readabilityone / epam-ketcher

Web-based molecule sketcher

Ketcher

Ketcher is an open-source web-based chemical structure editor incorporating high performance, good portability, light weight, and ability to easily integrate into a custom web-application. Ketcher is designed for chemists, laboratory scientists and technicians who draw structures and reactions.

Key Features

• ⚡️ Fast 2D structure representation that satisfies common chemical drawing standards
• 💠 3D structure visualization
• 📝 Template library (including custom and user's templates)
• 🔩 Add atom and bond basic properties and query features, add aliases and Generic groups
• 🌀 Stereochemistry support during editing, loading, and saving chemical structures
• ➿ Storing history of actions, with the ability to rollback to previous state
• 💾 Ability to load and save structures and reactions in MDL Molfile or RXN file format, InChI String, ChemAxon Extended SMILES, ChemAxon Extended CML file formats
• 🔬 Zoom in/out, hotkeys, cut/copy/paste
• 🔮 OCR - ability to recognize structures at pictures (image files) and reproduce them
• 📋 Copy and paste between different chemical editors
• 🛠️ Settings support (Rendering, Displaying, Debugging)
• 📷 Use of SVG to achieve best quality in-browser chemical structure rendering

Editor builtin tools:

• Atom Tool, Bond Tool, and Template Tool to draw and edit structures
• Aromatize/De-aromatize Tool
• Calculate CIP Descriptors Tool
• Structure Check Tool
• MW and Structure Parameters Calculate Tool
• Select, modify, and erase connected and unconnected atoms and bonds using Selection Tool, or using Shift key
• Advanced Structure Clean up Tool (+ stereochemistry checking and structure layout)
• Simple Structure Clean up Tool (checks bonds length, angles and spatial arrangement of atoms)
• Easy to use R-Group and S-Group tools (Generic, Multiple group, SRU polymer, peratom, Data S-Group)
• Reaction Tool (reaction generating, manual and automatic atom-to-atom mapping)
• Flip/Rotate Tool

Installation and usage

At this moment Ketcher can be embedded into your application in two ways:

• as a react component library
• as ready-to-run application (to find desired version please look at Assets block of releases). The application can be injected as IFrame or a separate page.

FAQ

How to use react component library

Look at the following link for details.

Configure indigo service

You can find the instruction for service installation here.

Packages

Project	Status	Description
ketcher-core		Core functionality: domain, shared services, functions and interface declarations
ketcher-standalone		Contains only the functionality necessary to start Ketcher in standalone mode
ketcher-react		Package contains only the functionality necessary to define components.

3D Viewer

Ketcher uses Miew-React for viewing and editing data in 3D.

You can find the latest version of Miew-React here. The last checked version - 1.0.0.

Ketcher API

Ketcher can return drawn structures using the following methods:

getSmiles(isExtended = false): Promise<string> – returns string representation of drawn structure in SMILES format.
Parameters: isExtended: boolean. By default, false. Indicates, whether extended SMILES format needs to be used.

getMolfile(molfileFormat): Promise<string> – returns string representation of drawn structure in MOL-format.
Parameters: molfileFormat: 'v2000' | 'v3000'. Optional, by default, 'auto'. Indicates, in which format result will be returned. If no desired format is provided, then it is chosen automatically, depending on drawn structure.

getRxn(molfileFormat): Promise<string> – returns string representation of drawn structure in RXN-format.
Parameters: molfileFormat: 'v2000' | 'v3000'. Optional, by default, 'v2000'. Indicates, in which format result will be returned.

getKet(): Promise<string> – returns string representation of drawn structure in internal Ket-format.

getSmarts(): Promise<string> – returns string representation of drawn structure in Smarts-format.

getCml(): Promise<string> – returns string representation of drawn structure in Cml-format.

getSdf(molfileFormat): Promise<string> – returns string representation of drawn structure in Sdf-format.
Parameters: molfileFormat: 'v2000' | 'v3000'. Optional, by default, 'v2000'. Indicates, in which format result will be returned.

getCDXml(): Promise<string> – returns string representation of drawn structure in CDXml-format.

getCDX(): Promise<string> – returns string representation of drawn structure in CDX-format.

getInchi(withAuxInfo = false): Promise<string> – returns string representation of drawn structure in Inchi-format.
Parameters: withAuxInfo: boolean. Optional, by default, false.

getInchiKey(): Promise<string> – returns string representation of drawn structure in InChiKey-format.

containsReaction(): boolean – returns true, in case drawn structure contains reaction; false otherwise.

isQueryStructureSelected(): boolean – returns true, in case selected structure has query.

setMolecule(structure: string): Promise<void> – draws passed structure on the canvas. Before drawing passed structure, current structure is removed.
Parameters: structure: string. Structure is a string in any supported format.

addFragment(structure: string): Promise<void> – adds passed structure on the canvas. Current structure is not changed.
Parameters: structure: string. Structure is a string in any supported format.

layout(): Promise<void> – performs layout algorithm for drawn structure.

recognize(image: Blob, version?: string): Promise<Struct> – recognizes a structure from image.
Parameters: image: Blob – image to recognize. Returns Struct – object, which represents recognized structure.

generateImage(data: string, options: {  
    outputFormat: 'png' | 'svg';
    backgroundColor: string;
    bondThickness: number;
}): Promise<Blob>

Generates image from passed structure.
Parameters:
data – string representation of structure in any supported format.
options – object with the following properties:
* outputFormat – can be 'png' or 'svg'
* backgroundColor – image background color
* bondThickness – thickness of bonds in output structure

Settings

You can add extra configuration in editor.setSetting

Allowed parameters:

• disableQueryElements: Disable the elements from the Extended Table

ketcher.setSettings({ "disableQueryElements": ["Pol", "CYH", "CXH"] })

• general.dearomatize-on-load: Dearomatize the molecule when ketcher application starts

ketcher.setSettings({ "general.dearomatize-on-load": true })

• ignoreChiralFlag: Ignore the chiral flag from .mol files

ketcher.setSettings({ "ignoreChiralFlag": true })

Contribution

See Contributing Guide.

License

Apache 2.0

Please read LICENSE and NOTICE for details.

Copyright (c) 2021 EPAM Systems, Inc.