Batch Analysis

SDF import for multi-molecule files

Import an SDF file containing multiple molecules. ChemStitch loads the first molecule onto the canvas and displays a persistent notification bar showing "Loaded molecule 1 of N."

SDF (Structure-Data File) is the standard container format for multi-molecule datasets. It is widely used for compound libraries, screening collections, and database exports.

Batch property computation

Click "Analyze All (N)" in the SDF notification bar to compute properties for every molecule in the file. The backend processes up to 500 molecules, calculating molecular weight, logP, hydrogen bond donors, hydrogen bond acceptors, TPSA, and rotatable bonds for each structure.

Individual molecule failures are shown inline in the results table — a single problematic structure does not fail the entire batch.

Results table

Batch results appear in a sortable table. Click any column header to sort by that property.

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)" — the Wildman-Crippen method is a fragment-based approach for estimating the octanol-water partition coefficient, and is the standard logP method used in RDKit.

Enriched SDF export

After batch analysis, export an enriched SDF file with computed properties appended to each molecule record. This file can be imported into other cheminformatics tools, databases, or visualization platforms with all properties intact.