Metadata-Version: 2.3
Name: residuum
Version: 0.1.0a2
Summary: Converting peptidoforms to residue SMILES using the PSI-MOD CV
Keywords: proteomics,peptides,residues,proforma,smiles,psi-mod,mass-spectrometry
Author: Ralf Gabriels
License: Apache-2.0
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Requires-Dist: pronto>=2.7.0
Requires-Dist: rdkit>=2023.0.0
Requires-Dist: pyteomics>=4.6.0
Requires-Python: >=3.11
Project-URL: Documentation, https://residuum.readthedocs.io
Project-URL: Homepage, https://github.com/CompOmics/residuum
Project-URL: Issues, https://github.com/CompOmics/residuum/issues
Project-URL: Repository, https://github.com/CompOmics/residuum
Description-Content-Type: text/markdown

# Residuum

Converting peptidoforms to residue SMILES using the PSI-MOD CV

## Overview

Residuum converts peptide sequences in ProForma notation to a list of residue-level SMILES
representations. It resolves modifications through the PSI-MOD ontology, supporting multiple
modification formats.

## Features

- **ProForma parsing**: Leverage Pyteomics for full ProForma v2 support
- **PSI-MOD resolving**: Query modifications by accession, name, or synonym
- **Multiple formats**: Support MOD:XXXXX, UNIMOD:XXX, modification names, custom SMILES
- **Smart matching**: Exact, approximate (parent terms), and fallback strategies
- **Terminal handling**: Automatic N-term/C-term SMILES reformatting to add H2N- and -COOH groups

## Installation

```bash
pip install residuum
```
