CodeEntropy 2.2.1__py3-none-any.whl → 2.2.3__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__ = "2.2.1"
+__version__ = "2.2.3"

CodeEntropy/entropy/nodes/vibrational.py

@@ -323,7 +323,7 @@ class VibrationalEntropyNode:
             EntropyPair containing translational entropy (from force covariance) and
             rotational entropy (from torque covariance).
         """
-        if fmat is None or tmat is None:
+        if fmat is None and tmat is None:
             return EntropyPair(trans=0.0, rot=0.0)
 
         f = self._mat_ops.filter_zero_rows_columns(
@@ -333,7 +333,7 @@ class VibrationalEntropyNode:
             np.asarray(tmat), atol=self._zero_atol
         )
 
-        if f.size == 0 or t.size == 0:
+        if f.size == 0 and t.size == 0:
             return EntropyPair(trans=0.0, rot=0.0)
 
         s_trans = ve.vibrational_entropy_calculation(

CodeEntropy/levels/dihedrals.py

@@ -219,7 +219,9 @@ class ConformationStateBuilder:
         Returns:
             List of peaks per dihedral (peak_values[dihedral_index] -> list of peaks).
         """
-        rep_mol = self._universe_operations.extract_fragment(data_container, 0)
+        rep_mol = self._universe_operations.extract_fragment(
+            data_container, molecules[0]
+        )
         number_frames = len(rep_mol.trajectory)
         num_residues = len(rep_mol.residues)
 
@@ -421,7 +423,9 @@ class ConformationStateBuilder:
         Returns:
             List of state labels (strings).
         """
-        rep_mol = self._universe_operations.extract_fragment(data_container, 0)
+        rep_mol = self._universe_operations.extract_fragment(
+            data_container, molecules[0]
+        )
         number_frames = len(rep_mol.trajectory)
         num_residues = len(rep_mol.residues)
 

{codeentropy-2.2.1.dist-info → codeentropy-2.2.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: CodeEntropy
-Version: 2.2.1
+Version: 2.2.3
 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-2.2.1.dist-info → codeentropy-2.2.3.dist-info}/RECORD

@@ -1,4 +1,4 @@
-CodeEntropy/__init__.py,sha256=mszxPVgJwIy0vuxnybAASyk_oZBgH4lI7HaOEiP8zdc,404
+CodeEntropy/__init__.py,sha256=bIbDv3369PKnJutP6FoFTDwcsNE9SYVGEBP1lDeLJzg,404
 CodeEntropy/__main__.py,sha256=5i_ZrxQaq0q2aPllbB4SZ6BApV6oUFCgx0cGyjfMPrU,108
 CodeEntropy/cli.py,sha256=xgSgagCV6HQ3CoXUpG7p7Ef5hCExgxp7orz6dZZWA6c,960
 CodeEntropy/config/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -17,10 +17,10 @@ CodeEntropy/entropy/nodes/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJW
 CodeEntropy/entropy/nodes/aggregate.py,sha256=4SyXP1_bM0IesOuqflRLvPgEfFu0PmKiEm4EFgnNxwg,3062
 CodeEntropy/entropy/nodes/configurational.py,sha256=-3j2ji_p-twPjZyjQ1T3tgN0pYLSIof9any1w5NI2as,7135
 CodeEntropy/entropy/nodes/orientational.py,sha256=yPN_XRJ1LOxJ7hOE2cnsjIbgQlI2avM1g3mFbGhW6fM,2481
-CodeEntropy/entropy/nodes/vibrational.py,sha256=6ILiFV7MMn5sY4JWqXQbu4AF6imZdxJ10mQKvQu1A8E,16976
+CodeEntropy/entropy/nodes/vibrational.py,sha256=3uhRqaMpK8u7QK2SDQ6RLRcr2rS3sPh6-GlTaNdTFWw,16978
 CodeEntropy/levels/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 CodeEntropy/levels/axes.py,sha256=776jtKiv9n3crGHnqSUA15X_5HYRQWDODFL-Hyp890w,25335
-CodeEntropy/levels/dihedrals.py,sha256=AkIoXYVj4Wo6xC5Mby5uL3LV4BgLdfDXVnyJO7hUJFM,19811
+CodeEntropy/levels/dihedrals.py,sha256=lAd0HnI-P_cJ7XX7nqhJkF8hM6PVkSICThuMW8onGDk,19877
 CodeEntropy/levels/forces.py,sha256=c7XnNIBTFCHHXllr1WxTIrxEV_CkUB2b1vdFO8hUofY,11595
 CodeEntropy/levels/frame_dag.py,sha256=695ETWeFASLwlKaN3iZuHfKBYWLvJfjZ6BuIJ8uKoRg,3767
 CodeEntropy/levels/hierarchy.py,sha256=3cd4t6Tywg7VMgw4TboFF5VAHdhG4FaGBXsMptchisY,5158
@@ -41,8 +41,8 @@ CodeEntropy/molecules/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3h
 CodeEntropy/molecules/grouping.py,sha256=rlRVbRcxS_bPCZV8yoOCZKSpLS1F5AdpdIhaK2nWf1U,6426
 CodeEntropy/results/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 CodeEntropy/results/reporter.py,sha256=ZmCEKhh_h7-0JGumlyrpH0Y-FaG8aGv-KkzdRAamEAQ,18368
-codeentropy-2.2.1.dist-info/entry_points.txt,sha256=8Oa3H9ErsrGtx5Hc6hIHOw73wK3Ylkvfgtl_4cBb_GU,52
-codeentropy-2.2.1.dist-info/licenses/LICENSE,sha256=hgMaAAVW1Q6dL586OHoz8vFO-6BYn-d2aAFBpVQylFc,1072
-codeentropy-2.2.1.dist-info/WHEEL,sha256=G2gURzTEtmeR8nrdXUJfNiB3VYVxigPQ-bEQujpNiNs,82
-codeentropy-2.2.1.dist-info/METADATA,sha256=7VSdw314wdwy2NZeNC1_8nlQmTCkFO9573Kq3NmGWNk,6490
-codeentropy-2.2.1.dist-info/RECORD,,
+codeentropy-2.2.3.dist-info/entry_points.txt,sha256=8Oa3H9ErsrGtx5Hc6hIHOw73wK3Ylkvfgtl_4cBb_GU,52
+codeentropy-2.2.3.dist-info/licenses/LICENSE,sha256=hgMaAAVW1Q6dL586OHoz8vFO-6BYn-d2aAFBpVQylFc,1072
+codeentropy-2.2.3.dist-info/WHEEL,sha256=G2gURzTEtmeR8nrdXUJfNiB3VYVxigPQ-bEQujpNiNs,82
+codeentropy-2.2.3.dist-info/METADATA,sha256=uRD4hVFTXQQ9x8zs8xWhYig6HVUnFtJ5aaOmF8yI1rE,6490
+codeentropy-2.2.3.dist-info/RECORD,,