LabLog's builtin molecule and reactions editor is powered by JSME Molecule Editor -developed by Bruno Bienfait and Peter Ertl at the Novartis Institutes for BioMedical Research [Ref: https://jcheminf.biomedcentral.com/articles/10.1186/1758-2946-5-24].
To launch the editor select a method or task inside your LabLog account, then create or select a step. In the step editor page click on the Molecule icon in the top menu.
The editor menu contains a rich set of tools for drawing molecules and reactions. Input of reactions is also supported, including generation of reaction SMILES and SMIRKS. Copying of molecule SMILES or a Molfile into system clipboard and pasting Molfile from clipboard into the editor is also supported.
Use the tools available in the editor menu to draw and edit molecules:
1- Rings are by default connected by a single bond when not added to a terminal atom. To add a spiro ring press Shift when adding a ring.
2- Click on existing single bond changes it to turn it into a double bond.
3- Use the chain tool to draw chains, saturated rings and by clicking on single bond change it to a double bond.
4- Move molecules by clicking and dragging inside a free space. To rotate press the Shift key and drag.
The editor supports stereochemistry at C4 centers, double bonds and allenes. Use the up / down wedge bonds to indicate stereochemistry at the C4 centers. Remember, that only bonds with a "sharp point" towards the atom are considered. When creating SMILES the editor tries to guess missing stereo features, in unresolvable cases an error message is issued and the SMILES without stereo information is created.
When the "autoez" option is set, SMILES with E,Z stereochemistry on all non-ring double bonds will be generated automatically. Without this keyword (or for ring double bonds) you have to mark a double bond as stereo by clicking on it with the stereo bond button selected. The bond color will change to magenta.
Stereochemistry may be completely disabled by the "nostereo" option.
To enable atom numbering toggle the menu button marked with the Numbers icon (enabled by default):
Press a number key on your keyboard (i.e. 2 or 12), then click on an atom to mark an atom. To delete the number press 0 on your keyboard and click on the numbered atom.
Copy and Paste
Right click on a molecule to open the Copy and Paste context menu. You can copy the molecule as SMILES or MOL file or paste MOL , SDF, or RXN files into the editor.
The editor also supports the shortcuts Ctrl C (for copy) and Ctrl V (for paste).
Saving files and version tracking
To save your drawing, type a name in the editor text box and click Save. The drawing will be attached to the selected step as a version-tracked file. To edit a saved drawing, click on the name in the file list.
LabLog automatically tracks the saved edits and assigns a version number to the files.
LabLog appends a .LLSmiles extension to the name you assign to your drawings. This indicated that the file contains canonical SMILES data strings saved by LabLog.
If you want to report a problem with the JSME or have a suggestion how to improve the molecule editor, contact the LabLog support team or send mail to JSME creators:
[email protected] and [email protected]