5i_ZrxQaq0q2aPllbB4SZ6BApV6oUFCgx0cGyjfMPrU,108
 CodeEntropy/cli.py,sha256=nSshc8P7F7n3jAW36vzwXsFdffLfFdCpkfLvA-tJb3c,1318
 CodeEntropy/config/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -20,7 +20,7 @@ CodeEntropy/entropy/nodes/configurational.py,sha256=-3j2ji_p-twPjZyjQ1T3tgN0pYLS
 CodeEntropy/entropy/nodes/orientational.py,sha256=yPN_XRJ1LOxJ7hOE2cnsjIbgQlI2avM1g3mFbGhW6fM,2481
 CodeEntropy/entropy/nodes/vibrational.py,sha256=3uhRqaMpK8u7QK2SDQ6RLRcr2rS3sPh6-GlTaNdTFWw,16978
 CodeEntropy/levels/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-CodeEntropy/levels/axes.py,sha256=wmotkCwWcc7RzicWJQzXVwYFqkyw9WqWpyeRF1NB3zU,50338
+CodeEntropy/levels/axes.py,sha256=2ws9a_n45ZHH4ya4DCttqEosHSqN_TrJO6dPHSbEeKE,47839
 CodeEntropy/levels/forces.py,sha256=c7XnNIBTFCHHXllr1WxTIrxEV_CkUB2b1vdFO8hUofY,11595
 CodeEntropy/levels/hierarchy.py,sha256=3cd4t6Tywg7VMgw4TboFF5VAHdhG4FaGBXsMptchisY,5158
 CodeEntropy/levels/linalg.py,sha256=PJlrKtIOYcYDycW3Tbetm6k94FKFZTq-hm28qiu_tS0,3565
@@ -47,7 +47,7 @@ CodeEntropy/levels/nodes/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZ
 CodeEntropy/levels/nodes/accumulators.py,sha256=XM7phCAIo0RK9YAtx2wrdo2oinmpwXYrH9mp1_LQD7U,6259
 CodeEntropy/levels/nodes/axes_topology.py,sha256=QzrWbCL9YA8fzF4_WWpQGaIAAsOnjY6cVH7INDE40dk,11285
 CodeEntropy/levels/nodes/beads.py,sha256=9Ow065FY4jrIqPKCZJCvDNfIekJ17OBSX-bmEFsxtbc,8010
-CodeEntropy/levels/nodes/covariance.py,sha256=EY_-Ps-e4qtI9RIhV47j7cuvP3znJovGt6kK6yC77sU,30294
+CodeEntropy/levels/nodes/covariance.py,sha256=T42iaL3AEswDp6qvI5uuTTKzksnjaJdEuQvNqsQjT_M,30100
 CodeEntropy/levels/nodes/detect_levels.py,sha256=YrM5SSceLiMqbOhr8Fy6SV-E_zkKRpvgHfDT8Grbin8,1864
 CodeEntropy/levels/nodes/detect_molecules.py,sha256=jILCddEicVngA7FjvQzafbG8HslaRICpT6hj2Uyi6YY,3059
 CodeEntropy/molecules/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -58,8 +58,8 @@ CodeEntropy/trajectory/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3
 CodeEntropy/trajectory/frames.py,sha256=MSx_swzFjo4TgkZTR1y6W-1zuKNPg_C36I_uFqvOKpk,4354
 CodeEntropy/trajectory/mda.py,sha256=epKpAzxkNQi3rE7HJc_tsK_ZY4c575LdXmWewJoP1qE,16954
 CodeEntropy/trajectory/source.py,sha256=NfYsdm1amr29h2tmJP-RKyCp3phb1SOAtAELJmGm740,1475
-codeentropy-2.6.0.dist-info/entry_points.txt,sha256=8Oa3H9ErsrGtx5Hc6hIHOw73wK3Ylkvfgtl_4cBb_GU,52
-codeentropy-2.6.0.dist-info/licenses/LICENSE,sha256=hgMaAAVW1Q6dL586OHoz8vFO-6BYn-d2aAFBpVQylFc,1072
-codeentropy-2.6.0.dist-info/WHEEL,sha256=lqN8jXt_QloFOGcx9kStvWbryhfEXoI2F2z-YURm350,81
-codeentropy-2.6.0.dist-info/METADATA,sha256=dDomybrlzZoHk5m116Ap4v8TI9QtKclsW6XIJhSkQ5E,6547
-codeentropy-2.6.0.dist-info/RECORD,,
+codeentropy-2.7.0.dist-info/entry_points.txt,sha256=8Oa3H9ErsrGtx5Hc6hIHOw73wK3Ylkvfgtl_4cBb_GU,52
+codeentropy-2.7.0.dist-info/licenses/LICENSE,sha256=hgMaAAVW1Q6dL586OHoz8vFO-6BYn-d2aAFBpVQylFc,1072
+codeentropy-2.7.0.dist-info/WHEEL,sha256=lqN8jXt_QloFOGcx9kStvWbryhfEXoI2F2z-YURm350,81
+codeentropy-2.7.0.dist-info/METADATA,sha256=emvj_HvZSa0vFbaVwumBcY5NoK2Bb_VFW8Ees52sp00,6547
+codeentropy-2.7.0.dist-info/RECORD,,