diff options
| -rw-r--r-- | ChangeLog | 6 | ||||
| -rw-r--r-- | DESCRIPTION | 2 | ||||
| -rw-r--r-- | R/chent.R | 39 | ||||
| -rw-r--r-- | man/chent.Rd | 4 |
4 files changed, 40 insertions, 11 deletions
@@ -1,3 +1,9 @@ +commit 4bd4606c76dfc152547e0f5899a98494a4290d33 +Author: Johannes Ranke <jranke@uni-bremen.de> +Date: 2018-03-01 09:48:02 +0100 + + Rebuild static documentation with current pkdown + commit 3f82707cd1e974848185b1141c69734e2573594d Author: Johannes Ranke <jranke@uni-bremen.de> Date: 2017-06-13 16:05:39 +0200 diff --git a/DESCRIPTION b/DESCRIPTION index 05af50c..f2b4656 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: chents Type: Package Title: Chemical Entities as R Objects Version: 0.2-6 -Date: 2018-02-27 +Date: 2018-05-16 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de")) Description: Utilities for dealing with chemical entities and associated @@ -1,4 +1,4 @@ -# Copyright (C) 2016 Johannes Ranke +# Copyright (C) 2016,2017,2018 Johannes Ranke # Contact: jranke@uni-bremen.de # This file is part of the R package chents @@ -39,6 +39,8 @@ #' @field Picture Graph as a \code{\link{picture}} object obtained using grImport #' @field Pict_font_size Font size as extracted from the intermediate PostScript file #' @field pdf_height Height of the MediaBox in the pdf after cropping +#' @field p0 Vapour pressure in Pa +#' @field cwsat Water solubility in mg/L #' @field chyaml List of information obtained from a YAML file #' @field degradation List of degradation endpoints #' @example inst/examples/octanol.R @@ -57,6 +59,8 @@ chent <- R6Class("chent", Picture = NULL, Pict_font_size = NULL, pdf_height = NULL, + p0 = NULL, + cwsat = NULL, chyaml = NULL, degradation = NULL, initialize = function(identifier, smiles = NULL, smiles_source = 'user', @@ -241,6 +245,21 @@ chent <- R6Class("chent", message("web repositories not implemented") } }, + add_p0 = function(p0, T = NA, source = NA, page = NA, remark = "") { + self$p0 <- p0 + attr(self$p0, "T") <- T + attr(self$p0, "source") <- source + attr(self$p0, "page") <- page + attr(self$p0, "remark") <- remark + }, + add_cwsat = function(cwsat, T = NA, pH = NA, source = NA, page = NA, remark = "") { + self$cwsat <- cwsat + attr(self$cwsat, "T") <- T + attr(self$cwsat, "pH") <- pH + attr(self$cwsat, "source") <- source + attr(self$cwsat, "page") <- page + attr(self$cwsat, "remark") <- remark + }, TPs = list(), add_TP = function(x, smiles = NULL) { if (inherits(x, "chent")) { @@ -259,7 +278,7 @@ chent <- R6Class("chent", pages = character(0), stringsAsFactors = FALSE), add_transformation = function(study_type, TP_identifier, max_occurrence, - comment = "", source = NA, pages = NA) { + remark = "", source = NA, pages = NA) { TP_name = make.names(TP_identifier) if (!inherits(self$TPs[[TP_name]], "chent")) { stop(paste("Please add the TP", TP_identifier, "first using chent$add_TP()")) @@ -271,34 +290,34 @@ chent <- R6Class("chent", data.frame(study_type = study_type, TP_identifier = TP_identifier, max_occurrence = max_occurrence, - comment = comment, + remark = remark, source = source, pages = pages, stringsAsFactors = FALSE)) }, soil_degradation_endpoints = data.frame(destination = character(0), DT50 = numeric(0), - comment = character(0), + remark = character(0), pages = character(0), stringsAsFactors = FALSE), add_soil_degradation_endpoints = function(destination, DT50 = NA, - comment = "", pages = NA) { + remark = "", pages = NA) { if (length(pages) > 1) pages = paste(pages, collapse = ", ") i <- nrow(self$soil_degradation_endpoints) + 1 - self$soil_degradation_endpoints[i, c("destination", "comment", "pages")] <- - c(destination, comment, pages) + self$soil_degradation_endpoints[i, c("destination", "remark", "pages")] <- + c(destination, remark, pages) self$soil_degradation_endpoints[i, "DT50"] <- DT50 }, ff = data.frame(from = character(0), to = character(0), ff = numeric(0), - comment = character(0), pages = character(0), + remark = character(0), pages = character(0), stringsAsFactors = FALSE), - add_ff = function(from = "parent", to, ff = 1, comment = "", pages = NA) { + add_ff = function(from = "parent", to, ff = 1, remark = "", pages = NA) { i <- nrow(self$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$ff[i, ] <- c(from, to, ff, comment, pages) + self$ff[i, ] <- c(from, to, ff, remark, pages) }, pdf = function(file = paste0(self$identifier, ".pdf"), dir = "structures/pdf", template = NULL) { diff --git a/man/chent.Rd b/man/chent.Rd index 1deb434..f5ed2dc 100644 --- a/man/chent.Rd +++ b/man/chent.Rd @@ -37,6 +37,10 @@ configured for use with PythonInR} \item{\code{pdf_height}}{Height of the MediaBox in the pdf after cropping} +\item{\code{p0}}{Vapour pressure in Pa} + +\item{\code{cwsat}}{Water solubility in mg/L} + \item{\code{chyaml}}{List of information obtained from a YAML file} \item{\code{degradation}}{List of degradation endpoints} |