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Merge branch 'master' into specify-temp
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‎.Rbuildignore‎

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^Meta$
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^cran-comments\.md$
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^CRAN-SUBMISSION$
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^data-raw$

‎.github/workflows/R-CMD-check.yaml‎

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fail-fast: false
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matrix:
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config:
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- {os: macos-latest, r: 'release'}
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- {os: windows-latest, r: 'release'}
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- {os: macos-13, r: 'release'} #TODO remove some day when ChemmineOB works on Apple silicon
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- {os: macos-latest, r: 'release'}
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- {os: windows-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
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- {os: ubuntu-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'oldrel-1'}
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http-user-agent: ${{ matrix.config.http-user-agent }}
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use-public-rspm: true
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- name: macOS openbabel
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if: matrix.config.os == 'macos-latest'
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if: contains(matrix.config.os, 'macos')
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run: |
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brew install open-babel
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- name: ubuntu openbabel

‎.github/workflows/test-coverage.yaml‎

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- name: Upload test results
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if: failure()
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uses: actions/upload-artifact@v3
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uses: actions/upload-artifact@v4
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with:
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name: coverage-test-failures
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path: ${{ runner.temp }}/package

‎DESCRIPTION‎

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<doi:10.5194/acp-8-2773-2008> or modified SIMPOL.1 method as in
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Meredith et al. (2023) <doi:10.5194/acp-8-2773-2008>.
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License: MIT + file LICENSE
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URL: https://meredith-lab.github.io/volcalc/
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URL: https://meredith-lab.github.io/volcalc/, https://cct-datascience.r-universe.dev/volcalc
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BugReports: https://github.com/Meredith-Lab/volcalc/issues
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Imports:
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ChemmineOB,
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fs,
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glue,
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httr2,
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KEGGREST,
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magrittr,
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purrr,
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rlang,
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Encoding: UTF-8
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Roxygen: list(markdown = TRUE)
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RoxygenNote: 7.3.2
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Depends:
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R (>= 2.10)
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LazyData: true

‎NEWS.md‎

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* Added a `validate = TRUE` option to `calc_vol()` and `get_fx_groups()` that returns `NA`s 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`
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* 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.
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* 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.
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* adds a dataset, `smarts_simpol1`, describing how functional groups are defined for the SIMPOL.1 and Meredith et al. methods
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* `KEGGREST` is no longer a dependency of `volcalc` (previously used in `get_mol_kegg()`)
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# volcalc 2.1.2
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‎R/data.R‎

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#' Search patterns used for SIMPOL.1 functional groups
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#'
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#' This dataframe documents how functional groups for the SIMPOL.1 and Meredith
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#' et al. method are defined using SMARTS strings or `ChemmineR` functions.
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#'
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#' @format
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#' \describe{
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#' \item{method}{Either "simpol1" for functional groups only used with the SIMPOL.1 method, or "meredith" for additional groups used in the Meredith et al. method.}
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#' \item{functional_groups}{These correspond to matching column names in the results of [get_fx_groups()].}
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#' \item{description}{Functional group description from Table 5 of Pankow & Asher (2008)}
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#' \item{smarts}{SMARTS strings used to capture groups, when applicable}
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#' \item{fun}{The function used to capture the functional group. When `smarts` is not `NA`, this is always "[ChemmineR::smartsSearchOB]". Other groups are captured with other `ChemmineR` functions or as calculations using other functional groups.}
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#' \item{notes}{Notes including how any functional group counts are corrected when there is overlap. E.g. when one SMARTS pattern is a subset of another pattern, but the two groups are counted separately without overlap in the SIMPOL.1 method.}
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#' }
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#'
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#' @references
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#' Meredith L, Ledford S, Riemer K, Geffre P, Graves K, Honeker L, LeBauer D,
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#' Tfaily M, Krechmer J. 2023. Automating methods for estimating metabolite
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#' volatility. Frontiers in Microbiology. \doi{10.3389/fmicb.2023.1267234}
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#'
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#' Pankow, J.F., Asher, W.E. 2008. SIMPOL.1: a simple group
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#' contribution method for predicting vapor pressures and enthalpies of
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#' vaporization of multifunctional organic compounds. Atmos. Chem. Phys.
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#' \doi{10.5194/acp-8-2773-2008}
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#'
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"smarts_simpol1"

‎R/get_fx_groups.R‎

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#' risk! Validation is not available on Windows. See **Details** for more
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#' information.
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#'
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#' @details It is unfortunately difficult to capture errors and warnings
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#' produced by the command line tool OpenBabel used by `ChemmineOB`, a
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#' dependency of `volcalc`. These errors and warnings are printed to the R
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#' console, but they are *not* R errors and do not stop code from running and
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#' producing potentially incorrect data. `validate = TRUE` checks the output
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#' of certain OpenBabel procedures for the *symptoms* of these errors, namely
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#' missing values for InChI and molecular formula. Unfortunately, since InChI
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#' @details For more details on how functional groups are defined, see the
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#' [smarts_simpol1] data set.
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#'
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#' It is unfortunately difficult to capture errors and warnings produced by
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#' the command line tool OpenBabel used by `ChemmineOB`, a dependency of
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#' `volcalc`. These errors and warnings are printed to the R console, but they
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#' are *not* R errors and do not stop code from running and producing
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#' potentially incorrect data. `validate = TRUE` checks the output of certain
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#' OpenBabel procedures for the *symptoms* of these errors, namely missing
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#' values for InChI and molecular formula. Unfortunately, since InChI
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#' generation is not available with the Windows version of `ChemmineOB`, this
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#' validation step cannot be performed on Windows and `validate = TRUE` will
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#' simply print a warning that can be silenced by setting `validate = FALSE`.
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carbon_dbl_count <- tibble::add_row(carbon_dbl_count, n = 0)
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}
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# *_pattern are SMARTS strings: https://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html
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carbon_dbl_bonds_pattern <- "C=C" #non-aromatic carbon double bonds
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CCCO_pattern <- "C(C=C[AR1])(=O)[AR1]" #C=C-C=O in a non-aromatic ring
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# ether_alkyl_pattern <- "[OD2]([C!R1])[C!R1]" #currently unused--ether_alkly calculated as total - other ethers
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ether_alicyclic_pattern <- "[OD2]([C!R0])[C!R0]"
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ether_aromatic_pattern <- "O(c)[C,c]" #only one of the carbons has to be aromatic
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nitro_pattern <- "[$([NX3](=O)=O),$([NX3+](=O)[O-])][!#8]"
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hydroxyl_aromatic_pattern <- "[OX2H]c"
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nitrate_pattern <- "[$([NX3](=[OX1])(=[OX1])O),$([NX3+]([OX1-])(=[OX1])O)]"
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#TODO need patterns for amines that don't pick up amides
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amine_primary_pattern <- "[NX3;H2;!$(NC=[!#6]);!$(NC#[!#6])][#6X4]"
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amine_secondary_pattern <- "[NX3H1!$(NC=[!#6])!$(NC#[!#6])]([#6X4])[#6X4]"
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amine_tertiary_pattern <- "[NX3H0!$(NC=[!#6])!$(NC#[!#6])]([#6X4])([#6X4])[#6X4]"
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amine_aromatic_pattern <- "[NX3;!$(NO)]c"
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amide_primary_pattern <- "[CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H2]"
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amide_secondary_pattern <- "[CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H1][#6;!$(C=[O,N,S])]"
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amide_tertiary_pattern <-
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"[CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])]"
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# amide_total_pattern <- "[CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]"
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carbonylperoxynitrate_pattern <- "*C(=O)OO[N+1](=O)[O-1]"
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peroxide_pattern <- "[OX2D2][OX2D2]" #this captures carbonylperoxynitrates too
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hydroperoxide_pattern <- "[OX2][OX2H,OX1-]" #this captures peroxyacids too
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carbonylperoxyacid_pattern <- "[CX3;$([R0][#6]),$([H1R0])](=[OX1])[OX2][$([OX2H]),$([OX1-])]"
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nitroester_pattern <- "C(=O)(OC)C~[NX3](-,=[OX1])-,=[OX1]"
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# This captures OH groups on a ring that also has a nitro group (para, ortho, or meta). Need to correct aromatic hydroxyl count later.
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nitrophenol_pattern <-
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"[OX2H][$(c1ccccc1[$([NX3](=O)=O),$([NX3+](=O)[O-])]),$(c1cccc(c1)[$([NX3](=O)=O),$([NX3+](=O)[O-])]),$(c1ccc(cc1)[$([NX3](=O)=O),$([NX3+](=O)[O-])])]"
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phosphoric_acid_pattern <-
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"[$(P(=[OX1])([$([OX2H]),$([OX1-]),$([OX2]P)])([$([OX2H]),$([OX1-]),$([OX2]P)])[$([OX2H]),$([OX1-]),$([OX2]P)]),$([P+]([OX1-])([$([OX2H]),$([OX1-]),$([OX2]P)])([$([OX2H]),$([OX1-]),$([OX2]P)])[$([OX2H]),$([OX1-]),$([OX2]P)])]"
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phosphoric_ester_pattern <-
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"[$(P(=[OX1])([OX2][#6])([$([OX2H]),$([OX1-]),$([OX2][#6])])[$([OX2H]),$([OX1-]),$([OX2][#6]),$([OX2]P)]),$([P+]([OX1-])([OX2][#6])([$([OX2H]),$([OX1-]),$([OX2][#6])])[$([OX2H]),$([OX1-]),$([OX2][#6]),$([OX2]P)])]"
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sulfate_pattern <-
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"[$([#16X4](=[OX1])(=[OX1])([OX2H,OX1H0-])[OX2][#6]),$([#16X4+2]([OX1-])([OX1-])([OX2H,OX1H0-])[OX2][#6])]"
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#sulfonate groups; sulfonate ions, and conjugate acid, sulfonic acids
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sulfonate_pattern <-
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"[#16X4](=[OX1])(=[OX1])([#6])[*$([O-1]),*$([OH1]),*$([OX2H0])]"
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thiol_pattern <- "[#16X2H]"
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carbothioester_pattern <- "S([#6])[CX3](=O)[#6]"
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smarts <- smarts_patterns_simpol1
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fx_groups_df <-
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dplyr::tibble(
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rings_aromatic = as.integer(rings$AROMATIC),
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rings_total = as.integer(rings$RINGS),
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rings_aliphatic = NA_integer_, #calculated below
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carbon_dbl_bonds_aliphatic = ChemmineR::smartsSearchOB(compound_sdf, carbon_dbl_bonds_pattern),
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CCCO_aliphatic_ring = ChemmineR::smartsSearchOB(compound_sdf, CCCO_pattern), # C=C-C=O in a non-aromatic ring
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carbon_dbl_bonds_aliphatic = ChemmineR::smartsSearchOB(compound_sdf, smarts$carbon_dbl_bonds_aliphatic),
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CCCO_aliphatic_ring = ChemmineR::smartsSearchOB(compound_sdf, smarts$CCCO_aliphatic_ring),
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hydroxyl_total = groups$ROH,
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hydroxyl_aromatic = ChemmineR::smartsSearchOB(compound_sdf, hydroxyl_aromatic_pattern, uniqueMatches = FALSE),
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hydroxyl_aromatic = ChemmineR::smartsSearchOB(compound_sdf, smarts$hydroxyl_aromatic, uniqueMatches = FALSE),
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hydroxyl_aliphatic = NA_integer_, #calculated below
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aldehydes = groups$RCHO,
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ketones = groups$RCOR,
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carbox_acids = groups$RCOOH,
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ester = groups$RCOOR,
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ether_total = groups$ROR,
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# ether_alkyl = ChemmineR::smartsSearchOB(compound_sdf, ether_alkyl_pattern),
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ether_alkyl = NA_integer_,
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ether_alicyclic = ChemmineR::smartsSearchOB(compound_sdf, ether_alicyclic_pattern),
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ether_aromatic = ChemmineR::smartsSearchOB(compound_sdf, ether_aromatic_pattern),
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nitrate = ChemmineR::smartsSearchOB(compound_sdf, nitrate_pattern),
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nitro = ChemmineR::smartsSearchOB(compound_sdf, nitro_pattern),
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amine_primary = ChemmineR::smartsSearchOB(compound_sdf, amine_primary_pattern),
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amine_secondary = ChemmineR::smartsSearchOB(compound_sdf, amine_secondary_pattern),
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amine_tertiary = ChemmineR::smartsSearchOB(compound_sdf, amine_tertiary_pattern),
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amine_aromatic = ChemmineR::smartsSearchOB(compound_sdf, amine_aromatic_pattern),
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amide_primary = ChemmineR::smartsSearchOB(compound_sdf, amide_primary_pattern),
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amide_secondary = ChemmineR::smartsSearchOB(compound_sdf, amide_secondary_pattern),
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amide_tertiary = ChemmineR::smartsSearchOB(compound_sdf, amide_tertiary_pattern),
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carbonylperoxynitrate = ChemmineR::smartsSearchOB(compound_sdf, carbonylperoxynitrate_pattern),
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peroxide = ChemmineR::smartsSearchOB(compound_sdf, peroxide_pattern),
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hydroperoxide = ChemmineR::smartsSearchOB(compound_sdf, hydroperoxide_pattern),
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carbonylperoxyacid = ChemmineR::smartsSearchOB(compound_sdf, carbonylperoxyacid_pattern),
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nitrophenol = ChemmineR::smartsSearchOB(compound_sdf, nitrophenol_pattern),
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nitroester = ChemmineR::smartsSearchOB(compound_sdf, nitroester_pattern),
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ether_alkyl = NA_integer_, #calculated below
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ether_alicyclic = ChemmineR::smartsSearchOB(compound_sdf, smarts$ether_alicyclic),
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ether_aromatic = ChemmineR::smartsSearchOB(compound_sdf, smarts$ether_aromatic),
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nitrate = ChemmineR::smartsSearchOB(compound_sdf, smarts$nitrate),
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nitro = ChemmineR::smartsSearchOB(compound_sdf, smarts$nitro),
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amine_primary = ChemmineR::smartsSearchOB(compound_sdf, smarts$amine_primary),
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amine_secondary = ChemmineR::smartsSearchOB(compound_sdf, smarts$amine_secondary),
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amine_tertiary = ChemmineR::smartsSearchOB(compound_sdf, smarts$amine_tertiary),
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amine_aromatic = ChemmineR::smartsSearchOB(compound_sdf, smarts$amine_aromatic),
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amide_primary = ChemmineR::smartsSearchOB(compound_sdf, smarts$amide_primary),
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amide_secondary = ChemmineR::smartsSearchOB(compound_sdf, smarts$amide_secondary),
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amide_tertiary = ChemmineR::smartsSearchOB(compound_sdf, smarts$amide_tertiary),
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carbonylperoxynitrate = ChemmineR::smartsSearchOB(compound_sdf, smarts$carbonylperoxynitrate),
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peroxide = ChemmineR::smartsSearchOB(compound_sdf, smarts$peroxide),
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hydroperoxide = ChemmineR::smartsSearchOB(compound_sdf, smarts$hydroperoxide),
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carbonylperoxyacid = ChemmineR::smartsSearchOB(compound_sdf, smarts$carbonylperoxyacid),
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nitrophenol = ChemmineR::smartsSearchOB(compound_sdf, smarts$nitrophenol),
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nitroester = ChemmineR::smartsSearchOB(compound_sdf, smarts$nitroester),
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# Additional groups from Meredith et al. 2023
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phosphoric_acids = ChemmineR::smartsSearchOB(compound_sdf, phosphoric_acid_pattern),
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phosphoric_esters = ChemmineR::smartsSearchOB(compound_sdf, phosphoric_ester_pattern),
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sulfates = ChemmineR::smartsSearchOB(compound_sdf, sulfate_pattern),
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sulfonates = ChemmineR::smartsSearchOB(compound_sdf, sulfonate_pattern),
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thiols = ChemmineR::smartsSearchOB(compound_sdf, thiol_pattern),
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carbothioesters = ChemmineR::smartsSearchOB(compound_sdf, carbothioester_pattern),
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phosphoric_acids = ChemmineR::smartsSearchOB(compound_sdf, smarts$phosphoric_acids),
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phosphoric_esters = ChemmineR::smartsSearchOB(compound_sdf, smarts$phosphoric_esters),
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sulfates = ChemmineR::smartsSearchOB(compound_sdf, smarts$sulfates),
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sulfonates = ChemmineR::smartsSearchOB(compound_sdf, smarts$sulfonates),
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thiols = ChemmineR::smartsSearchOB(compound_sdf, smarts$thiols),
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carbothioesters = ChemmineR::smartsSearchOB(compound_sdf, smarts$carbothioesters),
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oxygens = atoms[["O"]] %||% 0L,
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chlorines = atoms[["Cl"]] %||% 0L,
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nitrogens = atoms[["N"]] %||% 0L,

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