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Arki05 commited on
Commit
ccbce37
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1 Parent(s): fec2648

Splitting large SMILES files @1GB size

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  1. README.md +65 -0
  2. emolecules/free/2024-10-01/{version.smi → version.part01.smi} +2 -2
  3. emolecules/{ordersc/2024-10-01/parent.smi → free/2024-10-01/version.part02.smi} +2 -2
  4. emolecules/ordersc/2024-10-01/{version.smi → parent.part01.smi} +2 -2
  5. gdb/GDB-13s.smi → emolecules/ordersc/2024-10-01/parent.part02.smi +2 -2
  6. emolecules/ordersc/2024-10-01/version.part01.smi +3 -0
  7. emolecules/ordersc/2024-10-01/version.part02.smi +3 -0
  8. gdb/GDB-13s.part01.smi +3 -0
  9. gdb/GDB-13s.part02.smi +3 -0
  10. gdb/GDB-13s.part03.smi +3 -0
  11. gdb/GDB13_Subset-AB.part01.smi +3 -0
  12. gdb/GDB13_Subset-AB.part02.smi +3 -0
  13. gdb/GDB13_Subset-AB.part03.smi +3 -0
  14. gdb/GDB13_Subset-AB.part04.smi +3 -0
  15. gdb/GDB13_Subset-AB.part05.smi +3 -0
  16. gdb/GDB13_Subset-AB.part06.smi +3 -0
  17. gdb/GDB13_Subset-AB.part07.smi +3 -0
  18. gdb/GDB13_Subset-AB.part08.smi +3 -0
  19. gdb/GDB13_Subset-AB.part09.smi +3 -0
  20. gdb/GDB13_Subset-AB.part10.smi +3 -0
  21. gdb/GDB13_Subset-AB.part11.smi +3 -0
  22. gdb/GDB13_Subset-AB.part12.smi +3 -0
  23. gdb/GDB13_Subset-AB.part13.smi +3 -0
  24. gdb/GDB13_Subset-AB.part14.smi +3 -0
  25. gdb/GDB13_Subset-AB.part15.smi +3 -0
  26. gdb/GDB13_Subset-AB.part16.smi +3 -0
  27. gdb/GDB13_Subset-AB.smi +0 -3
  28. gdb/GDB17.50000000.part01.smi +3 -0
  29. gdb/GDB17.50000000.part02.smi +3 -0
  30. gdb/GDB17.50000000.smi +0 -3
  31. gdb/gdb13/12.part01.smi +3 -0
  32. gdb/gdb13/12.part02.smi +3 -0
  33. gdb/gdb13/12.part03.smi +3 -0
  34. gdb/gdb13/12.smi +0 -3
  35. gdb/gdb13/13.part01.smi +3 -0
  36. gdb/gdb13/13.part02.smi +3 -0
  37. gdb/gdb13/13.part03.smi +3 -0
  38. gdb/gdb13/13.part04.smi +3 -0
  39. gdb/gdb13/13.part05.smi +3 -0
  40. gdb/gdb13/13.part06.smi +3 -0
  41. gdb/gdb13/13.part07.smi +3 -0
  42. gdb/gdb13/13.part08.smi +3 -0
  43. gdb/gdb13/13.part09.smi +3 -0
  44. gdb/gdb13/13.part10.smi +3 -0
  45. gdb/gdb13/13.part11.smi +3 -0
  46. gdb/gdb13/13.part12.smi +3 -0
  47. gdb/gdb13/13.part13.smi +3 -0
  48. gdb/gdb13/13.part14.smi +3 -0
  49. gdb/gdb13/13.part15.smi +3 -0
  50. gdb/gdb13/13.part16.smi +3 -0
README.md ADDED
@@ -0,0 +1,65 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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+ ## SMILES Splitter Script
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+
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+ The file splitter script (`split_file.sh`) is used to split large SMILES files into smaller parts.
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+
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+ ### Usage
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+
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+ ```bash
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+ ./split_smi.sh <input_file> [max_size_mb]
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+ ```
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+
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+ - `<input_file>`: The SMILES file to split
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+ - `[max_size_mb]`: Optional. The maximum size of each part in MB (default: 1024)
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+
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+ ### Running with xargs for parallel processing
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+
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+ To split multiple files in parallel:
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+
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+ ```bash
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+ find . -name "*.smi" | xargs -n1 -P$(nproc) ./split_file.sh
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+ ```
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+
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+ To specify a custom size (e.g., 500 MB):
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+
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+ ```bash
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+ find . -name "*.smi" | xargs -n2 -P$(nproc) ./split_file.sh {} 500
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+ ```
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+
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+ Note: This script will delete the original file if it was split successfully.
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+
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+ ## SELFIES Converter Script
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+
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+ The SELFIES converter script (`selfies_converter.py`) converts SMILES files to SELFIES format.
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+
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+ ### Usage
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+
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+ ```bash
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+ python selfies_converter.py <input_file> [-v] [-b BATCH_SIZE]
38
+ ```
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+
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+ - `<input_file>`: The SMILES file to convert
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+ - `-v, --verbose`: Optional. Increase output verbosity
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+ - `-b BATCH_SIZE, --batch-size BATCH_SIZE`: Optional. Batch size for processing (default: 10000)
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+
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+ ### Running with find and xargs for parallel processing
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+
46
+ To convert all .smi files in parallel:
47
+
48
+ ```bash
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+ find . -name "*.smi" | xargs -I {} -P$(nproc) sh -c 'python selfies_converter.py {}'
50
+ ```
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+
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+ To convert files and remove the original .smi files after successful conversion:
53
+
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+ ```bash
55
+ find . -name "*.smi" | xargs -I {} -P$(nproc) sh -c 'python selfies_converter.py {} && rm {}'
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+ ```
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+
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+ Note: Be cautious when using the command that removes original files. Ensure you have backups before running it.
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+
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+ ## Output
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+
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+ Both scripts will create output files in the same directory as the input files:
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+
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+ - The file splitter creates `<original_name>.part01.smi`, `<original_name>.part02.smi`, etc.
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+ - The SELFIES converter creates `<original_name>.selfies` for the converted file and `<original_name>.alph` for the alphabet file.
emolecules/free/2024-10-01/{version.smi → version.part01.smi} RENAMED
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emolecules/{ordersc/2024-10-01/parent.smi → free/2024-10-01/version.part02.smi} RENAMED
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