ScopeMap

Generate Space
File Upload
Checkpoint Control
Upload Substrates

Usage Guide

Generate Space

Purpose: Create a molecular space from natural language descriptions.

How to use:

  1. Enter a description of desired molecular scaffolds (e.g., "aromatic aldehydes", "biphenyl scaffolds")
  2. Click Submit to generate SMARTS patterns
  3. Review extracted substructures and adjust molecular weight filters if needed
  4. Click Search Molecules to find matching compounds
  5. Click Use Space to generate the chemical space
File Upload

Purpose: Upload your own molecular dataset for sampling.

How to use:

  1. Prepare a CSV file with at least a SMILES column
  2. Optional: Include Index column (auto-generated if missing)
  3. Click Choose File and select your CSV
  4. Click Upload to process the data
  5. Wait for descriptor calculation and UMAP visualization

Note: Large datasets may take several minutes to process.

Sampling Control

Purpose: Intelligently sample molecules from your chemical space.

How to use:

  1. Set Batch Size (molecules per iteration)
  2. Set Target Samples (total desired molecules)
  3. Adjust Repulsion Strength (higher = more diverse sampling)
  4. Click Start Sampling to begin
  5. Review proposed molecules and mark as Keep/Exclude
  6. Repeat until target is reached
Checkpoint Management

Purpose: Save and restore sampling progress.

Download Checkpoint:

  • Click Download Checkpoint to save current progress
  • File includes all sampling decisions and current state

Upload Checkpoint:

  • Select a previously saved checkpoint file
  • Click Upload to restore that sampling state
  • Continue sampling from where you left off
Evaluation Tools

Purpose: Assess the quality of your sampling strategy.

How to use:

  1. Prepare a CSV file with your selected molecules
  2. Click Choose File in the Evaluation section
  3. Click Evaluate Sampling to analyze
  4. Review U-Score, R-Score
Quick Start

Method 1 - Generate from Description:

Generate Space → Enter "aromatic aldehydes with biphenyl scaffolds" → Submit → Search → Use Space → Start Sampling

Method 2 - Upload Your Data:

File Upload → Choose CSV file → Upload → Start Sampling → Review and select molecules