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MoleditPy
A desktop editor for drawing chemical structures, editing 3D molecules, and preparing computational chemistry inputs.
Open source. 43 of 65 checklist features confirmed.
Official demo
Main canvas
Dark interface retains a white drawing canvas.
Default drawings
Caffeine
Paclitaxel
Cholesterol in 3D
- SMILES import automatically laid out and fitted all three 2D structures.
- Default 2D atom labels use blue nitrogen and red oxygen.
- Cholesterol generated a ball-and-stick model with explicit hydrogens.
- SVG export defaults to transparent background and can include hover highlights.
- Default PNG output was 918×522 pixels at 72 dpi.
Facts
- GitHub stars
- 11 stars on 6 Nov 2026
- First commit
- 30 Sept 2025
- Repository activity
- 2,162 commits, 6 contributors, last push 5 Nov 2026
- Latest version
- v5.1.3
- Version we tested
- 5.1.3
- Runs on
- macOS, Windows, Linux
- License
- GNU Lesser General Public License version 3 or later.
- Price
- Free
- Relies on
- RDKit. Custom Qt scene; RDKit supplies chemistry and molecular data conversion.
- Draws with
- Qt QGraphicsScene/QPainter for 2D; QSvgGenerator for SVG; PyVista/VTK for 3D.
- Chemistry from
- RDKit
- Interface
- PySide6 (Qt 6)
- Main language
- Python
- Other languages
- C++: Native RDKit chemistry
- Renderer
- Original: MoleditPy Qt AtomItem/BondItem renderer
- Third-party licenses
- Includes LGPL-3.0 (PySide6/Qt/Shiboken6) and GPL-2.0-or-later with the PyInstaller bootloader exception; RDKit and VTK use BSD-3-Clause.
- Download
- 180 MB
- Installed
- 738 MB
- Reaction layouts and several advanced chemistry functions require separately installed plugins.
- Standalone bundles cannot run plugins requiring additional Python packages.
- Core SDF is import-only; native export writes MOL despite broader README claims.
In use
Screenshots from our test of this version.
Single, double and triple bonds
Single, double, and triple bonds on the drawing canvas.
Wedge, hash and wavy bonds
Solid and hashed wedge bonds on the drawing canvas.
Ring tools
Cyclohexane and benzene on the canvas beneath ring tools.
Template library
Ring template tools and two rings on the canvas.
Charges, isotopes and atom labels
A structure with nitrogen and oxygen labels and element tools.
2D structure cleanup
The Clean Up 2D button beneath a drawing.
Formula and mass
Molecule analysis displays the formula, molecular weight, and exact mass.
Property estimates
Molecule analysis displays LogP and TPSA values.
3D model view
A ball-and-stick 3D model in the viewer.
MOL and SDF
A MOL file imported into the drawing canvas.
SMILES
Molecule analysis displays a SMILES field and Copy button.
InChI
Molecule analysis displays InChI and InChIKey fields.
Plugins
Plugin Manager shows installation instructions and plugin controls.
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, tested by running it: Drew single, double, triple bonds; changed existing bond orders. Opens the screenshot.Single, double and triple bondsDrew single, double, triple bonds; changed existing bond orders.hiroyokoyama.github.io
- Partly: Solid and hashed wedges drawn; no wavy bond control found. Opens the screenshot.Wedge, hash and wavy bondsSolid and hashed wedges drawn; no wavy bond control found.github.com
- Not establishedDative, hydrogen and quadruple bonds
- Not establishedChoose double-bond side
- Yes, tested by running it: Placed cyclohexane and benzene with dedicated toolbar tools. Opens the screenshot.Ring toolsPlaced cyclohexane and benzene with dedicated toolbar tools.github.com
- Not establishedChair and Haworth rings
- Yes, tested by running it: Dragging the alkyl-chain tool created a zigzag chain. Opens the cited page.Chain toolDragging the alkyl-chain tool created a zigzag chain.hiroyokoyama.github.io
- Partly: Ring templates work; User Templates contains no built-in structures. Opens the screenshot.Template libraryRing templates work; User Templates contains no built-in structures.github.com
- Yes, according to the manual: Save current structure as a reusable user template. Opens the cited page.Save your own templatesSave current structure as a reusable user template.hiroyokoyama.github.io
- Yes, according to the manual: Requires Group Template plugin; abbreviations place expanded chemical structures. Opens the cited page.Group abbreviationsRequires Group Template plugin; abbreviations place expanded chemical structures.github.com
- Partly: Charges and periodic-table elements; isotope editing unverified. Opens the cited page.Charges, isotopes and atom labelsCharges and periodic-table elements; isotope editing unverified.hiroyokoyama.github.io
- Yes, according to the manual: Toggle one or two radical electrons on an atom. Opens the cited page.Radicals and lone pairsToggle one or two radical electrons on an atom.hiroyokoyama.github.io
- Partly: N selected nitrogen mode; selected atom did not change. Opens the cited page.Keyboard drawingN selected nitrogen mode; selected atom did not change.hiroyokoyama.github.io
- Partly: Rectangle selection; rotate and plugin flips; lasso and molecular resizing unverified. Opens the cited page.Lasso select and transformsRectangle selection; rotate and plugin flips; lasso and molecular resizing unverified.github.com
- Yes, according to the manual: Requires 3D Molecule on 2D plugin for canvas rotation. Opens the cited page.Tilt drawings in perspectiveRequires 3D Molecule on 2D plugin for canvas rotation.hiroyokoyama.github.io
Reactions and mechanisms
- Yes, according to the manual: Requires Reaction Sketcher plugin: forward, equilibrium, resonance and retrosynthetic arrows. Opens the cited page.Reaction arrowsRequires Reaction Sketcher plugin: forward, equilibrium, resonance and retrosynthetic arrows.hiroyokoyama.github.io
- Yes, according to the manual: Requires Reaction Sketcher plugin; editable full-head and fishhook curved arrows. Opens the cited page.Curved mechanism arrowsRequires Reaction Sketcher plugin; editable full-head and fishhook curved arrows.hiroyokoyama.github.io
- Not establishedMachine-readable reactions
- Not establishedAtom mapping
- Not establishedOrbitals and symbols
Figures and layout
- Yes, according to the manual: Requires Reaction Sketcher plugin: fonts, subscript and superscript text formatting. Opens the cited page.Rich text captionsRequires Reaction Sketcher plugin: fonts, subscript and superscript text formatting.github.com
- Yes, according to the manual: Requires Reaction Sketcher plugin: editable shapes and square, round, curly brackets. Opens the cited page.Shapes, brackets and curvesRequires Reaction Sketcher plugin: editable shapes and square, round, curly brackets.hiroyokoyama.github.io
- Yes, according to the manual: Requires Reaction Sketcher plugin; align and distribute selected objects. Opens the cited page.Align and distributeRequires Reaction Sketcher plugin; align and distribute selected objects.hiroyokoyama.github.io
- Yes, according to the manual: Requires Reaction Sketcher plugin; group and ungroup molecular items and annotations. Opens the cited page.Group and ungroupRequires Reaction Sketcher plugin; group and ungroup molecular items and annotations.hiroyokoyama.github.io
- Yes, according to the manual: Clean Up 2D tidies molecular drawing coordinates. Opens the cited page.2D structure cleanupClean Up 2D tidies molecular drawing coordinates.hiroyokoyama.github.io
- Not establishedJournal drawing styles
- Yes, according to the manual: Settings Saver plugin saves and reloads drawing-settings presets. Opens the cited page.Reusable custom stylesSettings Saver plugin saves and reloads drawing-settings presets.github.com
- Yes, according to the manual: Requires Reaction Sketcher plugin; individually colors text and annotation objects. Opens the cited page.Color controlRequires Reaction Sketcher plugin; individually colors text and annotation objects.github.com
- Partly: Reaction Sketcher plugin adds selection halos; PNG/SVG exports remove them. Opens the cited page.Color highlightingReaction Sketcher plugin adds selection halos; PNG/SVG exports remove them.github.com
- Not establishedPage layout and multipage
- Not establishedImported pictures
- Not establishedTLC plates and tables
Chemistry intelligence
- Yes, according to the manual: Flags valence problems before 3D conversion. Opens the cited page.Structure checkingFlags valence problems before 3D conversion.github.com
- Yes, according to the manual: Computes R/S and E/Z; checks converted stereochemistry. Opens the cited page.R/S and E/Z labelsComputes R/S and E/Z; checks converted stereochemistry.hiroyokoyama.github.io
- Yes, tested by running it: Cholesterol C27H46O; molecular weight 386.6640; exact mass 386.3549. Opens the screenshot.Formula and massCholesterol C27H46O; molecular weight 386.6640; exact mass 386.3549.hiroyokoyama.github.io
- Yes, tested by running it: Cholesterol LogP 7.389 and TPSA 20.23 displayed. Opens the screenshot.Property estimatesCholesterol LogP 7.389 and TPSA 20.23 displayed.hiroyokoyama.github.io
- No: No naming tool; SMILES importer rejected ethanol. Opens the cited page.Name to structureNo naming tool; SMILES importer rejected ethanol.github.com
- Partly: PubChem Structure Identifier plugin retrieves IUPAC names for database matches. Opens the cited page.Structure to namePubChem Structure Identifier plugin retrieves IUPAC names for database matches.github.com
- Yes, according to the manual: Requires NMR Predictor (nmrshiftdb2); coverage depends on reference data. Opens the cited page.NMR predictionRequires NMR Predictor (nmrshiftdb2); coverage depends on reference data.github.com
- Not establishedR-groups and query structures
- Not establishedPolymers and repeat units
- Not establishedPeptides and nucleic acids
- Yes, according to the manual: Requires DECIMER Image Importer plugin and model dependencies. Opens the cited page.Image to structureRequires DECIMER Image Importer plugin and model dependencies.github.com
- Yes, according to the manual: Requires PubChem Name Resolver plugin. Opens the cited page.Online structure lookupRequires PubChem Name Resolver plugin.github.com
- Yes, tested by running it: SMILES conversion succeeded; dragging rotated cholesterol in depth. Opens the screenshot.3D model viewSMILES conversion succeeded; dragging rotated cholesterol in depth.hiroyokoyama.github.io
- Yes, according to the manual: Requires CIF Viewer plugin; supports unit cells and supercells. Opens the cited page.Crystal structuresRequires CIF Viewer plugin; supports unit cells and supercells.github.com
Files and exchange
- No: Opening CDXML probe rejected; required PME project extension. Opens the cited page.CDXML import and exportOpening CDXML probe rejected; required PME project extension.
- Not establishedCDX import and export
- Yes, tested by running it: MOL round-trip succeeded; cholesterol SDF loaded in 3D. Opens the screenshot.MOL and SDFMOL round-trip succeeded; cholesterol SDF loaded in 3D.hiroyokoyama.github.io
- Yes, tested by running it: Imported all fixtures; generated and copied cholesterol SMILES in Analysis. Opens the screenshot.SMILESImported all fixtures; generated and copied cholesterol SMILES in Analysis.hiroyokoyama.github.io
- Yes, tested by running it: Analysis generated cholesterol InChI and InChIKey. Opens the screenshot.InChIAnalysis generated cholesterol InChI and InChIKey.hiroyokoyama.github.io
- Not establishedRXN files
- Yes, tested by running it: Native transparent SVG exports saved for all fixtures. Opens the cited page.SVG exportNative transparent SVG exports saved for all fixtures.hiroyokoyama.github.io
- No: No PDF/Print command; Command-P opened no dialog. Opens the cited page.PDF exportNo PDF/Print command; Command-P opened no dialog.
- Partly: PNG saved at 918×522 pixels, 72 dpi; no resolution control. Opens the cited page.High-resolution PNGPNG saved at 918×522 pixels, 72 dpi; no resolution control.github.com
- Partly: Windows Paste from ChemDraw plugin imports only; no reverse copy. Opens the cited page.Paste to and from ChemDrawWindows Paste from ChemDraw plugin imports only; no reverse copy.github.com
- Not establishedEditable in Word or PowerPoint
- Not establishedWindows Office OLE
APIs and automation
- Yes, according to the manual: Documented in-process Python PluginContext API drives the editor. Opens the cited page.Python APIDocumented in-process Python PluginContext API drives the editor.github.com
- Not establishedJavaScript or TypeScript API
- Partly: Launcher and plugin installer; no headless conversion or rendering. Opens the cited page.Command-line toolLauncher and plugin installer; no headless conversion or rendering.github.com
- Yes, according to the manual: Requires MCP Server plugin; controls the running editor. Opens the cited page.AI agent controlRequires MCP Server plugin; controls the running editor.github.com
- Yes, according to the manual: Requires Chat with Molecule Neo plugin and configured model access. Opens the cited page.Built-in AI assistantRequires Chat with Molecule Neo plugin and configured model access.github.com
Embedding and extension
- Yes, according to the manual: Python plugins extend menus, file handling, analysis and rendering. Opens the cited page.PluginsPython plugins extend menus, file handling, analysis and rendering.hiroyokoyama.github.io
- Not established: Standalone Python package; no editor embedding API confirmed.Embed in your own appStandalone Python package; no editor embedding API confirmed.github.com