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Then run:\n\n```bash\npip install -e .\n```\n\n## Command-line usage\n\n**schemist**  provides command-line utlities. The list of commands can be checked like so:\n\n```bash\n$ schemist --help\nusage: schemist [-h] [--version] {clean,convert,featurize,collate,dedup,enumerate,react,split} ...\n\nTools for cleaning, collating, and augmenting chemical datasets.\n\noptions:\n  -h, --help            show this help message and exit\n  --version, -v         show program's version number and exit\n\nSub-commands:\n  {clean,convert,featurize,collate,dedup,enumerate,react,split}\n                        Use these commands to specify the tool you want to use.\n    clean               Clean and normalize SMILES column of a table.\n    convert             Convert between string representations of chemical structures.\n    featurize           Convert between string representations of chemical structures.\n    collate             Collect disparate tables or SDF files of libraries into a single table.\n    dedup               Deduplicate chemical structures and retain references.\n    enumerate           Enumerate bio-chemical structures within length and sequence constraints.\n    react               React compounds in silico in indicated columns using a named reaction.\n    split               Split table based on chosen algorithm, optionally taking account of chemical structure during splits.\n```\n\nEach command is designed to work on large data files in a streaming fashion, so that the entire file is not held in memory at once. One caveat is that the scaffold-based splits are very slow with tables of millions of rows.\n\nAll commands (except `collate`) take from the input table a named column with a SMILES, SELFIES, amino-acid sequence, HELM, or InChI representation of compounds.\n\nThe tools complete specific tasks which \ncan be easily composed into analysis pipelines, because the TSV table output goes to\n`stdout` by default so they can be piped from one tool to another.\n\nTo get help for a specific command, do\n\n```bash\nschemist \u003ccommand\u003e --help\n```\n\nFor the Python API, [see below](#python-api).\n\n\n## Python API\n\n**schemist** can be imported into Python to help make custom analyses.\n\n```python\n\u003e\u003e\u003e import schemist as sch\n```\n\n## Documentation\n\nFull API documentation is at [ReadTheDocs](https://schemist.readthedocs.org).","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fscbirlab%2Fschemist","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fscbirlab%2Fschemist","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fscbirlab%2Fschemist/lists"}