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-rw-r--r--ChangeLog6
-rw-r--r--DESCRIPTION2
-rw-r--r--R/chent.R39
-rw-r--r--man/chent.Rd4
4 files changed, 40 insertions, 11 deletions
diff --git a/ChangeLog b/ChangeLog
index ec197d8..cfb6411 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -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
diff --git a/R/chent.R b/R/chent.R
index 3e89e14..ad3bc3c 100644
--- a/R/chent.R
+++ b/R/chent.R
@@ -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}

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