GCIdentifier.jl

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GCIdentifier.jl

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

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# 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.

![](https://raw.githubusercontent.com/ClapeyronThermo/GCIdentifier.jl/main/paper/figures/ibuprofen.svg)

## Basis Usage
Once installed (more details below), GCIdentifier can easy be called upon:
```julia
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
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](https://github.com/longemen3000/ChemicalIdentifiers.jl) where one can simply specify the molecule name:
```julia
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](https://github.com/ClapeyronThermo/Clapeyron.jl) to be used to obtain our desired properties:
```julia
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](https://clapeyronthermo.github.io/GCIdentifier.jl/dev/) 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
> julia
```

Hit the ```]``` key to enter Pkg mode, then type

```julia
Pkg> add GCIdentifier
```
Exit Pkg mode by hitting backspace.

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

```julia
using GCIdentifier
```

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

```julia
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.
* General support: If you have questions regarding the usage of this package or are having difficulties getting started, feel free to open a Discussion on GitHub or contact us directly on Zulip (link in badge above)!

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