https://github.com/scbirlab/schemist

⬢⬢⬢ Organizing and processing tables of chemical structures.
https://github.com/scbirlab/schemist

cheminformatics chemistry selfies smiles smiles-strings

Last synced: 4 months ago
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⬢⬢⬢ Organizing and processing tables of chemical structures.

• Host: GitHub
• URL: https://github.com/scbirlab/schemist
• Owner: scbirlab
• License: mit
• Created: 2024-02-21T10:20:10.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2025-11-14T13:25:39.000Z (8 months ago)
• Last Synced: 2025-12-15T09:21:25.223Z (7 months ago)
• Topics: cheminformatics, chemistry, selfies, smiles, smiles-strings
• Language: Python
• Homepage: https://schemist.readthedocs.org
• Size: 286 KB
• Stars: 2
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# ⬢⬢⬢ schemist

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Cleaning, collating, and augmenting chemical datasets.

- [Installation](#installation)

- [Command-line usage](#command-line-usage)

- [Python API](#python-api)

- [Documentation](#documentation)

## Installation

### The easy way

Install the pre-compiled version from PyPI:

```bash

pip install schemist

```

### From source

Clone the repository, then `cd` into it. Then run:

```bash

pip install -e .

```

## Command-line usage

**schemist**  provides command-line utlities. The list of commands can be checked like so:

```bash

$ schemist --help

usage: schemist [-h] [--version] {clean,convert,featurize,collate,dedup,enumerate,react,split} ...

Tools for cleaning, collating, and augmenting chemical datasets.

options:

  -h, --help            show this help message and exit

  --version, -v         show program's version number and exit

Sub-commands:

  {clean,convert,featurize,collate,dedup,enumerate,react,split}

                        Use these commands to specify the tool you want to use.

    clean               Clean and normalize SMILES column of a table.

    convert             Convert between string representations of chemical structures.

    featurize           Convert between string representations of chemical structures.

    collate             Collect disparate tables or SDF files of libraries into a single table.

    dedup               Deduplicate chemical structures and retain references.

    enumerate           Enumerate bio-chemical structures within length and sequence constraints.

    react               React compounds in silico in indicated columns using a named reaction.

    split               Split table based on chosen algorithm, optionally taking account of chemical structure during splits.

```

Each 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.

All commands (except `collate`) take from the input table a named column with a SMILES, SELFIES, amino-acid sequence, HELM, or InChI representation of compounds.

The tools complete specific tasks which 

can be easily composed into analysis pipelines, because the TSV table output goes to

`stdout` by default so they can be piped from one tool to another.

To get help for a specific command, do

```bash

schemist  --help

```

For the Python API, [see below](#python-api).

## Python API

**schemist** can be imported into Python to help make custom analyses.

```python

>>> import schemist as sch

```

## Documentation

Full API documentation is at [ReadTheDocs](https://schemist.readthedocs.org).