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How many combinations do you believe could be produced from the same molecular formula? Actually, It depends on the formula itself.
Here, We will experience and see all possible molecular structures of a certain molecular formula. Let's say benzene and Phenol.
- Introducing Surge
Surge is a fast open-source chemical graph generator that generate all possible molecular structures of a molecular formula.
You can find Surge's article is published in Journal of Cheminformatics
- Usage
Surge is a command line tool. Running surge -u C10H16O will generate the 452458 isomers of C10H16O in 0.1s.
Running surge -S C10H16O outputs those structurs in SMILES format. You can either use surge -S C10H16O > myresults.smi to redirect the output into a result file, or use the -o switch to provide a filename. Further formats supported are SD Files (SDF) and a concise Surge-specific format.
Usage: surge [-oFILE] [-z] [-u|-A|-S] formula
formula = a formula like C8H6N2
-S Output in SMILES format
-A Output in alphabetical format
-u Just count, don't write
-oFILE Write the output to the given file rather than to stdout.
-z Write output in gzip format (only if compiled with zlib)
- How to generate molecules ?
At first, get the program from here.
Then, generate molecules from formula C6H6 by writing the following prompt (consider that I'm using Windows)
The command above will generate benzene.sdf.
Then, we checked all generated structures.
Here are the generated molecules for C6H6 formula. There are more than 200 molecules.
And for Phenol molecular formula C6H5O, there were more than 2200 molecules !!!!
If you wanna go deeper, you should go with Users’ manual for molecule generator surge
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