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 ChemmineOBvolcalc is now published in Frontiers in Microbiology 🎉. DOI: 10.3389/fmicb.2023.1267234browseVignettes("volcalc") or on the package website?mol_example()mol_example() no longer takes any arguments and just returns file paths to all example .mol filescalc_vol() as a vector of SMILES strings with from = "smiles".environment parameter of calc_vol().simpol1() to avoid double-counting amides.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.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).mass column renamed to molecular_weight and addition of an exact_mass column.hydroxyl_total and hydroxyl_aliphatic instead of hydroxyl_groupsrings_total and rings_aliphatic instead of ringssimpol1():
ether to ether_alkyl and added ether_total (matching any R-O-R)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.
get_fx_groups() and calc_vol() from data frame to tibbleget_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.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()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)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)get_mol_kegg(), replaces save_compound_mol() for downloading mol files from KEGGget_fx_groups() now only counts the smallest set of smallest rings (#57)get_fx_groups now counts aromatic hydroxyl groups (e.g. phenols) to more closely align with Pankow & Asher (2008) (#46)volcalc introduced by a bug-fix in ChemmineR v3.53.1 (#54)volatility column in the output of calc_vol() has been renamed to rvi (relative volatility index)calc_vol()---remove amines functional group to avoid double counting with primary amines (#49)calc_vol()---use 293.15K for temperature (instead of 293K) to match the temperature used in Pankow & Asher (2008)volcalc. This is the version of the code used in an in-prep manuscript. Version 2.0.0 will include breaking changesNEWS.md file to track changes to the package.