| Name | schemist JSON |
| Version |
0.0.1
JSON |
| download |
| home_page | None |
| Summary | Organizing and processing tables of chemical structures. |
| upload_time | 2024-10-12 17:37:09 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.8 |
| license | MIT License Copyright (c) [year] [fullname] Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |
| keywords |
science
chemistry
smiles
selfies
cheminformatics
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# ⬢⬢⬢ schemist
[](https://huggingface.co/spaces/scbirlab/chem-converter)
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 <command> --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).
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"description": "# \u2b22\u2b22\u2b22 schemist\n\n\n\n\n[](https://huggingface.co/spaces/scbirlab/chem-converter)\n\nCleaning, collating, and augmenting chemical datasets.\n\n- [Installation](#installation)\n- [Command-line usage](#command-line-usage)\n- [Python API](#python-api)\n- [Documentation](#documentation)\n\n## Installation\n\n### The easy way\n\nInstall the pre-compiled version from PyPI:\n\n```bash\npip install schemist\n```\n\n### From source\n\nClone the repository, then `cd` into it. 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 <command> --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>>> import schemist as sch\n```\n\n## Documentation\n\nFull API documentation is at [ReadTheDocs](https://schemist.readthedocs.org).\n",
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