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MolGenDraw
A Windows application for drawing molecular structures and editing multi-record SDF and SMILES databases.
Free. 14 of 65 checklist features confirmed.
Main canvas
Needs Windows
Needs Windows
Default drawings
Needs Windows
Caffeine
Needs Windows
Paclitaxel
Needs Windows
Cholesterol in 3D
Facts
- GitHub stars
- 0 stars on 6 Nov 2026
- First commit
- 27 Jul 2026
- Repository activity
- 17 commits, 1 contributor, last push 30 Oct 2026
- Latest version
- v1.176
- Runs on
- Windows
- License
- Proprietary freeware; all rights reserved.
- Price
- Free
- Relies on
- RDKit. Vendor documents RDKit; canvas provenance is not publicly established.
- Chemistry from
- RDKit
- Interface
- PySide6
- Main language
- C++
- Other languages
- Python: Application and custom Pillow 3D renderer; Java: Local OPSIN name parsing
- Renderer
- Borrowed: RDKit MolDraw2D Cairo
- Third-party licenses
- Not established
- Download
- 150 MB
- Windows 10/11 64-bit only; executable is unsigned.
- Advanced reaction drawing and arrow tools are planned.
- Vector PDF output and PNG print resolution are undocumented.
Features
- Tested by running it
- Seen in the app
- The manual says yes
- Partly, with the reason shown
- Not supported
- Not established, which is not the same as no
Select a mark for its proof. A filled mark opens our screenshot, or the manual if the check left nothing to picture. A ring opens the manual.
Drawing structures
- Yes, according to the manual: vendor claim; manually cycle single, double and triple bonds. Opens the cited page.Single, double and triple bondsvendor claim; manually cycle single, double and triple bonds.github.com
- Not establishedWedge, hash and wavy bonds
- Not establishedDative, hydrogen and quadruple bonds
- Not establishedChoose double-bond side
- Yes, according to the manual: vendor claim; benzene, cyclohexane and cyclopentane ring tools. Opens the cited page.Ring toolsvendor claim; benzene, cyclohexane and cyclopentane ring tools.github.com
- Not establishedChair and Haworth rings
- Not establishedChain tool
- Yes, according to the manual: Phenolphthalein template shown in the structure library. Opens the cited page.Template libraryPhenolphthalein template shown in the structure library.github.com
- Yes, according to the manual: Save the current molecule as a reusable template. Opens the cited page.Save your own templatesSave the current molecule as a reusable template.github.com
- Not establishedGroup abbreviations
- Not established: Element and charge controls shown; isotope editing undocumented.Charges, isotopes and atom labelsElement and charge controls shown; isotope editing undocumented.
- Not establishedRadicals and lone pairs
- Not establishedKeyboard drawing
- Not established: Selection, rotation and flips documented; resizing unverified.Lasso select and transformsSelection, rotation and flips documented; resizing unverified.
- Not establishedTilt drawings in perspective
Reactions and mechanisms
- No: Advanced reaction drawing and arrow tools are planned. Opens the cited page.Reaction arrowsAdvanced reaction drawing and arrow tools are planned.raw.githubusercontent.com
- Not establishedCurved mechanism arrows
- Not establishedMachine-readable reactions
- Not establishedAtom mapping
- Not establishedOrbitals and symbols
Figures and layout
- Not establishedRich text captions
- Not establishedShapes, brackets and curves
- Not establishedAlign and distribute
- Not establishedGroup and ungroup
- Not established2D structure cleanup
- Not establishedJournal drawing styles
- Not established: Bond-width controls documented; reusable styles unverified.Reusable custom stylesBond-width controls documented; reusable styles unverified.
- Not establishedColor control
- Not establishedColor highlighting
- Not established: Only single-page A4 report export documented.Page layout and multipageOnly single-page A4 report export documented.
- Not establishedImported pictures
- Not establishedTLC plates and tables
Chemistry intelligence
- Yes, according to the manual: vendor claim; real-time RDKit sanitization errors flag invalid structures. Opens the cited page.Structure checkingvendor claim; real-time RDKit sanitization errors flag invalid structures.github.com
- Not establishedR/S and E/Z labels
- Yes, according to the manual: Formula, molecular weight and exact mass displayed. Opens the cited page.Formula and massFormula, molecular weight and exact mass displayed.github.com
- Not establishedProperty estimates
- Yes, according to the manual: PubChem name lookup and IUPAC-to-SMILES batch generation. Opens the cited page.Name to structurePubChem name lookup and IUPAC-to-SMILES batch generation.github.com
- Yes, according to the manual: IUPAC name generation requires an internet connection. Opens the cited page.Structure to nameIUPAC name generation requires an internet connection.github.com
- Not establishedNMR prediction
- Not establishedR-groups and query structures
- Not establishedPolymers and repeat units
- Not establishedPeptides and nucleic acids
- Yes, according to the manual: Batch PNG/JPG recognition exports editable MOL files. Opens the cited page.Image to structureBatch PNG/JPG recognition exports editable MOL files.github.com
- Yes, according to the manual: PubChem retrieval loads structures onto the canvas. Opens the cited page.Online structure lookupPubChem retrieval loads structures onto the canvas.github.com
- Yes, according to the manual: Mouse rotation; wireframe, sticks and ball-and-stick display modes. Opens the cited page.3D model viewMouse rotation; wireframe, sticks and ball-and-stick display modes.github.com
- Not establishedCrystal structures
Files and exchange
- Not establishedCDXML import and export
- Not establishedCDX import and export
- Yes, according to the manual: Reads/writes MOL and SDF; includes multi-record database editing. Opens the cited page.MOL and SDFReads/writes MOL and SDF; includes multi-record database editing.github.com
- Yes, according to the manual: Reads/writes SMILES, including multi-record SMI collections. Opens the cited page.SMILESReads/writes SMILES, including multi-record SMI collections.github.com
- Yes, according to the manual: Generates InChI and InChIKey offline. Opens the cited page.InChIGenerates InChI and InChIKey offline.github.com
- Not establishedRXN files
- Not establishedSVG export
- Not established: PDF reports documented; vector output unverified.PDF exportPDF reports documented; vector output unverified.
- Not established: Transparent PNG export documented; 300 dpi output unverified.High-resolution PNGTransparent PNG export documented; 300 dpi output unverified.
- Not establishedPaste to and from ChemDraw
- Not establishedEditable in Word or PowerPoint
- Not establishedWindows Office OLE
APIs and automation
- Not establishedPython API
- Not establishedJavaScript or TypeScript API
- Not establishedCommand-line tool
- Not establishedAI agent control
- Not establishedBuilt-in AI assistant
Embedding and extension
- Not establishedPlugins
- Not established: Standalone Windows executable; no embedding interface documented.Embed in your own appStandalone Windows executable; no embedding interface documented.github.com