solvation-analysis 0.3.2__py3-none-any.whl → 0.3.3a0__py3-none-any.whl

solvation_analysis/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2023-04-06T09:11:57-0700",
+ "date": "2023-04-09T10:45:35-0700",
  "dirty": false,
  "error": null,
- "full-revisionid": "b721d96f7a5494ce90657facec62d22bebb0229d",
- "version": "v0.3.2"
+ "full-revisionid": "7133ecc6ffd3dfca4e85abd2eeb6ec850fabb41d",
+ "version": "v0.3.3-alpha"
 }
 '''  # END VERSION_JSON
 

solvation_analysis/coordination.py

@@ -123,11 +123,12 @@ class Coordination:
         type_fractions = type_counts[SOLVENT_ATOM_IX] / solvent_counts_list
         type_fractions.name = FRACTION
         # change index type
-        type_fractions = (type_fractions
-                         .reset_index(ATOM_TYPE)
-                         .astype({ATOM_TYPE: str})
-                         .set_index(ATOM_TYPE, append=True)
-                         )
+        type_fractions = (
+            type_fractions
+            .reset_index(ATOM_TYPE)
+            .astype({ATOM_TYPE: str})
+            .set_index(ATOM_TYPE, append=True)
+        )
         return type_fractions[type_fractions[FRACTION] > tol]
 
     def _calculate_coordination_vs_random(self):
@@ -141,9 +142,10 @@ class Coordination:
         average_shell_size = sum(self.coordination_numbers.values())
         total_solvents = sum(self.solvent_counts.values())
         coordination_vs_random = {}
-        for solvent, count in self.solvent_counts.items():
+        for solvent, cn in self.coordination_numbers.items():
+            count = self.solvent_counts[solvent]
             random = count * average_shell_size / total_solvents
-            vs_random = self.coordination_numbers[solvent] / random
+            vs_random = cn / random
             coordination_vs_random[solvent] = vs_random
         return coordination_vs_random
 

solvation_analysis/tests/test_coordination.py

@@ -18,8 +18,7 @@ def test_coordination_from_solute(run_solute):
     ],
 )
 def test_coordination(name, cn, solvation_data, run_solute):
-    atoms = run_solute.u.atoms
-    coordination = Coordination(solvation_data, 10, 49, atoms)
+    coordination = Coordination.from_solute(run_solute)
     np.testing.assert_allclose(cn, coordination.coordination_numbers[name], atol=0.05)
     assert len(coordination.coordination_numbers_by_frame) == 3
 
@@ -33,8 +32,7 @@ def test_coordination(name, cn, solvation_data, run_solute):
     ],
 )
 def test_coordinating_atoms(name, atom_type, fraction, solvation_data, run_solute):
-    atoms = run_solute.u.atoms
-    coordination = Coordination(solvation_data, 10, 49, atoms)
+    coordination = Coordination.from_solute(run_solute)
     calculated_fraction = coordination._coordinating_atoms.loc[(name, atom_type)]
     np.testing.assert_allclose(fraction, calculated_fraction, atol=0.05)
 

{solvation_analysis-0.3.2.dist-info → solvation_analysis-0.3.3a0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: solvation-analysis
-Version: 0.3.2
+Version: 0.3.3a0
 Summary: A toolkit to analyze solvation structure in molecular dynamics trajectories.
 Author: Orion Cohen
 Author-email: Orion Cohen <orioncohen@berkeley.edu>
@@ -606,7 +606,6 @@ Requires-Dist: numpy (>=1.20.0)
 Requires-Dist: pandas
 Requires-Dist: mdanalysis (>=2.0.0)
 Requires-Dist: pytest
-Requires-Dist: pathlib
 Requires-Dist: matplotlib
 Requires-Dist: scipy
 Requires-Dist: statsmodels

{solvation_analysis-0.3.2.dist-info → solvation_analysis-0.3.3a0.dist-info}/RECORD

@@ -1,8 +1,8 @@
 solvation_analysis/__init__.py,sha256=nilCtSfGTLm40kUA9syYdl9pGF4XWpNJ2lV3rFyZI2w,335
 solvation_analysis/_column_names.py,sha256=wK9GN1_Pzve4cI3o86R7NQGdSLfhENXct0J036nS2c8,728
 solvation_analysis/_utils.py,sha256=XkdmglL0JjXsyAS-owZU_Vo1rCSdRD0Hz3P8rfWQ3po,8016
-solvation_analysis/_version.py,sha256=kmFSUv-a8NhnCUJxR1Oin3MUUIDxyHS4MoFncOUpdaE,498
-solvation_analysis/coordination.py,sha256=WsoCl65Y98jINEW2Wx92qsUW4epP6DaiF0J7gBs9QLs,6593
+solvation_analysis/_version.py,sha256=CeTQhwfxdqvxY5Pzehas2dwwJRCXrUik12wq6ckZpSA,504
+solvation_analysis/coordination.py,sha256=AE628q-dsHTzVXnsip953CHf-clqJnHPYQurPhyck3w,6570
 solvation_analysis/networking.py,sha256=PjN_bUGenxYs2dAcjGvnQb4C6dCU2rz4C2AyjhCTtuk,10777
 solvation_analysis/pairing.py,sha256=vAvhj4aPAnDACwEUOi-PS8TC-EiVzeSceOyycpDa7qQ,5709
 solvation_analysis/plotting.py,sha256=YtzU3TlQcsOlB0qASUAxviZ4s2g9ZPcP5xml7C9NRiY,13759
@@ -13,7 +13,7 @@ solvation_analysis/speciation.py,sha256=rLZCSXGbZ6-P80N-MopLN79_eGnl1feJDFrlv7Mx
 solvation_analysis/tests/__init__.py,sha256=tlIleLX_7zJFwQuwnqP9fJ0nQXdD1uA-l8uX8w4KUKM,112
 solvation_analysis/tests/conftest.py,sha256=2cMepIZ0rLza_wnaXpu-mH_Ld2fqxq7tKoQXdm-Cj1Y,9536
 solvation_analysis/tests/datafiles.py,sha256=4vOiZsRWtIpWhq8aEyfMpR8JQWPwkppqNwbTjx2sCVc,2601
-solvation_analysis/tests/test_coordination.py,sha256=LaQ6t3pqqPFp989k6JiDSQU_x3eh3NqHF5dxW96zQbU,1672
+solvation_analysis/tests/test_coordination.py,sha256=hrqV5y7yLDi3ysEbL7oNGCDbdVJ26brzDhGAuNAAwO8,1596
 solvation_analysis/tests/test_networking.py,sha256=AcHm1A_ZeIsBSqnl1KV9IzJc3EwkP4pfFRdNyBQnM0k,867
 solvation_analysis/tests/test_pairing.py,sha256=D9haGZGkswmrevOa_GPGXd0KqmusAGjzUcJCYdeKTPY,1516
 solvation_analysis/tests/test_plotting.py,sha256=AshDnsmn3W1Y_AkEnQVGTrNu9oWfWic2k3QxbB4fLqk,10037
@@ -109,8 +109,8 @@ solvation_analysis/tests/data/rdf_vs_li_hard/rdf_pf6_all_bins.npz,sha256=Z1knlSh
 solvation_analysis/tests/data/rdf_vs_li_hard/rdf_pf6_all_data.npz,sha256=yKRJ2BGnvWAfRnP9HLdK1USv1RPcwTW54Vk_Z8EqomA,864
 solvation_analysis/tests/data/rdf_vs_li_hard/rdf_universe_all_bins.npz,sha256=Z1knlShdL77EiFMvmh4FXzlkTCM2ziZKUuqYgtg_tZw,864
 solvation_analysis/tests/data/rdf_vs_li_hard/rdf_universe_all_data.npz,sha256=di1BmbLd0oca23XY5sW_M60Xi3Q8leIhHtJ61wDTTGs,864
-solvation_analysis-0.3.2.dist-info/LICENSE,sha256=-mQWu786dxXc5-JBLEYYgWZ2BTFaAueDVwUpzSRfbxI,34684
-solvation_analysis-0.3.2.dist-info/METADATA,sha256=c3NHIDUqqu3_FwOOiad8PwidPGiNDZ9s4axQMpWE3T8,45010
-solvation_analysis-0.3.2.dist-info/WHEEL,sha256=pkctZYzUS4AYVn6dJ-7367OJZivF2e8RA9b_ZBjif18,92
-solvation_analysis-0.3.2.dist-info/top_level.txt,sha256=M6YFLMMaJsIEeRqw1v_9jvSq7oXa8GWU5x6nNNc6zbU,19
-solvation_analysis-0.3.2.dist-info/RECORD,,
+solvation_analysis-0.3.3a0.dist-info/LICENSE,sha256=-mQWu786dxXc5-JBLEYYgWZ2BTFaAueDVwUpzSRfbxI,34684
+solvation_analysis-0.3.3a0.dist-info/METADATA,sha256=i5xRZTAAJuAlGJM8o7eFMyqUHwQfUprCYJKN2EoPsok,44989
+solvation_analysis-0.3.3a0.dist-info/WHEEL,sha256=pkctZYzUS4AYVn6dJ-7367OJZivF2e8RA9b_ZBjif18,92
+solvation_analysis-0.3.3a0.dist-info/top_level.txt,sha256=M6YFLMMaJsIEeRqw1v_9jvSq7oXa8GWU5x6nNNc6zbU,19
+solvation_analysis-0.3.3a0.dist-info/RECORD,,