From fd1609aafd2f40266c1e29d8dfdf5e08e8838d35 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sun, 24 May 2015 03:52:28 +0200 Subject: Start of a pfm_chent data object --- pkg/R/pfm_chent.R | 266 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 266 insertions(+) create mode 100644 pkg/R/pfm_chent.R (limited to 'pkg/R/pfm_chent.R') diff --git a/pkg/R/pfm_chent.R b/pkg/R/pfm_chent.R new file mode 100644 index 0000000..13a883b --- /dev/null +++ b/pkg/R/pfm_chent.R @@ -0,0 +1,266 @@ +# Copyright (C) 2015 Johannes Ranke +# Contact: jranke@uni-bremen.de +# This file is part of the R package pfm + +# This program is free software: you can redistribute it and/or modify it under +# the terms of the GNU General Public License as published by the Free Software +# Foundation, either version 3 of the License, or (at your option) any later +# version. + +# This program is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more +# details. + +# You should have received a copy of the GNU General Public License along with +# this program. If not, see + +#' R6 class for holding a chemical entity +#' +#' An R6 class for holding information about a chemical entity +#' +#' @docType class +#' @importFrom R6 R6Class +#' @export +#' @format An \code{\link{R6Class}} generator object. +#' @field acronym Acronym for local use +#' @field smiles SMILES code +#' @field mw Molecular weight +#' @field main_source Main source of information +#' @field transformations +#' @field sorption_endpoints +#' @examples +#' atrazine <- pfm_chent("atrazine", smiles = "Clc1nc(nc(n1)NC(C)C)NCC", mw = 215.68) +#' print(atrazine) +#' @keywords data + +pfm_chent <- R6Class("pfm_chent", + public <- list( + acronym = NULL, + smiles = NULL, + mw = NULL, + main_source = NULL, + initialize = function(acronym, smiles = NULL, mw = NULL, main_source = NULL) { + self$acronym <- acronym + self$smiles <- smiles + self$mw <- mw + self$main_source <- main_source + }, + p0 = data.frame(p0 = numeric(0), T = numeric(0), + comment = character(0), + source = character(0), pages = character(0), + stringsAsFactors = FALSE), + add_p0 = function(p0, T = 25, comment = "", source, pages = NA) { + i <- nrow(self$p0) + 1 + self$p0[i, c("p0", "T")] <- c(p0, T) + self$p0[i, c("comment", "pages")] <- c(comment, pages) + if (!missing(source)) self$p0[i, "source"] <- source + }, + cwsat = data.frame(cwsat = numeric(0), T = numeric(0), + pH = numeric(0), comment = character(0), + source = character(0), pages = character(0), + stringsAsFactors = FALSE), + add_cwsat = function(cwsat, T = NA, pH = NA, comment = "", source, pages = NA) { + i <- nrow(self$cwsat) + 1 + self$cwsat[i, c("cwsat", "T", "pH")] <- c(cwsat, T, pH) + self$cwsat[i, c("comment", "pages")] <- c(comment, pages) + if (!missing(source)) self$cwsat[i, "source"] <- source + }, + TPs = list(), + add_TP = function(x, smiles = NULL, mw = NULL, main_source = NULL) { + if (inherits(x, "pfm_chent")) { + chent_name <- deparse(substitute(x)) + chent <- x + } else { + chent_name <- make.names(x) + chent <- pfm_chent$new(x, smiles, mw, main_source) + } + self$TPs[[chent_name]] <- chent + }, + transformations = data.frame(study_type = character(0), + acronym = character(0), + max_occurrence = numeric(0), + source = character(0), + pages = character(0), + stringsAsFactors = FALSE), + add_transformations = function(study_type, TPs, max_occurrence, + comment = "", source, pages = NA) { + TP_names = make.names(TPs) + TP_is_chent = sapply(self$TPs[TP_names], function(x) inherits(x, "pfm_chent")) + if (!all(TP_is_chent)) { + stop(paste("Please add all TPs using pfm_chent$add_TP()", print(TP_is_chent))) + } + chents <- self$TPs[TP_names] + if (missing(source)) source <- self$main_source + if (is.numeric(pages)) pages <- paste(pages, collapse = ", ") + transformations <- data.frame(study_type = study_type, + acronym = sapply(chents, function(x) x$acronym), + max_occurrence = max_occurrence, + comment = comment, + source = source, + pages = pages, + row.names = NULL, + stringsAsFactors = FALSE) + self$transformations <- rbind(self$transformations, transformations) + }, + soil_degradation_endpoints = data.frame(destination = character(0), + DT50 = numeric(0), + comment = character(0), + pages = character(0), + stringsAsFactors = FALSE), + add_soil_degradation_endpoints = function(destination, DT50 = NA, + comment = "", pages = NA) { + i <- nrow(self$soil_degradation_endpoints) + 1 + self$soil_degradation_endpoints[i, c("destination", "comment", "pages")] <- + c(destination, comment, pages) + self$soil_degradation_endpoints[i, "DT50"] <- DT50 + }, + ws_degradation_endpoints = data.frame(destination = character(0), + DT50 = numeric(0), + comment = character(0), + tier = character(0), + pages = character(0), + stringsAsFactors = FALSE), + add_ws_degradation_endpoints = function(destination, DT50 = NA, tier = NA, + comment = "", pages = NA) { + i <- nrow(self$ws_degradation_endpoints) + 1 + self$ws_degradation_endpoints[i, c("destination", "tier", "comment", "pages")] <- + c(destination, tier, comment, pages) + self$ws_degradation_endpoints[i, "DT50"] <- DT50 + }, + water_degradation_endpoints = data.frame(destination = character(0), + DT50 = numeric(0), + tier = character(0), + comment = character(0), + pages = character(0), + stringsAsFactors = FALSE), + add_water_degradation_endpoints = function(destination, DT50 = NA, tier = NA, + comment = "", pages = NA) { + i <- nrow(self$water_degradation_endpoints) + 1 + self$water_degradation_endpoints[i, c("destination", "tier", "comment", "pages")] <- + c(destination, tier, comment, pages) + self$water_degradation_endpoints[i, "DT50"] <- DT50 + }, + sediment_degradation_endpoints = data.frame(destination = character(0), + DT50 = numeric(0), + tier = character(0), + comment = character(0), + pages = character(0), + stringsAsFactors = FALSE), + add_sediment_degradation_endpoints = function(destination, DT50 = NA, tier = NA, + comment = "", pages = NA) { + i <- nrow(self$sediment_degradation_endpoints) + 1 + self$sediment_degradation_endpoints[i, c("destination", "tier", "comment", "pages")] <- + c(destination, tier, comment, pages) + self$sediment_degradation_endpoints[i, "DT50"] <- DT50 + }, + sorption_endpoints = data.frame(Kfoc = numeric(0), f1.n = numeric(0), + type = character(0), + comment = character(0), + pages = character(0), + stringsAsFactors = FALSE), + add_sorption_endpoints = function(Kfoc, f1.n = 1, type = "arithmetic mean", + comment = "", pages = NA) { + i <- nrow(self$sorption_endpoints) + 1 + self$sorption_endpoints[i, c("Kfoc", "f1.n")] <- c(Kfoc, f1.n) + self$sorption_endpoints[i, c("type", "comment", "pages")] <- c(type, comment, pages) + }, + print = function(TPs = TRUE) { + cat(" with acronym", self$acronym, "\n") + if (!is.null(self$smiles)) cat ("SMILES:", self$smiles, "\n") + if (!is.null(self$mw)) cat ("Molecular weight:", round(self$mw, 1), "\n") + if (!is.null(self$main_source)) cat ("Main source of information:", self$main_source, "\n") + if (TPs) { + if (length(self$TPs) > 0) { + cat("\nTransformation products:\n") + print(self$TPs) + } + if (nrow(self$transformations) > 0) { + cat("\nTransformations:\n") + print(self$transformations[order(self$transformations$study_type), ], row.names = FALSE) + } + } + } + ) +) + +#' R6 class for holding active ingredients +#' +#' An R6 class for holding information about active ingredients +#' +#' @docType class +#' @importFrom R6 R6Class +#' @importFrom pfm pfm_chent +#' @export +#' @format An \code{\link{R6Class}} generator object. +#' @field iso ISO common name +#' @examples +#' atrazine <- pfm_ai("atrazine", smiles = "Clc1nc(nc(n1)NC(C)C)NCC", mw = 215.68) +#' print(atrazine) +#' @keywords data + +pfm_ai <- R6Class("pfm_ai", + inherit = pfm_chent, + public <- list( + iso = NULL, + initialize = function(iso, acronym = iso, smiles = NULL, mw = NULL, main_source = NULL) { + super$initialize(acronym = acronym, smiles = smiles, mw = mw, main_source = main_source) + self$iso <- iso + }, + ff = data.frame(from = character(0), to = character(0), ff = numeric(0), + comment = character(0), pages = character(0), + stringsAsFactors = FALSE), + add_ff = function(from = "parent", to, ff = 1, comment = "", pages = NA) { + i <- nrow(self$ff) + 1 + if (from != "parent") { + if (!exists(from, self$TPs)) stop(from, " was not found in TPs") + } + if (!exists(to, self$TPs)) stop(to, " was not found in TPs") + self$ff[i, ] <- c(from, to, ff, comment, pages) + }, + print = function() { + if (is.null(self$iso)) cat(" with acronym", self$acronym, "\n") + else cat(" with ISO common name", self$iso, "\n") + super$print() + } + ) +) + +#' R6 class for holding a product with at least one active ingredient +#' +#' An R6 class for holding information about a product with at least one active ingredient +#' +#' @docType class +#' @importFrom R6 R6Class +#' @export +#' @format An \code{\link{R6Class}} generator object. +#' @field name The name of the product +#' @field ais A list of active ingredients +#' @field concentrations The concentration of the ais +#' @field concentration_units Defaults to g/L +#' @keywords data + +pfm_product <- R6Class("pfm_product", + public <- list( + name = NULL, + ais = list(), + concentrations = NULL, + concentration_units = NULL, + density = NULL, + density_units = "g/L", + initialize = function(name, ..., concentrations, concentration_units = "g/L", + density = 1000, density_units = "g/L") { + self$name <- name + self$ais <- list(...) + self$concentrations <- concentrations + self$density <- density + self$density_units <- density_units + names(self$concentrations) <- names(self$ais) + self$concentration_units <- concentration_units + }, + print = function() { + cat(" named", self$name, "\n") + } + ) +) + -- cgit v1.2.1