VirMolAnalyte V2.0 modules

Five GUI Modules

A compact map of the current desktop interface: guided AI workflow, molecular screening, fragment attribution, database creation, and standalone structure drawing.

View module list See workflow map

This section documents the current main tabs in virmol_gui.py. The order below matches the GUI tab order:

1. AI Assistant
2. Molecular Analysis
3. Fragment Analysis
4. Database Management
5. Other Tool

For a first run, most users should start with Molecular Analysis unless they want the guided workflow in AI Assistant.

Module list

GUI order	Tab name	Main purpose	Manual
1	AI Assistant	Guided screening workflow, preflight diagnosis, offline tools, and optional cloud LLM interpretation	Open
2	Molecular Analysis	13C/DEPT preprocessing, manual peak input, database screening, hit table, compound details, and export	Open
3	Fragment Analysis	Masking AAS attribution, positive fragment extraction, spectrum maps, fusion, and fragment-level AI review	Open
4	Database Management	Build custom .npz molecular libraries from SMILES files	Open
5	Other Tool	Standalone SMILES structure drawing and HD SVG/PNG export	Open

Recommended workflow

flowchart LR
  A["AI Assistant (optional guided entry)"] --> B["Molecular Analysis"]
  B --> C["Fragment Analysis"]
  D["Database Management"] -. "custom .npz" .-> B
  E["Other Tool (standalone drawing)"]

1. AI Assistant: optional guided entry point for users who want workflow help or LLM-assisted interpretation.
2. Molecular Analysis: required for database screening and the main source of candidate hits.
3. Fragment Analysis: optional downstream evidence workflow after screening results exist.
4. Database Management: independent utility for creating custom databases used by Molecular Analysis.
5. Other Tool: independent SMILES drawing/export utility.

Demo run screenshots

These screenshots were captured from the live GUI after running the bundled demo Bruker data (test/NMRsample/4/pdata/1, test/NMRsample/8/pdata/1, test/NMRsample/6/pdata/1) with the default peak-picking thresholds, Plant database, CNF/CTNF filters, and the default FPAACS evaluator.

AI Assistant tab with workflow status and offline/LLM actions.

Molecular Analysis before running the demo data.

Peak detection view after clicking Submit.

Merged 13C/DEPT spectrum and generated peak table.

Default Plant database screening results.

Top-hit Compound Details window with structure and shift comparison.

Fragment Analysis tab after screening results are available.

Database Management tab.

Other Tool tab for SMILES structure drawing.

Global menus

The current GUI uses a top menu bar and no default toolbar.

Menu	Main actions
File	New / Open / Save project, import NMR or SMILES, export results to CSV, exit
Edit	Preferences for AI / LLM provider and API key
View	Status bar toggle, reset layout
Tools	Peak Detection, Data Analysis, Database Management, Settings placeholder
Help	Documentation, About VirMolAnalyte

Shared output directory

Automatic outputs are written to:

GUI_result_files/

Common files include:

File	Typical source
NMR-1D.csv	Molecular Analysis Merge, solvent removal, impurity removal, or export
Result.csv	Molecular Analysis Start Analysis or Export Results Folder
analysis_parameters.txt	Export Results Folder
Top20_structures_5x4.png	Export Results Folder
ai_log.jsonl	AI Assistant LLM actions