File Formats
Import formats
ChemStitch imports structures from seven formats:
| Format | Extension | Notes |
|---|---|---|
| SMILES | .smi, .smiles | Line notation, widely used |
| MOL V2000 | .mol | Standard 2D connection table |
| MOL V3000 | .mol | Extended format for large molecules |
| SDF | .sdf, .sd | Multi-molecule container; loads first molecule, notification shows "Loaded molecule 1 of N" |
| InChI | .inchi | IUPAC International Chemical Identifier |
| CDXML | .cdxml | ChemDraw XML format — import preserves structure; a stereochemistry warning notes that some ChemDraw-specific display properties may render differently |
| RXN | .rxn | Reaction scheme format with reactants and products |
Formats are auto-detected from file extension or content. Drag a file onto the browser window or use the import dialog.
Export formats
Export your structures from the download dropdown in the toolbar:
- • MOL V2000 — Standard 2D connection table
- • MOL V3000 — Extended format for large molecules
- • SDF — Multi-molecule container with properties
- • RXN — Reaction scheme format (available in reaction mode)
For publication-quality images, see the Publication Export section.
Note: CDXML export is not currently supported — ChemDraw XML is import-only. If you need to send structures to a ChemDraw user, export as MOL V2000 (universally compatible).
Clipboard operations
Copy your structure to the clipboard in three representations using the Copy dropdown:
- • SMILES — Compact line notation, ideal for pasting into databases or scripts
- • InChI — IUPAC International Chemical Identifier, useful for database searches
- • InChIKey — Fixed-length hash of the InChI, used for exact-match lookups in PubChem and other databases
Each copy operation shows a toast confirmation specifying the format (e.g., "SMILES copied"). If a structure has valence errors that prevent InChI generation, the toast explains the issue.
Format auto-detection
When you import a file, ChemStitch identifies the format automatically from the file extension or content structure. You do not need to select a format manually — drag the file in and the correct parser activates.