Chemical Drawing

Draw chemical structure

Overview

Chemical Drawing widgets allow you to draw chemical structures including chemical compounds, reactions, Markush structures. The Chemical drawing widgets can also perform the chemical substructure search and similarity search.

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

Widget

Type

Description

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

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.

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.

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+bc)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 new tab, select a table to search

  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.

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 [email protected] 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 [email protected]

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