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

Marvin JS (Web Services)

Section

Marvin JS with web services support

SMILES Drawer

Section

Display chemical structure from SMILES

Common Functions

Here are a few common functions across all drawing widgets.

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.

You can also perform a similarity search with the chemical drawing widgets. Labii uses the Tanimoto coefficient for the similarity search. On 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.

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 Marvin JS user guide can be found here.

Save

Remember to click the Save to save. The save button from the Marvin JS interface could not save the data to Labii.

Readonly

The edit interface will be hidden in the read-only interface, instead, a picture will be displayed.

Edit picture size

The size of the read-only picture can be modified. Click Edit icon to modify. Default to 400px X 300px.

License

Please reach out to sales@labii.com to request the information regarding the license of Marvin JS.

Marvin JS (Web Services)

Marvin JS (Web Services) providing additional tools for transforming, exporting, converting chemical structures.

All other functions are identical to Marvin JS.

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.