Chemical Drawing

Draw chemical structure

Overview

Labii Chemical Drawing Widgets are a set of interactive tools designed to facilitate the creation and manipulation of chemical structures and reactions. These widgets are commonly used in scientific research, chemical education, and drug discovery processes.

The Labii Chemical Drawing Widgets offer a user-friendly interface that allows scientists, chemists, and students to draw chemical structures and reactions using a variety of input methods. These may include mouse and keyboard input, as well as touch-based interactions for touchscreen devices.

The widgets provide a comprehensive set of features to represent various types of molecules, including organic compounds, inorganic compounds, peptides, and polymers. Users can draw structures by selecting and placing atoms, bonds, functional groups, and other chemical entities from a pre-defined library or by manually constructing them using drawing tools.

In addition to drawing structures, the widgets enable users to modify and manipulate existing molecules and reactions. This can involve editing the connectivity of atoms, changing bond types, adding or removing functional groups, and applying transformations such as ring formation or breaking.

Labii Chemical Drawing Widgets also support the annotation of structures with chemical properties, such as stereochemistry, charges, isotopes, and reactions conditions. Users can input and display this information alongside the molecular structure to provide a more comprehensive representation. The Chemical drawing widgets are equipped with the capability to conduct chemical substructure searches and similarity searches as well.

Furthermore, these widgets often include features for visualizing 3D molecular structures, generating 2D and 3D depictions of chemical reactions, and calculating chemical properties like molecular weight, formula, and stereochemistry analysis. They may also integrate with external databases and tools, allowing users to search for additional information about specific compounds or perform advanced analyses.

Labii Chemical Drawing Widgets serve as powerful tools for chemical scientists and students, providing an intuitive and efficient way to create, modify, and analyze chemical structures and reactions in a digital environment.

Here is a list of Chemical Drawing widgets that supported in Labii:

Marvin JS	Section	Draw and modify chemical structures
Kekule	Section	Draw, edit, compare and search molecule structures
JSME Molecular Editor	Section	Drawing and editing of molecules and reactions
ChemDraw	Section	ChemDraw integration
SMILES Drawer	Section	Display chemical structure from SMILES
LabSketch	Section	Draw chemical structures and simulate experimental processes

Common Functions

Here are a few common functions across all drawing widgets.

Save

Click the Save button to save your molecular or reaction.

File import

Most of the drawers support a certain type of molecular file. Labii added an additional file import function to support common file types. Here is a list of file types that are currently supported:

• *.mol

• *.sdf / *.sd

• *.cml

• *.inchi

• *.smi / *.smiles

Please reach out to us to request other file types to be supported.

To import a file, click the cloud icon or drag and drop a file to the cloud icon.

Sub-structure Search

Use the substructure search to return records that match to exact structure or the substructure stored in one of the Drawer widgets.

Labii's substructure search enables you to return a registered chemical or the experiment that processed a reaction. To enable the structure to be searchable, the structures have to be stored with one of the chemical drawing widgets.

Labii first generates the molecular fingerprints for each structure with Open Babel, and then the fingerprints are used to perform the substructure search.

To perform the substructure search:

1. Draw a structure

2. Click Save

3. Click Substructure Search

4. In the new tab, select a table to search

5. The results will be displayed in the tab.

Different drawers process a molecular differently, please ALWAYS use one same drawer to get consistent search results.

Similarity Search

You can also perform a similarity search with the chemical drawing widgets. Labii uses the Tanimoto coefficient for the similarity search. By default, Labii returns the results with >65% similarity.

$$SIMab = c/(a+b-c)$$

• c bits set in common in the two fingerprints

• a and b bits set in the fingerprints for A and B

To perform the similarity search:

1. Draw a structure

2. Click Save

3. Click Similarity Search

4. In the dropdown, select a similarity percentage:

   1. 65%

   2. 75%

   3. 85%

   4. 95%

5. The results will be displayed in the tab.

Read-only view

The drawer interface will be hidden when read-only. Instead, a picture of the molecular/reaction will be displayed.

Generate chemial structure with AI

Labii simplifies the process of creating chemical structures by allowing users to input chemical names or CAS numbers. With Labii's intuitive interface, researchers can effortlessly generate accurate chemical structures by providing basic information about the compound they are working with. This streamlined approach saves time and ensures precise representation of the molecular structures for effective analysis and research purposes.

Marvin JS

Marvin JS is ChemAxon's novel chemical editor designed for the wider community. This revolutionary new product provides a clean, exciting, and user-oriented tool for the quick and convenient drawing of chemical structures as well as reactions/reaction mechanisms.

Labii has integrated Marvin JS in ELN & LIMS, users can create molecular structures with Marvin JS and can save the structure for later use. Detail of the Marvin JS user guide can be found here.

License

Please reach out to [e-mail] to request information regarding the license of Marvin JS.

Kekule

Kekule.js is molecule-centric, focusing on providing the ability to represent, draw, edit, compare and search molecule structures on web browsers.

JSME Molecular Editor

JSME is a free molecule editor written in JavaScript. JSME is a direct successor of the JME Molecule Editor applet. JSME supports the drawing and editing of molecules and reactions.

JSME is developed by B. Bienfait and P. Ertl and please cite the following article if you use JSME widget:

B. Bienfait and P. Ertl, JSME: a free molecule editor in JavaScript, J. Cheminformatics 5:24 (2013)

SMILES Drawer

SMILES Drawer is a function developed by the Reymond group to display the chemical structure from a SMILES string.

To add the structure, click Edit SMILES and input the SMIELS string. Click the Submit to show the structure.

ChemDraw

ChemDraw is a molecule editor sold to PerkinElmer. Labii is integrating ChemDraw functions to draw molecular structures.

This widget requires the ChemDraw JS License. Please consult with [e-mail].

This widget is not ready to use. Data created can not be saved.

LabSketch

LabSketch widget is a versatile tool that enables users to draw chemical structures and simulate experimental processes, providing a comprehensive solution for chemical research and analysis.