firecode 1.1.0__tar.gz → 1.1.2__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 (78) hide show
  1. {firecode-1.1.0 → firecode-1.1.2}/CHANGELOG.md +10 -0
  2. {firecode-1.1.0/firecode.egg-info → firecode-1.1.2}/PKG-INFO +12 -1
  3. {firecode-1.1.0 → firecode-1.1.2}/docs/conf.py +1 -2
  4. {firecode-1.1.0 → firecode-1.1.2}/firecode/__main__.py +3 -1
  5. firecode-1.1.2/firecode/eig_based_RMSD_test.ipynb +464 -0
  6. {firecode-1.1.0 → firecode-1.1.2}/firecode/embedder.py +45 -32
  7. {firecode-1.1.0 → firecode-1.1.2}/firecode/embedder_options.py +4 -0
  8. {firecode-1.1.0 → firecode-1.1.2}/firecode/hypermolecule_class.py +1 -0
  9. {firecode-1.1.0 → firecode-1.1.2}/firecode/operators.py +1 -0
  10. {firecode-1.1.0 → firecode-1.1.2}/firecode/optimization_methods.py +1 -1
  11. {firecode-1.1.0 → firecode-1.1.2}/firecode/torsion_module.py +1 -1
  12. {firecode-1.1.0 → firecode-1.1.2}/firecode/utils.py +295 -3
  13. {firecode-1.1.0 → firecode-1.1.2/firecode.egg-info}/PKG-INFO +12 -1
  14. {firecode-1.1.0 → firecode-1.1.2}/firecode.egg-info/SOURCES.txt +1 -1
  15. {firecode-1.1.0 → firecode-1.1.2}/firecode.egg-info/requires.txt +1 -0
  16. {firecode-1.1.0 → firecode-1.1.2}/setup.py +2 -1
  17. firecode-1.1.0/firecode/firecode_debug.log +0 -51
  18. {firecode-1.1.0 → firecode-1.1.2}/LICENSE +0 -0
  19. {firecode-1.1.0 → firecode-1.1.2}/MANIFEST.in +0 -0
  20. {firecode-1.1.0 → firecode-1.1.2}/README.md +0 -0
  21. {firecode-1.1.0 → firecode-1.1.2}/docs/examples.rst +0 -0
  22. {firecode-1.1.0 → firecode-1.1.2}/docs/index.rst +0 -0
  23. {firecode-1.1.0 → firecode-1.1.2}/docs/installation.rst +0 -0
  24. {firecode-1.1.0 → firecode-1.1.2}/docs/introduction.rst +0 -0
  25. {firecode-1.1.0 → firecode-1.1.2}/docs/license.rst +0 -0
  26. {firecode-1.1.0 → firecode-1.1.2}/docs/operators_keywords.rst +0 -0
  27. {firecode-1.1.0 → firecode-1.1.2}/docs/requirements.txt +0 -0
  28. {firecode-1.1.0 → firecode-1.1.2}/docs/usage.rst +0 -0
  29. {firecode-1.1.0 → firecode-1.1.2}/firecode/TEST_NOTEBOOK.ipynb +0 -0
  30. {firecode-1.1.0 → firecode-1.1.2}/firecode/__init__.py +0 -0
  31. {firecode-1.1.0 → firecode-1.1.2}/firecode/_gaussian.py +0 -0
  32. {firecode-1.1.0 → firecode-1.1.2}/firecode/algebra.py +0 -0
  33. {firecode-1.1.0 → firecode-1.1.2}/firecode/ase_manipulations.py +0 -0
  34. {firecode-1.1.0 → firecode-1.1.2}/firecode/atropisomer_module.py +0 -0
  35. {firecode-1.1.0 → firecode-1.1.2}/firecode/automep.py +0 -0
  36. {firecode-1.1.0 → firecode-1.1.2}/firecode/calculators/__init__.py +0 -0
  37. {firecode-1.1.0 → firecode-1.1.2}/firecode/calculators/_gaussian.py +0 -0
  38. {firecode-1.1.0 → firecode-1.1.2}/firecode/calculators/_mopac.py +0 -0
  39. {firecode-1.1.0 → firecode-1.1.2}/firecode/calculators/_openbabel.py +0 -0
  40. {firecode-1.1.0 → firecode-1.1.2}/firecode/calculators/_orca.py +0 -0
  41. {firecode-1.1.0 → firecode-1.1.2}/firecode/calculators/_xtb.py +0 -0
  42. {firecode-1.1.0 → firecode-1.1.2}/firecode/concurrent_test.py +0 -0
  43. {firecode-1.1.0 → firecode-1.1.2}/firecode/embeds.py +0 -0
  44. {firecode-1.1.0 → firecode-1.1.2}/firecode/errors.py +0 -0
  45. {firecode-1.1.0 → firecode-1.1.2}/firecode/graph_manipulations.py +0 -0
  46. {firecode-1.1.0 → firecode-1.1.2}/firecode/mep_relaxer.py +0 -0
  47. {firecode-1.1.0 → firecode-1.1.2}/firecode/modify_settings.py +0 -0
  48. {firecode-1.1.0 → firecode-1.1.2}/firecode/mprof.py +0 -0
  49. {firecode-1.1.0 → firecode-1.1.2}/firecode/multiembed.py +0 -0
  50. {firecode-1.1.0 → firecode-1.1.2}/firecode/nci.py +0 -0
  51. {firecode-1.1.0 → firecode-1.1.2}/firecode/numba_functions.py +0 -0
  52. {firecode-1.1.0 → firecode-1.1.2}/firecode/parameters.py +0 -0
  53. {firecode-1.1.0 → firecode-1.1.2}/firecode/pka.py +0 -0
  54. {firecode-1.1.0 → firecode-1.1.2}/firecode/profiler.py +0 -0
  55. {firecode-1.1.0 → firecode-1.1.2}/firecode/pruning.py +0 -0
  56. {firecode-1.1.0 → firecode-1.1.2}/firecode/pt.py +0 -0
  57. {firecode-1.1.0 → firecode-1.1.2}/firecode/quotes.json +0 -0
  58. {firecode-1.1.0 → firecode-1.1.2}/firecode/quotes.py +0 -0
  59. {firecode-1.1.0 → firecode-1.1.2}/firecode/reactive_atoms_classes.py +0 -0
  60. {firecode-1.1.0 → firecode-1.1.2}/firecode/references.py +0 -0
  61. {firecode-1.1.0 → firecode-1.1.2}/firecode/rmsd.py +0 -0
  62. {firecode-1.1.0 → firecode-1.1.2}/firecode/settings.py +0 -0
  63. {firecode-1.1.0 → firecode-1.1.2}/firecode/solvents.py +0 -0
  64. {firecode-1.1.0 → firecode-1.1.2}/firecode/tests/C2F2H4.xyz +0 -0
  65. {firecode-1.1.0 → firecode-1.1.2}/firecode/tests/C2H4.xyz +0 -0
  66. {firecode-1.1.0 → firecode-1.1.2}/firecode/tests/CH3Cl.xyz +0 -0
  67. {firecode-1.1.0 → firecode-1.1.2}/firecode/tests/HCOOH.xyz +0 -0
  68. {firecode-1.1.0 → firecode-1.1.2}/firecode/tests/HCOOOH.xyz +0 -0
  69. {firecode-1.1.0 → firecode-1.1.2}/firecode/tests/chelotropic.txt +0 -0
  70. {firecode-1.1.0 → firecode-1.1.2}/firecode/tests/cyclical.txt +0 -0
  71. {firecode-1.1.0 → firecode-1.1.2}/firecode/tests/dihedral.txt +0 -0
  72. {firecode-1.1.0 → firecode-1.1.2}/firecode/tests/string.txt +0 -0
  73. {firecode-1.1.0 → firecode-1.1.2}/firecode/tests/trimolecular.txt +0 -0
  74. {firecode-1.1.0 → firecode-1.1.2}/firecode/tests.py +0 -0
  75. {firecode-1.1.0 → firecode-1.1.2}/firecode.egg-info/dependency_links.txt +0 -0
  76. {firecode-1.1.0 → firecode-1.1.2}/firecode.egg-info/top_level.txt +0 -0
  77. {firecode-1.1.0 → firecode-1.1.2}/pyproject.toml +0 -0
  78. {firecode-1.1.0 → firecode-1.1.2}/setup.cfg +0 -0
@@ -4,6 +4,16 @@
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  <!-- - ... mep_relax> BETA
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  - ... IMAGES kw, also implement it for neb>-->
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+ ## FIRECODE 1.1.2 🔥 (April 29 2025)
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+ - Added CRESTLEVEL keyword to specify CREST theory level (i.e. "CRESTLEVEL=GFN2").
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+ - Updated aimnet2 bindings to only useunderscore in the module name calls and not hyphens.
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+ - Fixed bug with the default value for the attribute "charge".
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+
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+ ## FIRECODE 1.1.1 🔥 (January 2025)
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+ - Added pretty error traceback with rich.
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+ <!-- SMARTS Constraint class -->
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+
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+
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  ## FIRECODE 1.1.0 🔥 (December 24 2024)
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  - Implemented planar angle and dihedral constraints in ensemble optimization (only intra-file, but also available in embedding runs). These are propagated to xtb, ASE-mediated calculators and PyTorch models, as well as to operators like mtd> (CREST). These constraints can be specified in new input lines that start with a blank space under the reference molecule line, with the syntax "i1 i2 i3 \[i4\] target(float)" (i.e. "0 1 2 3 90.0" for dihedrals or "0 1 2 0.0" for planar angles). For now, these constraints are enforced at every step (as capital letter constraints, but not associated to any letter).
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  - Improved comments parsing: possible to comment in any input line (with "#", following a Pyhton-style syntax).
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: firecode
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- Version: 1.1.0
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+ Version: 1.1.2
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  Summary: Computational chemistry general purpose ensemble optimizer and transition state builder
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  Home-page: https://www.github.com/ntampellini/firecode
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  Author: Nicolò Tampellini
@@ -30,6 +30,7 @@ Requires-Dist: llvmlite==0.41.1
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  Requires-Dist: importlib-metadata==7.0.1
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  Requires-Dist: psutil==5.9.6
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  Requires-Dist: setuptools==75.3.0
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+ Requires-Dist: rich
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  ## FIRECODE: Filtering Refiner and Embedder for Conformationally Dense Ensembles.
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  Ensemble optimizer. Systematic generation of multimolecular arrangements for mono/bi/trimolecular transition states. Numerous utilities for conformational exploration, selection, pruning and constrained ensemble optimization.
@@ -40,6 +41,16 @@ Ensemble optimizer. Systematic generation of multimolecular arrangements for mon
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  <!-- - ... mep_relax> BETA
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  - ... IMAGES kw, also implement it for neb>-->
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+ ## FIRECODE 1.1.2 🔥 (April 29 2025)
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+ - Added CRESTLEVEL keyword to specify CREST theory level (i.e. "CRESTLEVEL=GFN2").
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+ - Updated aimnet2 bindings to only useunderscore in the module name calls and not hyphens.
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+ - Fixed bug with the default value for the attribute "charge".
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+
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+ ## FIRECODE 1.1.1 🔥 (January 2025)
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+ - Added pretty error traceback with rich.
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+ <!-- SMARTS Constraint class -->
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+
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+
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  ## FIRECODE 1.1.0 🔥 (December 24 2024)
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  - Implemented planar angle and dihedral constraints in ensemble optimization (only intra-file, but also available in embedding runs). These are propagated to xtb, ASE-mediated calculators and PyTorch models, as well as to operators like mtd> (CREST). These constraints can be specified in new input lines that start with a blank space under the reference molecule line, with the syntax "i1 i2 i3 \[i4\] target(float)" (i.e. "0 1 2 3 90.0" for dihedrals or "0 1 2 0.0" for planar angles). For now, these constraints are enforced at every step (as capital letter constraints, but not associated to any letter).
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  - Improved comments parsing: possible to comment in any input line (with "#", following a Pyhton-style syntax).
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  #
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  import os
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  import sys
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- from firecode.__main__ import __version__
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  # sys.path.insert(0, os.path.abspath('.'))
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  sys.path.insert(0, os.path.join(os.path.abspath('..'), 'firecode'))
@@ -26,7 +25,7 @@ author = 'Nicolò Tampellini'
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  # The full version, including alpha/beta/rc tags
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- release = __version__
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+ release = '1.1.0'
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  # release='latest'
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  # -- General configuration ---------------------------------------------------
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  import argparse
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  import os
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  import sys
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+ from rich.traceback import install
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+ install(show_locals=True)
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- __version__ = '1.1.0'
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+ __version__ = '1.1.2'
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  if __name__ == '__main__':
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