mdinterface 1.5.1__tar.gz → 1.5.2__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.
Files changed (94) hide show
  1. {mdinterface-1.5.1/mdinterface.egg-info → mdinterface-1.5.2}/PKG-INFO +1 -1
  2. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/__init__.py +2 -2
  3. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/externals/ligpargen.py +5 -2
  4. {mdinterface-1.5.1 → mdinterface-1.5.2/mdinterface.egg-info}/PKG-INFO +1 -1
  5. {mdinterface-1.5.1 → mdinterface-1.5.2}/LICENSE +0 -0
  6. {mdinterface-1.5.1 → mdinterface-1.5.2}/MANIFEST.in +0 -0
  7. {mdinterface-1.5.1 → mdinterface-1.5.2}/README.md +0 -0
  8. {mdinterface-1.5.1 → mdinterface-1.5.2}/assets/mdinterface.png +0 -0
  9. {mdinterface-1.5.1 → mdinterface-1.5.2}/docs/api/database.md +0 -0
  10. {mdinterface-1.5.1 → mdinterface-1.5.2}/docs/api/externals.md +0 -0
  11. {mdinterface-1.5.1 → mdinterface-1.5.2}/docs/api/io.md +0 -0
  12. {mdinterface-1.5.1 → mdinterface-1.5.2}/docs/api/polymer.md +0 -0
  13. {mdinterface-1.5.1 → mdinterface-1.5.2}/docs/api/simcell.md +0 -0
  14. {mdinterface-1.5.1 → mdinterface-1.5.2}/docs/api/specie.md +0 -0
  15. {mdinterface-1.5.1 → mdinterface-1.5.2}/docs/assets/mdinterface.png +0 -0
  16. {mdinterface-1.5.1 → mdinterface-1.5.2}/docs/guide/database.md +0 -0
  17. {mdinterface-1.5.1 → mdinterface-1.5.2}/docs/guide/logging.md +0 -0
  18. {mdinterface-1.5.1 → mdinterface-1.5.2}/docs/guide/polymer.md +0 -0
  19. {mdinterface-1.5.1 → mdinterface-1.5.2}/docs/guide/simcell.md +0 -0
  20. {mdinterface-1.5.1 → mdinterface-1.5.2}/docs/guide/specie.md +0 -0
  21. {mdinterface-1.5.1 → mdinterface-1.5.2}/docs/index.md +0 -0
  22. {mdinterface-1.5.1 → mdinterface-1.5.2}/docs/installation.md +0 -0
  23. {mdinterface-1.5.1 → mdinterface-1.5.2}/docs/quickstart.md +0 -0
  24. {mdinterface-1.5.1 → mdinterface-1.5.2}/docs/requirements.txt +0 -0
  25. {mdinterface-1.5.1 → mdinterface-1.5.2}/examples/electrode_interface.py +0 -0
  26. {mdinterface-1.5.1 → mdinterface-1.5.2}/examples/legacy/make_POSCAR.py +0 -0
  27. {mdinterface-1.5.1 → mdinterface-1.5.2}/examples/legacy/make_box.py +0 -0
  28. {mdinterface-1.5.1 → mdinterface-1.5.2}/examples/legacy/make_polymer.py +0 -0
  29. {mdinterface-1.5.1 → mdinterface-1.5.2}/examples/legacy/make_solvent_box.py +0 -0
  30. {mdinterface-1.5.1 → mdinterface-1.5.2}/examples/legacy/make_specie_ligpargen_resp.py +0 -0
  31. {mdinterface-1.5.1 → mdinterface-1.5.2}/examples/multilayer.py +0 -0
  32. {mdinterface-1.5.1 → mdinterface-1.5.2}/examples/multisolvent_box.py +0 -0
  33. {mdinterface-1.5.1 → mdinterface-1.5.2}/examples/polymer/polymer_piperion.py +0 -0
  34. {mdinterface-1.5.1 → mdinterface-1.5.2}/examples/sandwich_from_traj.py +0 -0
  35. {mdinterface-1.5.1 → mdinterface-1.5.2}/examples/solvent_box.py +0 -0
  36. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/build/__init__.py +0 -0
  37. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/build/box.py +0 -0
  38. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/build/builder.py +0 -0
  39. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/build/continuum2sim.py +0 -0
  40. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/build/polymerize.py +0 -0
  41. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/build/snippets.py +0 -0
  42. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/build/solvent.py +0 -0
  43. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/config.py +0 -0
  44. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/core/__init__.py +0 -0
  45. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/core/polymer.py +0 -0
  46. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/core/specie.py +0 -0
  47. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/core/topology.py +0 -0
  48. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/database/__init__.py +0 -0
  49. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/database/graphene.py +0 -0
  50. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/database/ions.py +0 -0
  51. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/database/metals.py +0 -0
  52. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/database/molecules.py +0 -0
  53. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/database/nobles.py +0 -0
  54. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/externals/__init__.py +0 -0
  55. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/externals/aimd.py +0 -0
  56. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/externals/ase.py +0 -0
  57. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/externals/obabel.py +0 -0
  58. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/externals/optimization.py +0 -0
  59. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/externals/pyscf.py +0 -0
  60. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/io/__init__.py +0 -0
  61. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/io/gromacswriter.py +0 -0
  62. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/io/lammpswriter.py +0 -0
  63. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/io/packmol.py +0 -0
  64. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/io/read.py +0 -0
  65. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/read/cp2ktraj.py +0 -0
  66. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/read/lammpstraj.py +0 -0
  67. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/read/read.py +0 -0
  68. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/read/trajectory.py +0 -0
  69. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/read/xyztraj.py +0 -0
  70. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/simulationbox.py +0 -0
  71. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/utils/__init__.py +0 -0
  72. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/utils/auxiliary.py +0 -0
  73. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/utils/draw.py +0 -0
  74. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/utils/graphs.py +0 -0
  75. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/utils/logger.py +0 -0
  76. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/utils/map.py +0 -0
  77. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/utils/poisson.py +0 -0
  78. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/utils/rings.py +0 -0
  79. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/utils/units.py +0 -0
  80. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface.egg-info/SOURCES.txt +0 -0
  81. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface.egg-info/dependency_links.txt +0 -0
  82. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface.egg-info/requires.txt +0 -0
  83. {mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface.egg-info/top_level.txt +0 -0
  84. {mdinterface-1.5.1 → mdinterface-1.5.2}/pyproject.toml +0 -0
  85. {mdinterface-1.5.1 → mdinterface-1.5.2}/requirements.txt +0 -0
  86. {mdinterface-1.5.1 → mdinterface-1.5.2}/setup.cfg +0 -0
  87. {mdinterface-1.5.1 → mdinterface-1.5.2}/setup.py +0 -0
  88. {mdinterface-1.5.1 → mdinterface-1.5.2}/tests/__init__.py +0 -0
  89. {mdinterface-1.5.1 → mdinterface-1.5.2}/tests/test_auxiliary.py +0 -0
  90. {mdinterface-1.5.1 → mdinterface-1.5.2}/tests/test_builder.py +0 -0
  91. {mdinterface-1.5.1 → mdinterface-1.5.2}/tests/test_database.py +0 -0
  92. {mdinterface-1.5.1 → mdinterface-1.5.2}/tests/test_solvent.py +0 -0
  93. {mdinterface-1.5.1 → mdinterface-1.5.2}/tests/test_specie.py +0 -0
  94. {mdinterface-1.5.1 → mdinterface-1.5.2}/tests/test_topology.py +0 -0
{mdinterface-1.5.1/mdinterface.egg-info → mdinterface-1.5.2}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: mdinterface
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- Version: 1.5.1
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+ Version: 1.5.2
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  Summary: Build Interface Systems for Molecular Dynamics Simulations
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  Author-email: Fabrice Roncoroni <fabrice.roncoroni@gmail.com>
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  License-Expression: Apache-2.0
{mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/__init__.py RENAMED
@@ -6,8 +6,8 @@ Initially developed to construct electrolyte/electrode interfaces, it is also we
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  """
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- __version__ = '1.5.1'
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- __date__ = '31 Mar. 2026'
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+ __version__ = '1.5.2'
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+ __date__ = '28 Apr. 2026'
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  __author__ = 'Fabrice Roncoroni'
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  __all__ = ['SimulationBox', 'SimCell', 'BoxBuilder', "Specie", "Polymer"]
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{mdinterface-1.5.1 → mdinterface-1.5.2}/mdinterface/externals/ligpargen.py RENAMED
@@ -379,8 +379,10 @@ def refine_large_specie_topology(specie, Nmax=12, ending="H", offset=True,
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  sn_sys, sn_atypes, sn_bonds, sn_angles, sn_dihs, sn_imps = \
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  run_ligpargen(capped, charge=sn_charge, is_snippet=True)
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- # Remap: real atoms -> original sids; caps -> placeholders
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- real_sids = list(specie._sids[seg_indices])
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+ # Remap: real atoms -> globally unique labels (original atom index
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+ # avoids collisions across segments); caps -> placeholders
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+ real_sids = [f"{sn_atypes[pos].symbol}_{seg_indices[pos]:03d}"
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+ for pos in range(n_real)]
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  cap_sids = [f"__cap_{seg_idx}_{c}__"
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  for c in range(len(sn_atypes) - n_real)]
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  original_idxs = np.array(real_sids + cap_sids)
@@ -399,6 +401,7 @@ def refine_large_specie_topology(specie, Nmax=12, ending="H", offset=True,
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  for pos, orig_idx in enumerate(seg_indices):
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  charges[orig_idx] = seg_charges[pos]
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  atom_types_ordered[orig_idx] = sn_atypes[pos]
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+ atom_types_ordered[orig_idx].set_label(real_sids[pos])
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  # ------------------------------------------------------------------
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  # 3. Rebuild topology from assembled segment results
{mdinterface-1.5.1 → mdinterface-1.5.2/mdinterface.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: mdinterface
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- Version: 1.5.1
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+ Version: 1.5.2
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  Summary: Build Interface Systems for Molecular Dynamics Simulations
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  Author-email: Fabrice Roncoroni <fabrice.roncoroni@gmail.com>
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  License-Expression: Apache-2.0
{mdinterface-1.5.1 → mdinterface-1.5.2}/LICENSE RENAMED
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{mdinterface-1.5.1 → mdinterface-1.5.2}/MANIFEST.in RENAMED
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{mdinterface-1.5.1 → mdinterface-1.5.2}/README.md RENAMED
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{mdinterface-1.5.1 → mdinterface-1.5.2}/docs/api/io.md RENAMED
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{mdinterface-1.5.1 → mdinterface-1.5.2}/docs/index.md RENAMED
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{mdinterface-1.5.1 → mdinterface-1.5.2}/pyproject.toml RENAMED
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{mdinterface-1.5.1 → mdinterface-1.5.2}/setup.cfg RENAMED
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{mdinterface-1.5.1 → mdinterface-1.5.2}/setup.py RENAMED
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