About ERROR: Could not find all groups

[felipe-mansoldo]

Dear all,

I'm trying your package. I decided to start with a famous molecule, Penicillin G. So I got its SMILES at: https://pubchem.ncbi.nlm.nih.gov/compound/Penicillin-G#section=Canonical-SMILES

Canonical SMILES = CC1(C(N2C(S1)C(C2=O)NC(=O)CC3=CC=CC=C3)C(=O)O)C

But I got error:

julia> (component,groups) = get_groups_from_smiles("CC1(C(N2C(S1)C(C2=O)NC(=O)CC3=CC=CC=C3)C(=O)O)C", UNIFACGroups)
ERROR: Could not find all groups for CC1(C(N2C(S1)C(C2=O)NC(=O)CC3=CC=CC=C3)C(=O)O)C
Stacktrace:
 [1] error(s::String)
   @ Base .\error.jl:35
 [2] get_groups_from_smiles(smiles::String, groups::Vector{GCPair}; connectivity::Bool, check::Bool)
   @ GCIdentifier C:\Users\admin\.julia\packages\GCIdentifier\V6P7e\src\group_search.jl:126
 [3] get_groups_from_smiles(smiles::String, groups::Vector{GCPair})
   @ GCIdentifier C:\Users\admin\.julia\packages\GCIdentifier\V6P7e\src\group_search.jl:111
 [4] top-level scope
   @ REPL[3]:1

Is it a bug or some limitation?

thanks,

[pw0908]

Hi Felipe,

This isn't really an error. It just means that UNIFAC doesnt have all the groups necessary to model Penicilin G. unfortunately... You can see which groups UNIFAC does have by adding check=false:

(component,groups) = get_groups_from_smiles("CC1(C(N2C(S1)C(C2=O)NC(=O)CC3=CC=CC=C3)C(=O)O)C", UNIFACGroups; check=false)
("CC1(C(N2C(S1)C(C2=O)NC(=O)CC3=CC=CC=C3)C(=O)O)C", ["COOH" => 1, "CH3" => 2, "ACH" => 5, "CY-CH" => 2, "CY-C" => 2, "CH2CO" => 1, "CHNH" => 1, "AC" => 1])

To see which groups are missing, you can use our find_missing_groups_from_smiles function:

groups = find_missing_groups_from_smiles("CC1(C(N2C(S1)C(C2=O)NC(=O)CC3=CC=CC=C3)C(=O)O)C", UNIFACGroups)
3-element Vector{GCPair}:
 GCPair("[NX3;H0;R]", "cN")
 GCPair("[SX2;H0;R]", "cS")
 GCPair("[OX1;H0;!R]", "O=")

Indeed, it looks like the cyclic sulfur and cyclic nitrogen groups haven't been fitted. The ketone oxygen is mainly due to the fact that there is a cyclic carbon which is double bonded to that oxygen.

Hope this helps!

Best regards,

Pierre

[felipe-mansoldo]

Hi Pierre, Thank you for your attention and response. Do you think about expanding support to other groups? My best regards,

[pw0908]

Hi Felipe,

We aren't the developers of UNIFAC so we don't really have much motivation / interest to expand the approach to other groups. This is something you could do yourself, however, using Clapeyron.

Feel free to raise an issue there if you'd like some guidance.

Best regards,

Pierre

[felipe-mansoldo]

Hi, ok, thank you very much! my best,