define SMARTS patterns in internal dataset rather than in get_fx_grou…

…ps() code

R/data.R

@@ -1,14 +1,14 @@
 #' Search patterns used for SIMPOL.1 functional groups
-#' 
+#'
 #' This dataframe documents how functional groups for the SIMPOL.1 and Meredith
 #' et al. method are defined using SMARTS strings or `ChemmineR` functions.
-#' 
+#'
 #' @format
 #' \describe{
 #'   \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.}
 #'   \item{functional_groups}{These correspond to matching column names in the results of [get_fx_groups()].}
 #'   \item{smarts}{SMARTS strings used to capture groups, when applicable}
-#'   \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.}
+#'   \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.}
 #'   \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.}
 #' }
 "smarts_simpol1"

R/get_fx_groups.R

@@ -100,48 +100,7 @@ Set `validate = FALSE` to silence this warning.")
     carbon_dbl_count <- tibble::add_row(carbon_dbl_count, n = 0)
   }
 
-  # *_pattern are SMARTS strings: https://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html
-  carbon_dbl_bonds_pattern <- "C=C" #non-aromatic carbon double bonds
-  CCCO_pattern <- "C(C=C[AR1])(=O)[AR1]" #C=C-C=O in a non-aromatic ring
-  # ether_alkyl_pattern <- "[OD2]([C!R1])[C!R1]" #currently unused--ether_alkly calculated as total - other ethers
-  ether_alicyclic_pattern <- "[OD2]([C!R0])[C!R0]"
-  ether_aromatic_pattern <- "O(c)[C,c]" #only one of the carbons has to be aromatic
-  nitro_pattern <- "[$([NX3](=O)=O),$([NX3+](=O)[O-])][!#8]"
-  hydroxyl_aromatic_pattern <- "[OX2H]c"
-  nitrate_pattern <- "[$([NX3](=[OX1])(=[OX1])O),$([NX3+]([OX1-])(=[OX1])O)]"
-
-  #TODO need patterns for amines that don't pick up amides
-  amine_primary_pattern <- "[NX3;H2;!$(NC=[!#6]);!$(NC#[!#6])][#6X4]"
-  amine_secondary_pattern <- "[NX3H1!$(NC=[!#6])!$(NC#[!#6])]([#6X4])[#6X4]"
-  amine_tertiary_pattern <- "[NX3H0!$(NC=[!#6])!$(NC#[!#6])]([#6X4])([#6X4])[#6X4]"
-  amine_aromatic_pattern <-  "[NX3;!$(NO)]c" 
-
-  amide_primary_pattern <- "[CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H2]"
-  amide_secondary_pattern <- "[CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H1][#6;!$(C=[O,N,S])]"
-  amide_tertiary_pattern <- 
-    "[CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])]"
-
-  # 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])])]"
-
-  carbonylperoxynitrate_pattern <- "*C(=O)OO[N+1](=O)[O-1]"
-  peroxide_pattern <- "[OX2D2][OX2D2]"  #this captures carbonylperoxynitrates too
-  hydroperoxide_pattern <- "[OX2][OX2H,OX1-]" #this captures peroxyacids too
-  carbonylperoxyacid_pattern <- "[CX3;$([R0][#6]),$([H1R0])](=[OX1])[OX2][$([OX2H]),$([OX1-])]" 
-  nitroester_pattern <- "C(=O)(OC)C~[NX3](-,=[OX1])-,=[OX1]" 
-  # This captures OH groups on a ring that also has a nitro group (para, ortho, or meta).  Need to correct aromatic hydroxyl count later.
-  nitrophenol_pattern <- 
-    "[OX2H][$(c1ccccc1[$([NX3](=O)=O),$([NX3+](=O)[O-])]),$(c1cccc(c1)[$([NX3](=O)=O),$([NX3+](=O)[O-])]),$(c1ccc(cc1)[$([NX3](=O)=O),$([NX3+](=O)[O-])])]"
-  phosphoric_acid_pattern <-
-    "[$(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-]),$([OX2]P)])]"
-  phosphoric_ester_pattern <-
-    "[$(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]),$([OX2]P)])]"
-  sulfate_pattern <-
-    "[$([#16X4](=[OX1])(=[OX1])([OX2H,OX1H0-])[OX2][#6]),$([#16X4+2]([OX1-])([OX1-])([OX2H,OX1H0-])[OX2][#6])]"
-  #sulfonate groups; sulfonate ions, and conjugate acid, sulfonic acids
-  sulfonate_pattern <-
-    "[#16X4](=[OX1])(=[OX1])([#6])[*$([O-1]),*$([OH1]),*$([OX2H0])]"
-  thiol_pattern <- "[#16X2H]"
-  carbothioester_pattern <- "S([#6])[CX3](=O)[#6]"
+  smarts <- smarts_patterns_simpol1
 
   fx_groups_df <- 
     dplyr::tibble(
@@ -157,43 +116,42 @@ Set `validate = FALSE` to silence this warning.")
       rings_aromatic = as.integer(rings$AROMATIC),
       rings_total = as.integer(rings$RINGS),
       rings_aliphatic = NA_integer_, #calculated below
-      carbon_dbl_bonds_aliphatic = ChemmineR::smartsSearchOB(compound_sdf, carbon_dbl_bonds_pattern),
-      CCCO_aliphatic_ring = ChemmineR::smartsSearchOB(compound_sdf, CCCO_pattern), # C=C-C=O in a non-aromatic ring
+      carbon_dbl_bonds_aliphatic = ChemmineR::smartsSearchOB(compound_sdf, smarts$carbon_dbl_bonds_aliphatic),
+      CCCO_aliphatic_ring = ChemmineR::smartsSearchOB(compound_sdf, smarts$CCCO_aliphatic_ring),
       hydroxyl_total = groups$ROH, 
-      hydroxyl_aromatic = ChemmineR::smartsSearchOB(compound_sdf, hydroxyl_aromatic_pattern, uniqueMatches = FALSE),
+      hydroxyl_aromatic = ChemmineR::smartsSearchOB(compound_sdf, smarts$hydroxyl_aromatic, uniqueMatches = FALSE),
       hydroxyl_aliphatic = NA_integer_, #calculated below
       aldehydes = groups$RCHO,
       ketones = groups$RCOR,
       carbox_acids = groups$RCOOH,
       ester = groups$RCOOR,
       ether_total = groups$ROR,
-      # ether_alkyl = ChemmineR::smartsSearchOB(compound_sdf, ether_alkyl_pattern),
-      ether_alkyl = NA_integer_,
-      ether_alicyclic = ChemmineR::smartsSearchOB(compound_sdf, ether_alicyclic_pattern),
-      ether_aromatic = ChemmineR::smartsSearchOB(compound_sdf, ether_aromatic_pattern),
-      nitrate = ChemmineR::smartsSearchOB(compound_sdf, nitrate_pattern),
-      nitro = ChemmineR::smartsSearchOB(compound_sdf, nitro_pattern),
-      amine_primary   = ChemmineR::smartsSearchOB(compound_sdf, amine_primary_pattern),
-      amine_secondary = ChemmineR::smartsSearchOB(compound_sdf, amine_secondary_pattern),
-      amine_tertiary  = ChemmineR::smartsSearchOB(compound_sdf, amine_tertiary_pattern),
-      amine_aromatic = ChemmineR::smartsSearchOB(compound_sdf, amine_aromatic_pattern),
-      amide_primary = ChemmineR::smartsSearchOB(compound_sdf, amide_primary_pattern),
-      amide_secondary = ChemmineR::smartsSearchOB(compound_sdf, amide_secondary_pattern),
-      amide_tertiary = ChemmineR::smartsSearchOB(compound_sdf, amide_tertiary_pattern),
-      carbonylperoxynitrate = ChemmineR::smartsSearchOB(compound_sdf, carbonylperoxynitrate_pattern),
-      peroxide = ChemmineR::smartsSearchOB(compound_sdf, peroxide_pattern),
-      hydroperoxide = ChemmineR::smartsSearchOB(compound_sdf, hydroperoxide_pattern),
-      carbonylperoxyacid = ChemmineR::smartsSearchOB(compound_sdf, carbonylperoxyacid_pattern),
-      nitrophenol = ChemmineR::smartsSearchOB(compound_sdf, nitrophenol_pattern),
-      nitroester = ChemmineR::smartsSearchOB(compound_sdf, nitroester_pattern),
+      ether_alkyl = NA_integer_, #calculated below
+      ether_alicyclic = ChemmineR::smartsSearchOB(compound_sdf, smarts$ether_alicyclic),
+      ether_aromatic = ChemmineR::smartsSearchOB(compound_sdf, smarts$ether_aromatic),
+      nitrate = ChemmineR::smartsSearchOB(compound_sdf, smarts$nitrate),
+      nitro = ChemmineR::smartsSearchOB(compound_sdf, smarts$nitro),
+      amine_primary   = ChemmineR::smartsSearchOB(compound_sdf, smarts$amine_primary),
+      amine_secondary = ChemmineR::smartsSearchOB(compound_sdf, smarts$amine_secondary),
+      amine_tertiary  = ChemmineR::smartsSearchOB(compound_sdf, smarts$amine_tertiary),
+      amine_aromatic = ChemmineR::smartsSearchOB(compound_sdf, smarts$amine_aromatic),
+      amide_primary = ChemmineR::smartsSearchOB(compound_sdf, smarts$amide_primary),
+      amide_secondary = ChemmineR::smartsSearchOB(compound_sdf, smarts$amide_secondary),
+      amide_tertiary = ChemmineR::smartsSearchOB(compound_sdf, smarts$amide_tertiary),
+      carbonylperoxynitrate = ChemmineR::smartsSearchOB(compound_sdf, smarts$carbonylperoxynitrate),
+      peroxide = ChemmineR::smartsSearchOB(compound_sdf, smarts$peroxide),
+      hydroperoxide = ChemmineR::smartsSearchOB(compound_sdf, smarts$hydroperoxide),
+      carbonylperoxyacid = ChemmineR::smartsSearchOB(compound_sdf, smarts$carbonylperoxyacid),
+      nitrophenol = ChemmineR::smartsSearchOB(compound_sdf, smarts$nitrophenol),
+      nitroester = ChemmineR::smartsSearchOB(compound_sdf, smarts$nitroester),
 
       # Additional groups from Meredith et al. 2023
-      phosphoric_acids = ChemmineR::smartsSearchOB(compound_sdf, phosphoric_acid_pattern),
-      phosphoric_esters = ChemmineR::smartsSearchOB(compound_sdf, phosphoric_ester_pattern),
-      sulfates = ChemmineR::smartsSearchOB(compound_sdf, sulfate_pattern),
-      sulfonates = ChemmineR::smartsSearchOB(compound_sdf, sulfonate_pattern),
-      thiols = ChemmineR::smartsSearchOB(compound_sdf, thiol_pattern),
-      carbothioesters = ChemmineR::smartsSearchOB(compound_sdf, carbothioester_pattern),
+      phosphoric_acids = ChemmineR::smartsSearchOB(compound_sdf, smarts$phosphoric_acids),
+      phosphoric_esters = ChemmineR::smartsSearchOB(compound_sdf, smarts$phosphoric_esters),
+      sulfates = ChemmineR::smartsSearchOB(compound_sdf, smarts$sulfates),
+      sulfonates = ChemmineR::smartsSearchOB(compound_sdf, smarts$sulfonates),
+      thiols = ChemmineR::smartsSearchOB(compound_sdf, smarts$thiols),
+      carbothioesters = ChemmineR::smartsSearchOB(compound_sdf, smarts$carbothioesters),
       oxygens   = atoms[["O"]] %||% 0L,
       chlorines = atoms[["Cl"]] %||% 0L,
       nitrogens = atoms[["N"]] %||% 0L,

data-raw/README.md

@@ -0,0 +1,4 @@
+In the future, if new methods are added, create a separate .csv file named smarts_<method>.csv.
+To turn this into a user-facing dataset, edit `make_data.R` to add another `usethis::use_data()` and document it by adding a new entry to `R/data.R`.  To also use this in internal data, it needs to be added as an argument to `usethis::use_data(..., internal = TRUE)` since only one sysdata.rda can exist for holding internal data.  E.g. `usethis::use_data(smarts_patterns_simpol1, smarts_patterns_newmethod, internal = TRUE, overwrite = TRUE)`
+
+Be sure to run the code in `make_data.R` and to run `devtools::document()` to update data and documentation.

data-raw/make_data.R

@@ -0,0 +1,14 @@
+## code to prepare `smarts` dataset goes here
+smarts_simpol1 <- readr::read_csv("data-raw/smarts_simpol1.csv")
+
+#create user-facing data.frame
+usethis::use_data(smarts_simpol1, overwrite = TRUE)
+
+#create internal named list with just SMARTS strings
+just_smarts_simpol1 <- 
+  smarts_simpol1 %>% 
+  dplyr::filter(!is.na(smarts)) 
+smarts_patterns_simpol1 <- as.list(just_smarts_simpol1$smarts)
+names(smarts_patterns_simpol1) <- just_smarts_simpol1$functional_group
+
+usethis::use_data(smarts_patterns_simpol1, internal = TRUE, overwrite = TRUE)

data-raw/smarts_simpol1.csv

@@ -4,7 +4,7 @@ simpol1,rings_aromatic,NA,ChemmineR::rings,
 simpol1,rings_total,NA,ChemmineR::rings,
 simpol1,rings_aliphatic,NA,rings_total - rings_aromatic,
 simpol1,carbon_dbl_bonds_aliphatic,C=C,ChemmineR::smartsSearchOB,
-simpol1,CCCO_aliphatic_ring,C(C=C[AR1])(=O)[AR1],ChemmineR::smartsSearchOB,
+simpol1,CCCO_aliphatic_ring,C(C=C[AR1])(=O)[AR1],ChemmineR::smartsSearchOB,Matches C=C-C=O in a non-aromatic ring
 simpol1,hydroxyl_total,NA,ChemmineR::groups,
 simpol1,hydroxyl_aromatic,[OX2H]c,ChemmineR::smartsSearchOB,"This pattern also captures nitrophenols, so the number of nitrophenols is subtracted"
 simpol1,hydroxyl_aliphatic,NA,hydroxyl_total - hydroxyl_aromatic,