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Changelog

Source: NEWS.md

volcalc (development version)

volcalc 2.2.0

  • Added a validate = TRUE option to calc_vol() and get_fx_groups() that returns NAs when there are suspected errors in parsing SMILES or .mol files. This is unfortunately not available on Windows due to differences in the windows version of ChemmineOB
  • Users can now supply a temperature at which to calculate volatility estimates. As a result, RVI values may now be slightly different compared to those from volcalc v2.1.2 due to rounding differences.
  • Inputs to calc_vol() supplied as a named vector of SMILES strings now properly pass the names to ChemmineR::smile2sdf() where they are used as the molecule name.
  • adds a dataset, smarts_simpol1, describing how functional groups are defined for the SIMPOL.1 and Meredith et al. methods
  • KEGGREST is no longer a dependency of volcalc (previously used in get_mol_kegg())

volcalc 2.1.2

  • There is no release for this version as it was a rejected CRAN submission.

volcalc 2.1.1

  • Added Dr. Laura Meredith as a package author as the concept for volcalc originated from her.
  • Added package contributors S. Marshall Ledford (our main user and beta tester since day 1!) and Tamás Stirling (for help with SMARTS patterns)
  • Updated citation files accordingly

volcalc 2.1.0

  • The manuscript associated with volcalc is now published in Frontiers in Microbiology 🎉. DOI: 10.3389/fmicb.2023.1267234
  • There are now two vignettes available which can be viewed with browseVignettes("volcalc") or on the package website

Miscelanous changes

  • New example .mol files were added. See ?mol_example()
  • mol_example() no longer takes any arguments and just returns file paths to all example .mol files

Changes to calc_vol() and simpol1()

  • It is now possible to supply input to calc_vol() as a vector of SMILES strings with from = "smiles".
  • Users can now choose from RVI thresholds for non-volatile, low, moderate, and high volatility for clean atmosphere, polluted atmosphere, or soil using the environment parameter of calc_vol().
  • A coefficient for amides has been removed from the “Meredith” method of simpol1() to avoid double-counting amides.
  • The default for the method argument to calc_vol() has now been renamed to "meredith". "simpol1" now uses the original SIMPOL.1 method without additional coefficients added in Meredith et al. (2023).
  • simpol1() gains an argument meredith that controls whether just the functional groups in the original SIMPOL.1 method (Pankow & Asher, 2008) is used or if additional coefficients used in Meredith et al. (2023) are also included.
  • simpol1() now takes into account amide functional groups.

Changes to get_mol_kegg()

  • The pathway_ids argument of get_mol_kegg() now also accepts pathway module IDs (e.g. “M00082”).
  • get_mol_kegg() got a significant speed improvement (#84).
  • get_mol_kegg() will skip downloading a .mol file if it is already present by default (override with force=TRUE).

Changes to get_fx_groups()

  • mass column renamed to molecular_weight and addition of an exact_mass column.
  • change to how non-aromatic carbon double bonds are counted. Now using SMARTS pattern “C=C”
  • now returns hydroxyl_total and hydroxyl_aliphatic instead of hydroxyl_groups
  • now returns rings_total and rings_aliphatic instead of rings
  • Now captures all functional groups in the SIMPOL.1 method except “number of carbons on the acid side of an amide”. This version adds these previously missing groups used by simpol1():
    • C=C-C=O in a non-aromatic ring
    • non-aromatic carbon double bonds
    • aromatic amines
    • primary, secondary, and tertiary amides
    • hydroperoxides
    • carbonylperoxyacids
    • carbonylperoxynitrates
    • alkyl, alicyclic, and aromatic ethers (in addition to total ethers)
    • nitrophenols
    • nitroesters
  • changed ether to ether_alkyl and added ether_total (matching any R-O-R)
  • slight change to the SMARTS pattern to capture sulfonate groups to also capture conjugate sulfonic acids

volcalc 2.0.0

This version includes big (breaking) changes in how the package works! Please read the changelog below carefully and check function documentation and examples to see the new usage of functions.

  • Change output of get_fx_groups() and calc_vol() from data frame to tibble
  • get_fx_groups() and calc_vol() no longer depend on KEGG or take KEGG compound IDs or pathway IDs. Instead, calc_vol() accepts a path to a .mol file as input.
  • calc_vol() is vectorized and accepts multiple compounds as input.
  • Moved SIMPOL.1 calculations out of calc_vol() and into to their own function, simpol1(), to pave the way for future expansions using other methods. The “manual” workflow is now .mol file |> ChemmineR::read.SDFset() |> get_fx_groups() |> simpol1()
  • The output of calc_vol() (and simpol1()) now contains a column called log10_P instead of log_Sum, equivalent to log_Sum + the coefficient for b_0(T)
  • Output of calc_vol() now contains a column with the inputs, named whatever is supplied to from (eg. a column called mol_path containing paths to mol files)
  • A new function, get_mol_kegg(), replaces save_compound_mol() for downloading mol files from KEGG
  • Added pkgdown website
  • get_fx_groups() now only counts the smallest set of smallest rings (#57)
  • Fixed a bug that caused the number of phenols to be miscounted. Rather than counting phenols, get_fx_groups now counts aromatic hydroxyl groups (e.g. phenols) to more closely align with Pankow & Asher (2008) (#46)
  • package now has a hex logo!
  • Fixes a bug in volcalc introduced by a bug-fix in ChemmineR v3.53.1 (#54)
  • The volatility column in the output of calc_vol() has been renamed to rvi (relative volatility index)

volcalc 1.0.2

  • Minor change in calculation in calc_vol()—remove amines functional group to avoid double counting with primary amines (#49)

volcalc 1.0.1

  • Minor change in calculation in calc_vol()—use 293.15K for temperature (instead of 293K) to match the temperature used in Pankow & Asher (2008)

volcalc 1.0.0

  • Initial release of volcalc. This is the version of the code used in an in-prep manuscript. Version 2.0.0 will include breaking changes

volcalc 0.0.0.9000

  • Added a NEWS.md file to track changes to the package.