OMNIDEPICT: 2D Chemical Structure Depiction of Complex Molecules ver. 2017-02-13
Automatic 2D structure diagram generation (SDG) from chemical format files (SMILES, Mol2, MDL Molfile, SDFile, etc.).
The main purpose is to support structures that may be too complex to be handled with other SDG methods. (see Gallery)
Upload a chemical file (e.g., .mol, .sdf, .mol2), or enter a SMILES string in the text field below. The file can contain up to 100 molecules, max. 2 MB.
Set a number of repetitions (1-20) for each molecule (see Notes below). Molecules with less than 13 atoms are not repeated.
Click on 'Proceed'.
You can view generated depictions or download the result Molfile. You can view/edit the file with one of many chemical viewers/editors (e.g., Marvin, Indigo, Open Babel).
This is a free service. However, publication or distribution of any data or results generated with this website should be properly cited.
You may also consider citing the following paper:
Frączek, T., "Simulation-Based Algorithm for Two-Dimensional Chemical Structure Diagram Generation of Complex Molecules and Ligand–Protein Interactions."
J. Chem. Inf. Model. 2016, 56, 2320-2335, DOI: 10.1021/acs.jcim.6b00391.
Up to 100 molecules with no more than 1000 atoms are supported.
Due to the stochastic nature of the SDG algorithm, it may generate a different result each time a given molecule is submitted.
If the result are not satisfactory, try to generate more depictions by increasing the number of repetitions.
Molecules written in file formats that do not explicitly define atom connectivity (e.g., .pdb, .cif, .xyz) may be split to smaller fragments.
To properly represent stereochemistry of molecules, appropriate 3D atom coordinates must be present in the input file. Otherwise, coordinates are not required.
Representation of chiral compounds contains some bugs. Work in progress.
The third-party InChI converter crashes when a stereochemistry layer is present. An in-house InChI interpreter is being written.