polyscript-pypi 0.1.0__py3-none-any.whl

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 (57) hide show
  1. MCP/server.py +770 -0
  2. polyscript/__init__.py +12 -0
  3. polyscript/brics/BRICSMod.py +1164 -0
  4. polyscript/brics/BRICS_utils.py +189 -0
  5. polyscript/brics/__init__.py +48 -0
  6. polyscript/classifier/__init__.py +270 -0
  7. polyscript/classifier/class_reference.py +951 -0
  8. polyscript/depolymerizer/__init__.py +576 -0
  9. polyscript/depolymerizer/mpi.py +390 -0
  10. polyscript/depolymerizer/reaction_reference.py +447 -0
  11. polyscript/polymerizer/__init__.py +22 -0
  12. polyscript/polymerizer/core.py +648 -0
  13. polyscript/polymerizer/mpi.py +860 -0
  14. polyscript/polymerizer/mpi_df.py +378 -0
  15. polyscript/polymerizer/utils.py +795 -0
  16. polyscript/utils/__init__.py +80 -0
  17. polyscript/utils/adapters.py +357 -0
  18. polyscript/utils/canon_analyze.py +193 -0
  19. polyscript/utils/executor.py +66 -0
  20. polyscript/utils/logger.py +331 -0
  21. polyscript/utils/mpi/__init__.py +33 -0
  22. polyscript/utils/mpi/checkpoint.py +263 -0
  23. polyscript/utils/mpi/logger.py +138 -0
  24. polyscript/utils/mpi/progress.py +134 -0
  25. polyscript/utils/mpi/protocol.py +113 -0
  26. polyscript/utils/mpi/resource.py +94 -0
  27. polyscript/utils/mpi/splitter.py +42 -0
  28. polyscript/utils/mpi_executor.py +167 -0
  29. polyscript/utils/mpi_validator.py +940 -0
  30. polyscript/utils/parsers.py +177 -0
  31. polyscript/utils/validators.py +201 -0
  32. polyscript_pypi-0.1.0.dist-info/METADATA +82 -0
  33. polyscript_pypi-0.1.0.dist-info/RECORD +57 -0
  34. polyscript_pypi-0.1.0.dist-info/WHEEL +5 -0
  35. polyscript_pypi-0.1.0.dist-info/licenses/LICENSE +21 -0
  36. polyscript_pypi-0.1.0.dist-info/top_level.txt +4 -0
  37. runners/adapt_dataframe.py +105 -0
  38. runners/brics_decompose.py +28 -0
  39. runners/canonicalization.py +46 -0
  40. runners/filter_candidates.py +54 -0
  41. runners/mpi_depolymerize.py +51 -0
  42. runners/mpi_runner.py +66 -0
  43. runners/mpi_runner_df.py +49 -0
  44. runners/mpi_validator.py +45 -0
  45. tests/conftest.py +10 -0
  46. tests/sample_gen.py +10 -0
  47. tests/test_brics.py +275 -0
  48. tests/test_classifier.py +201 -0
  49. tests/test_mpi_polymerize.py +170 -0
  50. tests/test_polymerize.py +206 -0
  51. tests/utils/test_adaptors.py +182 -0
  52. tests/utils/test_canonicalization.py +62 -0
  53. tests/utils/test_executor.py +101 -0
  54. tests/utils/test_logger.py +426 -0
  55. tests/utils/test_mpi_validator.py +159 -0
  56. tests/utils/test_parsers.py +150 -0
  57. tests/utils/test_validator.py +105 -0
polyscript/__init__.py ADDED
@@ -0,0 +1,12 @@
1
+ """PolyScript: A chemical notation format and toolkit for polymer sequences.
2
+
3
+ PolyScript encodes polymer synthesis information as a structured string
4
+ containing monomers (SMILES), a reaction (SMARTS), and the resulting
5
+ polymer (SMILES/PSMILES), e.g.::
6
+
7
+ ${monomer1}+{monomer2}=>{reaction_smarts}=>{polymer}$
8
+
9
+ The package provides utilities for parsing, validating, converting, and
10
+ analysing PolyScript sequences, including MPI-parallel batch validation
11
+ of large datasets.
12
+ """