moltosmiles function?

[richardskim111]

Hi! I'm new to MolecularGraph.jl. Does it currently support a function to convert a GraphMol instance into a SMILES string?

[mojaie]

Thank you for your interest.
Unfortunately, GraphMol to SMILES converter is not supported yet.

[hhaensel]

I just added a PR that supports molecule generation from inchi strings. During my research for a solution I stumbled across OpenBabel which is an amazing ChemConverter.
If you install it on your system, you can easily convert between any file formats, e.g.

babel_cmd = raw"C:\Temp\OpenBabel\obabel.exe" # or wherever your babel is located
smiles = rstrip(read(`$babel_cmd -:"InChI=1/C2H6O/c1-2-3/h3H,2H2,1H3" -iinchi -osmi`, String))
# "CCO"

using MolecularGraph

mol = smilestomol("CCO")
sdf = printv2mol(mol)
smiles = rstrip(read(`$babel_cmd -:"$sdf" -imol -osmi`, String))
# "CCO"

This still has some overhead in calling an external program but is still pretty fast.

It would be tempting to build an OpenBabel.jl package ...

[timoleistner]

Adding to @hhaensel's comment, with openbabel_jll one can use the ExecutableProduct, removing the overhead of calling an external program:

using openbabel_jll
inchi = "InChI=1/C2H6O/c1-2-3/h3H,2H2,1H3"
smiles = rstrip(readchomp(`$(obabel()) -:$inchi -i inchi -o smiles`))

I would love to see this approach applied more broadly in this package to enable more flexible format conversion.