solvation-analysis 0.3.2__tar.gz → 0.3.3a0__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Potentially problematic release.

This version of solvation-analysis might be problematic. Click here for more details.

Files changed (126) hide show
  1. {solvation-analysis-0.3.2/solvation_analysis.egg-info → solvation-analysis-0.3.3a0}/PKG-INFO +1 -1
  2. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/pyproject.toml +0 -1
  3. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/_version.py +3 -3
  4. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/coordination.py +9 -7
  5. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/test_coordination.py +2 -4
  6. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0/solvation_analysis.egg-info}/PKG-INFO +1 -1
  7. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis.egg-info/requires.txt +0 -1
  8. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/CODE_OF_CONDUCT.md +0 -0
  9. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/LICENSE +0 -0
  10. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/MANIFEST.in +0 -0
  11. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/README.md +0 -0
  12. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/requirements.txt +0 -0
  13. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/setup.cfg +0 -0
  14. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/setup.py +0 -0
  15. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/__init__.py +0 -0
  16. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/_column_names.py +0 -0
  17. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/_utils.py +0 -0
  18. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/networking.py +0 -0
  19. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/pairing.py +0 -0
  20. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/plotting.py +0 -0
  21. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/rdf_parser.py +0 -0
  22. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/residence.py +0 -0
  23. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/solute.py +0 -0
  24. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/speciation.py +0 -0
  25. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/__init__.py +0 -0
  26. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/conftest.py +0 -0
  27. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/.DS_Store +0 -0
  28. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/README.md +0 -0
  29. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/bn_fec_data/bn_fec.data +0 -0
  30. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/bn_fec_data/bn_fec_elements.csv +0 -0
  31. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/bn_fec_data/bn_fec_short_unwrap.dcd +0 -0
  32. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/bn_fec_data/bn_fec_short_wrap.dcd +0 -0
  33. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/bn_fec_data/bn_solv_df_large.csv +0 -0
  34. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/ea_fec_data/ea_fec.dcd +0 -0
  35. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/ea_fec_data/ea_fec.pdb +0 -0
  36. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/eax_data/ea/topology.pdb +0 -0
  37. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/eax_data/ea/trajectory_equil.dcd +0 -0
  38. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/eax_data/eaf/topology.pdb +0 -0
  39. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/eax_data/eaf/trajectory_equil.dcd +0 -0
  40. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/eax_data/fea/topology.pdb +0 -0
  41. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/eax_data/fea/trajectory_equil.dcd +0 -0
  42. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/eax_data/feaf/topology.pdb +0 -0
  43. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/eax_data/feaf/trajectory_equil.dcd +0 -0
  44. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/iba_data/isobutyric_acid.dcd +0 -0
  45. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/iba_data/isobutyric_acid.pdb +0 -0
  46. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_non_solvated/rdf_bn_N_vs_fec_F_bins.npz +0 -0
  47. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_non_solvated/rdf_bn_N_vs_fec_F_data.npz +0 -0
  48. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_non_solvated/rdf_bn_N_vs_fec_O_bins.npz +0 -0
  49. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_non_solvated/rdf_bn_N_vs_fec_O_data.npz +0 -0
  50. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_non_solvated/rdf_bn_N_vs_fec_all_bins.npz +0 -0
  51. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_non_solvated/rdf_bn_N_vs_fec_all_data.npz +0 -0
  52. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_non_solvated/rdf_bn_N_vs_pf6_F_bins.npz +0 -0
  53. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_non_solvated/rdf_bn_N_vs_pf6_F_data.npz +0 -0
  54. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_non_solvated/rdf_bn_N_vs_pf6_all_bins.npz +0 -0
  55. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_non_solvated/rdf_bn_N_vs_pf6_all_data.npz +0 -0
  56. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_non_solvated/rdf_fec_F_vs_bn_N_bins.npz +0 -0
  57. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_non_solvated/rdf_fec_F_vs_bn_N_data.npz +0 -0
  58. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_non_solvated/rdf_fec_F_vs_bn_all_bins.npz +0 -0
  59. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_non_solvated/rdf_fec_F_vs_bn_all_data.npz +0 -0
  60. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_non_solvated/rdf_fec_F_vs_pf6_F_bins.npz +0 -0
  61. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_non_solvated/rdf_fec_F_vs_pf6_F_data.npz +0 -0
  62. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_non_solvated/rdf_fec_F_vs_pf6_all_bins.npz +0 -0
  63. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_non_solvated/rdf_fec_F_vs_pf6_all_data.npz +0 -0
  64. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_non_solvated/rdf_fec_O_vs_bn_N_bins.npz +0 -0
  65. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_non_solvated/rdf_fec_O_vs_bn_N_data.npz +0 -0
  66. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_non_solvated/rdf_fec_O_vs_bn_all_bins.npz +0 -0
  67. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_non_solvated/rdf_fec_O_vs_bn_all_data.npz +0 -0
  68. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_non_solvated/rdf_fec_O_vs_pf6_F_bins.npz +0 -0
  69. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_non_solvated/rdf_fec_O_vs_pf6_F_data.npz +0 -0
  70. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_non_solvated/rdf_fec_O_vs_pf6_all_bins.npz +0 -0
  71. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_non_solvated/rdf_fec_O_vs_pf6_all_data.npz +0 -0
  72. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_non_solvated/rdf_pf6_F_vs_bn_N_bins.npz +0 -0
  73. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_non_solvated/rdf_pf6_F_vs_bn_N_data.npz +0 -0
  74. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_non_solvated/rdf_pf6_F_vs_bn_all_bins.npz +0 -0
  75. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_non_solvated/rdf_pf6_F_vs_bn_all_data.npz +0 -0
  76. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_non_solvated/rdf_pf6_F_vs_fec_F_bins.npz +0 -0
  77. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_non_solvated/rdf_pf6_F_vs_fec_F_data.npz +0 -0
  78. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_non_solvated/rdf_pf6_F_vs_fec_O_bins.npz +0 -0
  79. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_non_solvated/rdf_pf6_F_vs_fec_O_data.npz +0 -0
  80. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_non_solvated/rdf_pf6_F_vs_fec_all_bins.npz +0 -0
  81. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_non_solvated/rdf_pf6_F_vs_fec_all_data.npz +0 -0
  82. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_vs_li_easy/rdf_bn_N_bins.npz +0 -0
  83. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_vs_li_easy/rdf_bn_N_data.npz +0 -0
  84. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_vs_li_easy/rdf_bn_all_bins.npz +0 -0
  85. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_vs_li_easy/rdf_bn_all_data.npz +0 -0
  86. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_vs_li_easy/rdf_fec_F_bins.npz +0 -0
  87. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_vs_li_easy/rdf_fec_F_data.npz +0 -0
  88. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_vs_li_easy/rdf_fec_O_bins.npz +0 -0
  89. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_vs_li_easy/rdf_fec_O_data.npz +0 -0
  90. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_vs_li_easy/rdf_fec_all_bins.npz +0 -0
  91. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_vs_li_easy/rdf_fec_all_data.npz +0 -0
  92. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_vs_li_easy/rdf_pf6_F_bins.npz +0 -0
  93. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_vs_li_easy/rdf_pf6_F_data.npz +0 -0
  94. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_vs_li_easy/rdf_pf6_all_bins.npz +0 -0
  95. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_vs_li_easy/rdf_pf6_all_data.npz +0 -0
  96. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_vs_li_easy/rdf_universe_all_bins.npz +0 -0
  97. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_vs_li_easy/rdf_universe_all_data.npz +0 -0
  98. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_vs_li_hard/rdf_bn_N_bins.npz +0 -0
  99. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_vs_li_hard/rdf_bn_N_data.npz +0 -0
  100. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_vs_li_hard/rdf_bn_all_bins.npz +0 -0
  101. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_vs_li_hard/rdf_bn_all_data.npz +0 -0
  102. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_vs_li_hard/rdf_fec_F_bins.npz +0 -0
  103. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_vs_li_hard/rdf_fec_F_data.npz +0 -0
  104. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_vs_li_hard/rdf_fec_O_bins.npz +0 -0
  105. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_vs_li_hard/rdf_fec_O_data.npz +0 -0
  106. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_vs_li_hard/rdf_fec_all_bins.npz +0 -0
  107. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_vs_li_hard/rdf_fec_all_data.npz +0 -0
  108. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_vs_li_hard/rdf_pf6_F_bins.npz +0 -0
  109. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_vs_li_hard/rdf_pf6_F_data.npz +0 -0
  110. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_vs_li_hard/rdf_pf6_all_bins.npz +0 -0
  111. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_vs_li_hard/rdf_pf6_all_data.npz +0 -0
  112. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_vs_li_hard/rdf_universe_all_bins.npz +0 -0
  113. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/data/rdf_vs_li_hard/rdf_universe_all_data.npz +0 -0
  114. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/datafiles.py +0 -0
  115. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/test_networking.py +0 -0
  116. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/test_pairing.py +0 -0
  117. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/test_plotting.py +0 -0
  118. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/test_rdf_parser.py +0 -0
  119. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/test_residence.py +0 -0
  120. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/test_selection.py +0 -0
  121. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/test_solute.py +0 -0
  122. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/test_speciation.py +0 -0
  123. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis.egg-info/SOURCES.txt +0 -0
  124. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis.egg-info/dependency_links.txt +0 -0
  125. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis.egg-info/top_level.txt +0 -0
  126. {solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/versioneer.py +0 -0
{solvation-analysis-0.3.2/solvation_analysis.egg-info → solvation-analysis-0.3.3a0}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: solvation-analysis
3
- Version: 0.3.2
3
+ Version: 0.3.3a0
4
4
  Summary: A toolkit to analyze solvation structure in molecular dynamics trajectories.
5
5
  Author: Orion Cohen
6
6
  Author-email: Orion Cohen <orioncohen@berkeley.edu>
{solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/pyproject.toml RENAMED
@@ -32,7 +32,6 @@ dependencies = [
32
32
  'pandas',
33
33
  'mdanalysis>=2.0.0',
34
34
  'pytest',
35
- 'pathlib',
36
35
  'matplotlib',
37
36
  'scipy',
38
37
  'statsmodels',
{solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/_version.py RENAMED
@@ -8,11 +8,11 @@ import json
8
8
 
9
9
  version_json = '''
10
10
  {
11
- "date": "2023-04-06T09:11:57-0700",
11
+ "date": "2023-04-09T10:45:35-0700",
12
12
  "dirty": false,
13
13
  "error": null,
14
- "full-revisionid": "b721d96f7a5494ce90657facec62d22bebb0229d",
15
- "version": "v0.3.2"
14
+ "full-revisionid": "7133ecc6ffd3dfca4e85abd2eeb6ec850fabb41d",
15
+ "version": "v0.3.3-alpha"
16
16
  }
17
17
  ''' # END VERSION_JSON
18
18
 
{solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/coordination.py RENAMED
@@ -123,11 +123,12 @@ class Coordination:
123
123
  type_fractions = type_counts[SOLVENT_ATOM_IX] / solvent_counts_list
124
124
  type_fractions.name = FRACTION
125
125
  # change index type
126
- type_fractions = (type_fractions
127
- .reset_index(ATOM_TYPE)
128
- .astype({ATOM_TYPE: str})
129
- .set_index(ATOM_TYPE, append=True)
130
- )
126
+ type_fractions = (
127
+ type_fractions
128
+ .reset_index(ATOM_TYPE)
129
+ .astype({ATOM_TYPE: str})
130
+ .set_index(ATOM_TYPE, append=True)
131
+ )
131
132
  return type_fractions[type_fractions[FRACTION] > tol]
132
133
 
133
134
  def _calculate_coordination_vs_random(self):
@@ -141,9 +142,10 @@ class Coordination:
141
142
  average_shell_size = sum(self.coordination_numbers.values())
142
143
  total_solvents = sum(self.solvent_counts.values())
143
144
  coordination_vs_random = {}
144
- for solvent, count in self.solvent_counts.items():
145
+ for solvent, cn in self.coordination_numbers.items():
146
+ count = self.solvent_counts[solvent]
145
147
  random = count * average_shell_size / total_solvents
146
- vs_random = self.coordination_numbers[solvent] / random
148
+ vs_random = cn / random
147
149
  coordination_vs_random[solvent] = vs_random
148
150
  return coordination_vs_random
149
151
 
{solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis/tests/test_coordination.py RENAMED
@@ -18,8 +18,7 @@ def test_coordination_from_solute(run_solute):
18
18
  ],
19
19
  )
20
20
  def test_coordination(name, cn, solvation_data, run_solute):
21
- atoms = run_solute.u.atoms
22
- coordination = Coordination(solvation_data, 10, 49, atoms)
21
+ coordination = Coordination.from_solute(run_solute)
23
22
  np.testing.assert_allclose(cn, coordination.coordination_numbers[name], atol=0.05)
24
23
  assert len(coordination.coordination_numbers_by_frame) == 3
25
24
 
@@ -33,8 +32,7 @@ def test_coordination(name, cn, solvation_data, run_solute):
33
32
  ],
34
33
  )
35
34
  def test_coordinating_atoms(name, atom_type, fraction, solvation_data, run_solute):
36
- atoms = run_solute.u.atoms
37
- coordination = Coordination(solvation_data, 10, 49, atoms)
35
+ coordination = Coordination.from_solute(run_solute)
38
36
  calculated_fraction = coordination._coordinating_atoms.loc[(name, atom_type)]
39
37
  np.testing.assert_allclose(fraction, calculated_fraction, atol=0.05)
40
38
 
{solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0/solvation_analysis.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: solvation-analysis
3
- Version: 0.3.2
3
+ Version: 0.3.3a0
4
4
  Summary: A toolkit to analyze solvation structure in molecular dynamics trajectories.
5
5
  Author: Orion Cohen
6
6
  Author-email: Orion Cohen <orioncohen@berkeley.edu>
{solvation-analysis-0.3.2 → solvation-analysis-0.3.3a0}/solvation_analysis.egg-info/requires.txt RENAMED
@@ -2,7 +2,6 @@ numpy>=1.20.0
2
2
  pandas
3
3
  mdanalysis>=2.0.0
4
4
  pytest
5
- pathlib
6
5
  matplotlib
7
6
  scipy
8
7
  statsmodels