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Add graphical single-entry molecular workbench - #2

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PerinMu merged 4 commits into
mainfrom
agent/gui-modification-builder
Aug 4, 2026
Merged

Add graphical single-entry molecular workbench#2
PerinMu merged 4 commits into
mainfrom
agent/gui-modification-builder

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@PerinMu

@PerinMu PerinMu commented Aug 4, 2026

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Summary

  • add an optional bilingual Streamlit workbench for entering molecules and sequences one record at a time
  • provide a visual peptide editor for residue-position PTMs, N/C termini, backbone N-methylation, D residues, and editable generated notation
  • expose representation conversion, Morgan/RDKit/MACCS/Atom Pair/Torsion/k-mer fingerprints, and molecular descriptors
  • show result cards with formula, exact mass, charge, heavy atoms, canonical SMILES, 2D structure, and per-result downloads
  • retain successful entries in session history with individual removal and complete JSON/CSV export
  • add a custom side-chain/N-terminal/C-terminal modification library with shared runtime validation and registry import/export
  • expose both moltranscode gui and moltranscode-gui while keeping Streamlit optional
  • document installation, the manual workflow, local-only processing, and network-binding precautions

Validation

  • ruff check .
  • pytest: 64 passed
  • Streamlit AppTest: bilingual UI, visual multi-PTM peptide editing, terminal groups, InChIKey conversion, result metrics, 2D drawing, history, and downloads
  • Streamlit AppTest: custom AzidoLys registration immediately available in the peptide editor
  • Streamlit AppTest: single SMILES to MACCS fingerprint workflow
  • live local server health check on 127.0.0.1:8501
  • built moltranscode-0.2.0-py3-none-any.whl and verified GUI modules plus entry points are packaged

Notes

The GUI processes one record at a time and retains history only for the active session. Batch workflows remain in the CLI. It exports existing schema_version 1 registry JSON and does not upload structures to a hosted service.

@PerinMu PerinMu changed the title Add graphical modification builder Add graphical single-entry molecular workbench Aug 4, 2026
@PerinMu
PerinMu marked this pull request as ready for review August 4, 2026 13:27
@PerinMu
PerinMu merged commit 7cf34c2 into main Aug 4, 2026
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