moyner/gcidentifier.jl

tools to perform group contribution (GC) identification, given the SMILES of a compound

GCIdentifier.jl

Welcome to GCIdentifier! This module provides utilities needed to fragment a given molecular SMILES (or name) based on the groups provided in existing group-contribution methods (such as UNIFAC, Joback's method and SAFT-$\gamma$ Mie). Additional functionalities have been provided to automatically identify and propose new groups.

Basis Usage

Once installed (more details below), GCIdentifier can easy be called upon:

julia> using GCIdentifier

Let's consider the case where we want to get the groups for ibuprofen from the UNIFAC group-contribution method. The SMILES representation for ibuprofen is CC(Cc1ccc(cc1)C(C(=O)O)C)C. To get the corresponding groups, simply use:

julia> (component,groups) = get_groups_from_smiles("CC(Cc1ccc(cc1)C(C(=O)O)C)C", UNIFACGroups)
("CC(Cc1ccc(cc1)C(C(=O)O)C)C", ["COOH" => 1, "CH3" => 3, "CH" => 1, "ACH" => 4, "ACCH2" => 1, "ACCH" => 1])

If the SMILES representation is not known, it is possible to use GCIdentifier in conjunction with ChemicalIdentifiers where one can simply specify the molecule name:

julia> using ChemicalIdentifiers

julia> (component,groups) = get_groups_from_name("ibuprofen",UNIFACGroups)
("ibuprofen", ["COOH" => 1, "CH3" => 3, "CH" => 1, "ACH" => 4, "ACCH2" => 1, "ACCH" => 1])

These groups can then be used in packages such as Clapeyron to be used to obtain our desired properties:

julia> using Clapeyron

julia> model = UNIFAC(["water",(component,groups)])

julia> activity_coefficient(model,1e5,298.15,[1.,0.])
2-element Vector{Float64}:
      1.0
 421519.07740198134

More details have been provided in the docs where we provide additional details regarding how one can obtain the connectivity between groups, identifying new groups within a structure and how one could apply their own GC method.

Installing GCIdentifier

The minimum supported version is Julia 1.6. To install GCIdentifier, launch Julia with

> julia

Hit the ] key to enter Pkg mode, then type

Pkg> add GCIdentifier

Exit Pkg mode by hitting backspace.

Now you may begin using functions from the GCIdentifier library by entering the command

using GCIdentifier

To remove the package, hit the ] key to enter Pkg mode, then type

Pkg> rm GCIdentifier

Contributing

If you'd like to make a contribution to GCIdentifier, you can:

• Report an issue: If you encounter an error in which groups are assigned or any other type of error, feel free to raise an issue and one of the developers will try to address it. If you've found the source of the error and fixed it yourself, feel free to also open a Pull Request so that it can be reviewed and pushed to the main branch.
• Implement your own modifications: We are always open to making changes to the source code and documentation! If you'd like to add your own groups and/or functionalities to the package, feel free to open a pull request and one of the developers will review it before merging it with the main branch.