Skip to content

Quick Start

VirMolAnalyte molecular analysis results

Start with VirMolAnalyte V2.0

Choose the fastest path from Bruker spectra, a prepared peak list, or the AI Assistant into database screening and fragment evidence.

Watch video tutorials Choose a workflow

This page follows the current GUI layout and button names. The main tabs are: AI Assistant, Molecular Analysis, Fragment Analysis, Database Management, and Other Tool.

For most users, start from Molecular Analysis. Use AI Assistant when you want a guided workflow or LLM-assisted interpretation.

Video tutorials

1. Database search from raw data
Use Molecular Analysis with Bruker 1D NMR folders, run Submit / Merge, load a database, then click Start Analysis.

2. Database searching from peak list
Paste a peak list into Manual peak input, load a database, and run screening without spectral preprocessing.

3. Database searching from AI Agent
Use AI Assistant to run a guided screening workflow from pasted or loaded peak data.

4. Fragment Analysis
After screening, switch to Fragment Analysis, run Run masking attribution, then Extract positive fragments + map.

Legacy quick demo This older short demo shows bundled Bruker data, default peak-picking thresholds, Plant database, CNF/CTNF filters, and FPAACS ranking.

Choose a workflow

Your starting point GUI tab Recommended path
Bruker pdata/1 folders Molecular Analysis Path A
Existing ppm, type peak list Molecular Analysis Path B
Want guided automation AI Assistant Path C
Want fragment evidence after screening Fragment Analysis Path D
Only need to draw/export a structure Other Tool Path E

Path A: Raw Bruker 1D data -> Top hits

  1. Open Molecular Analysis.
  2. In Spectrum Preprocessing, set the three folders: 13C_NMR, DEPT90, and DEPT135. Each should usually point to a Bruker .../pdata/1 directory.
  3. Check Peak Detection Parameters. The demo values are already filled for the bundled example data.
  4. Click Submit to detect peaks.
  5. Click Merge to create the combined peak table. This writes GUI_result_files/NMR-1D.csv.
  6. Optional: use Solvent Removal or Impurity Removal, then click the corresponding Submit button.
  7. In Database Analysis, choose a database and click Load Database. For a custom .npz, use Load Other Database.
  8. Confirm filters and evaluator. Default screening uses CNF, CTNF, and FPAACS.
  9. Click Start Analysis.
  10. Review Analysis Results. Click a row to open Compound Details.
  11. Use Export Results Folder to save Result.csv, NMR-1D.csv, a Top-20 structure grid, and analysis parameters.
  12. Optional: click Copy methods text or AI: Top 5 ->.

Path B: Peak list only -> Top hits

  1. Open Molecular Analysis.
  2. In Database Analysis, paste peaks into Manual peak input.
  3. Use one peak per line:
131.2, s
116.3, d
36.8, t
27.1, q
  1. Accepted type labels are q, t, d, s; CH3, CH2, CH, and C are also accepted.
  2. Choose a database and click Load Database.
  3. Confirm filters and evaluator.
  4. Click Start Analysis.
  5. Review Analysis Results and open Compound Details if needed.

Path C: AI Assistant guided screening

  1. Open AI Assistant.
  2. Use Open file..., Use NMR-1D.csv, Example case, or paste peaks directly into the chat input.
  3. Check the workflow/default settings shown in the AI panel.
  4. Run the guided screening action from the AI Assistant.
  5. When the workflow finishes, results appear in Molecular Analysis and downstream fragment tools become available.
  6. For cloud LLM interpretation, open Preferences first and configure an API key.

Path D: Fragment Analysis after screening

  1. Finish Start Analysis in Molecular Analysis first. At least one hit is required.
  2. Open Fragment Analysis.
  3. Set Top N candidates to analyze and masking parameters if needed.
  4. Click Run masking attribution.
  5. Select a completed candidate from the candidate selector.
  6. Click Extract positive fragments + map.
  7. Optional: run intra-molecular fusion or Run fusion analysis (Top combinations).
  8. Use Save HD (SVG/PNG) for publication-quality structure exports.
  9. Optional: use the AI buttons for signal assignment or fragment evidence review.

Path E: Draw a structure only

  1. Open Other Tool.
  2. Paste a SMILES string.
  3. Click Draw Structure.
  4. Optional: enable atom index, rotate, or flip the structure.
  5. Click Save HD (SVG/PNG).

Before clicking Start Analysis

  • Database has been loaded. The button changes to a loaded state.
  • Peaks are available from GUI_result_files/NMR-1D.csv or Manual peak input.
  • At least one evaluator is selected. Default: FPAACS.
  • CNF / CTNF / MW filters match the sample and database scope.

Before Fragment Analysis

  • Start Analysis has finished successfully.
  • Analysis Results contains at least one candidate.
  • Experimental peaks are still available from manual input or GUI_result_files/NMR-1D.csv.
  • For AI review, configure Preferences if cloud LLM output is needed.

Output files

Default output folder:

GUI_result_files/

Common files:

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

Next steps

Goal Read
Every control on Molecular Analysis Molecular Analysis
Masking modes and fragment fusion Fragment Analysis
LLM/API setup AI Assistant
Custom .npz library Database Management
Standalone structure drawing Other Tool