diff --git a/R/get_fx_groups.R b/R/get_fx_groups.R index afacf95..f2d96f6 100644 --- a/R/get_fx_groups.R +++ b/R/get_fx_groups.R @@ -121,7 +121,7 @@ get_fx_groups <- function(compound_sdf) { carbons_asa = NA_integer_, #carbon number on the acid-side of amide rings_aromatic = as.integer(rings$AROMATIC), rings_total = as.integer(rings$RINGS), - rings_aliphatic = rings_total - rings_aromatic, + rings_aliphatic = .data$rings_total - .data$rings_aromatic, carbon_dbl_bonds = 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 hydroxyl_total = groups$ROH, @@ -132,7 +132,7 @@ get_fx_groups <- function(compound_sdf) { carbox_acids = groups$RCOOH, ester = groups$RCOOR, ether_total = groups$ROR, - ether_alkyl = ChemmineR::smartsSearchOB(compound_sdf, ether_pattern) - ester, + ether_alkyl = ChemmineR::smartsSearchOB(compound_sdf, ether_pattern) - .data$ester, ether_alicyclic = ChemmineR::smartsSearchOB(compound_sdf, ether_alicyclic_pattern), ether_aromatic = ChemmineR::smartsSearchOB(compound_sdf, ether_aromatic_pattern), nitrate = ChemmineR::smartsSearchOB(compound_sdf, nitrate_pattern), @@ -149,7 +149,7 @@ get_fx_groups <- function(compound_sdf) { hydroperoxide = ChemmineR::smartsSearchOB(compound_sdf, hydroperoxide_pattern), carbonylperoxyacid = ChemmineR::smartsSearchOB(compound_sdf, carbonylperoxyacid_pattern), #correction--hydroperoxide pattern also picks up peroxyacids - hydroperoxide = hydroperoxide - carbonylperoxyacid, + hydroperoxide = .data$hydroperoxide - .data$carbonylperoxyacid, nitrophenol = NA_integer_, #TODO: still confused about this one # nitrophenol = ChemmineR::smartsSearchOB(compound_sdf, nitrophenol_pattern), nitroester = NA_integer_, #TODO: still very confused about this one