Batch Analyze an SDF Library
Import a multi-molecule SDF file and compute properties for up to 500 compounds in one step.
What you'll accomplish
By the end of this guide, you'll have imported a multi-molecule SDF file, run batch property calculations on the entire library, sorted and reviewed results in a table, and exported an enriched SDF file with computed properties appended.
When to use batch analysis
Batch analysis is useful when you have a compound library and need to quickly characterize all molecules — for example, screening a virtual library for drug-likeness, reviewing a vendor catalog for Lipinski compliance, or preparing a table of properties for a publication or presentation.
ChemStitch processes up to 500 molecules per batch. For larger libraries, split your SDF file into chunks.
Step 1: Prepare your SDF file
SDF (Structure-Data File) is the standard container format for multi-molecule datasets. If your compounds are in a different format (SMILES list, CSV with SMILES column), convert them to SDF using a tool like Open Babel or RDKit before importing.
Each molecule in the SDF can have associated data fields, but only the structure itself is used for property computation.
Step 2: Import the SDF file
Drag your SDF file onto the browser window or use the import dialog (Ctrl+O). ChemStitch loads the first molecule onto the canvas and displays a persistent notification bar showing "Loaded molecule 1 of N" where N is the total count.
The notification bar stays visible until you dismiss it, giving you access to the batch analysis button.
Step 3: Run batch analysis
Click "Analyze All (N)" in the SDF notification bar. ChemStitch sends the entire library to the backend for processing. The backend computes six properties for each molecule: molecular weight, logP (Wildman-Crippen), hydrogen bond donors, hydrogen bond acceptors, topological polar surface area, and rotatable bonds.
Processing time depends on the library size. A 500-molecule library typically completes in a few seconds.
Step 4: Review results
Results appear in a sortable table. Click any column header to sort by that property — for example, click "MW" to sort by molecular weight, or "logP" to rank by lipophilicity.
The table includes a Lipinski evaluation column. Molecules that violate the Rule of Five show a warning icon with "FAIL" text, making it easy to identify compounds outside the drug-like chemical space. The logP column specifies the computational method: "logP (Wildman-Crippen)".
If an individual molecule has a structural issue (invalid SMILES, valence error), that row shows an error message. One problematic molecule does not fail the entire batch.
Step 5: Export enriched SDF
After batch analysis, export an enriched SDF file with computed properties appended to each molecule record. Click the export button to download the file.
The enriched SDF includes all original molecule data plus the six computed properties. This file can be imported directly into other cheminformatics tools (DataWarrior, KNIME, Pipeline Pilot), databases, or visualization platforms with all properties intact.
Tips for effective batch analysis
- • Sort by Lipinski column first — This immediately separates drug-like compounds from non-drug-like ones.
- • Use the enriched export — Downloading the enriched SDF preserves your analysis results. You don't need to re-run the computation if you return to the data later.
- • Combine with AI chat — After reviewing the table, click on an interesting molecule to load it onto the canvas. Then use the AI to explore it further — predict reactions, plan a synthesis route, or look up similar compounds in PubChem.