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GCIdentifier.jl

GCIdentifier.jl: A Julia package for identifying molecular fragments from SMILES - Published in JOSS (2024)

https://github.com/clapeyronthermo/gcidentifier.jl

Science Score: 95.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in JOSS metadata
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    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    1 of 7 committers (14.3%) from academic institutions
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

group-contribution joback smiles-strings unifac

Keywords from Contributors

mesh
Last synced: 6 months ago · JSON representation

Repository

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

Basic Info
  • Host: GitHub
  • Owner: ClapeyronThermo
  • License: mit
  • Language: Julia
  • Default Branch: main
  • Homepage:
  • Size: 906 KB
Statistics
  • Stars: 20
  • Watchers: 6
  • Forks: 4
  • Open Issues: 2
  • Releases: 13
Topics
group-contribution joback smiles-strings unifac
Created about 3 years ago · Last pushed 6 months ago
Metadata Files
Readme License Zenodo

README.md

Build Status codecov Dev project chat DOI

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 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 where one can simply specify the molecule name: ```julia julia> using ChemicalIdentifiers

julia> (component,groups) = getgroupsfrom_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 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

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)!

Owner

  • Name: Clapeyron
  • Login: ClapeyronThermo
  • Kind: organization

JOSS Publication

GCIdentifier.jl: A Julia package for identifying molecular fragments from SMILES
Published
April 05, 2024
DOI
Volume 9, Issue 96, Page 6453
Authors
Pierre J. Walker ORCID
Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States, Department of Chemical Engineering, Imperial College, London SW7 2AZ, United Kingdom
Andrés Riedemann
Departamento de Ingeniería Química, Universidad de Concepción, Concepción 4030000, Chile
Zhen-Gang Wang ORCID
Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
Editor
Bonan Zhu ORCID
Tags
Group-contribution Thermodynamics Molecular Design
View PDF Review Thread Software Archive

GitHub Events

Total
  • Create event: 6
  • Commit comment event: 11
  • Issues event: 5
  • Release event: 5
  • Watch event: 6
  • Delete event: 1
  • Issue comment event: 17
  • Push event: 28
  • Pull request review event: 1
  • Pull request event: 6
  • Fork event: 1
Last Year
  • Create event: 6
  • Commit comment event: 11
  • Issues event: 5
  • Release event: 5
  • Watch event: 6
  • Delete event: 1
  • Issue comment event: 17
  • Push event: 28
  • Pull request review event: 1
  • Pull request event: 6
  • Fork event: 1

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 135
  • Total Committers: 7
  • Avg Commits per committer: 19.286
  • Development Distribution Score (DDS): 0.474
Past Year
  • Commits: 25
  • Committers: 6
  • Avg Commits per committer: 4.167
  • Development Distribution Score (DDS): 0.56
Top Committers
Name Email Commits
pw0908 p****r@c****u 71
longemen3000 l****0@g****m 55
dependabot[bot] 4****] 3
princesswinnie e****g@g****m 2
Olav Møyner o****r@g****m 2
Thomas Vetter 8****t 1
Evangelos (Vangelis) Tsochantaris 1****h 1
Committer Domains (Top 20 + Academic)
caltech.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 8
  • Total pull requests: 27
  • Average time to close issues: about 19 hours
  • Average time to close pull requests: about 2 months
  • Total issue authors: 7
  • Total pull request authors: 7
  • Average comments per issue: 3.25
  • Average comments per pull request: 0.7
  • Merged pull requests: 21
  • Bot issues: 0
  • Bot pull requests: 10
Past Year
  • Issues: 4
  • Pull requests: 6
  • Average time to close issues: about 20 hours
  • Average time to close pull requests: 3 months
  • Issue authors: 3
  • Pull request authors: 3
  • Average comments per issue: 1.75
  • Average comments per pull request: 1.0
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 2
View more stats
Top Authors
Issue Authors
  • Tiger2Wings (2)
  • thomvet (1)
  • Vtsoch (1)
  • viniviena (1)
  • felipe-mansoldo (1)
  • CalCraven (1)
  • JuliaTagBot (1)
Pull Request Authors
  • dependabot[bot] (10)
  • longemen3000 (4)
  • moyner (4)
  • pw0908 (3)
  • princesswinnie1122 (2)
  • thomvet (2)
  • Vtsoch (2)
Top Labels
Issue Labels
Pull Request Labels
dependencies (10)

Packages

  • Total packages: 1
  • Total downloads:
    • julia 3 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 13
juliahub.com: GCIdentifier

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

  • Versions: 13
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 3 Total
Rankings
Dependent repos count: 9.8%
Average: 24.6%
Dependent packages count: 39.4%
Last synced: 6 months ago

Dependencies

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.github/workflows/TagBot.yml actions
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