From f4b487c7677c9c228bdc11851bc7f932c5311e38 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 11 Nov 2022 14:05:41 +0100 Subject: Update docs, use run.sh on travis --- man/chent.Rd | 102 +++++++++++++++++++++++++++++------------------------------ man/pai.Rd | 58 ++++++++++++++++----------------- man/pp.Rd | 18 +++++------ 3 files changed, 89 insertions(+), 89 deletions(-) (limited to 'man') diff --git a/man/chent.Rd b/man/chent.Rd index d94452e..15fbc54 100644 --- a/man/chent.Rd +++ b/man/chent.Rd @@ -69,28 +69,28 @@ if (!is.null(caffeine$Picture)) { \section{Methods}{ \subsection{Public methods}{ \itemize{ -\item \href{#method-new}{\code{chent$new()}} -\item \href{#method-try_pubchem}{\code{chent$try_pubchem()}} -\item \href{#method-get_pubchem}{\code{chent$get_pubchem()}} -\item \href{#method-get_rdkit}{\code{chent$get_rdkit()}} -\item \href{#method-get_chyaml}{\code{chent$get_chyaml()}} -\item \href{#method-add_p0}{\code{chent$add_p0()}} -\item \href{#method-add_cwsat}{\code{chent$add_cwsat()}} -\item \href{#method-add_PUF}{\code{chent$add_PUF()}} -\item \href{#method-add_TP}{\code{chent$add_TP()}} -\item \href{#method-add_transformation}{\code{chent$add_transformation()}} -\item \href{#method-add_soil_degradation}{\code{chent$add_soil_degradation()}} -\item \href{#method-add_soil_ff}{\code{chent$add_soil_ff()}} -\item \href{#method-add_soil_sorption}{\code{chent$add_soil_sorption()}} -\item \href{#method-pdf}{\code{chent$pdf()}} -\item \href{#method-png}{\code{chent$png()}} -\item \href{#method-emf}{\code{chent$emf()}} -\item \href{#method-clone}{\code{chent$clone()}} +\item \href{#method-chent-new}{\code{chent$new()}} +\item \href{#method-chent-try_pubchem}{\code{chent$try_pubchem()}} +\item \href{#method-chent-get_pubchem}{\code{chent$get_pubchem()}} +\item \href{#method-chent-get_rdkit}{\code{chent$get_rdkit()}} +\item \href{#method-chent-get_chyaml}{\code{chent$get_chyaml()}} +\item \href{#method-chent-add_p0}{\code{chent$add_p0()}} +\item \href{#method-chent-add_cwsat}{\code{chent$add_cwsat()}} +\item \href{#method-chent-add_PUF}{\code{chent$add_PUF()}} +\item \href{#method-chent-add_TP}{\code{chent$add_TP()}} +\item \href{#method-chent-add_transformation}{\code{chent$add_transformation()}} +\item \href{#method-chent-add_soil_degradation}{\code{chent$add_soil_degradation()}} +\item \href{#method-chent-add_soil_ff}{\code{chent$add_soil_ff()}} +\item \href{#method-chent-add_soil_sorption}{\code{chent$add_soil_sorption()}} +\item \href{#method-chent-pdf}{\code{chent$pdf()}} +\item \href{#method-chent-png}{\code{chent$png()}} +\item \href{#method-chent-emf}{\code{chent$emf()}} +\item \href{#method-chent-clone}{\code{chent$clone()}} } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-new}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-chent-new}{}}} \subsection{Method \code{new()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{chent$new( @@ -109,8 +109,8 @@ if (!is.null(caffeine$Picture)) { } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-try_pubchem}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-chent-try_pubchem}{}}} \subsection{Method \code{try_pubchem()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{chent$try_pubchem(query, from = "name")}\if{html}{\out{
}} @@ -118,8 +118,8 @@ if (!is.null(caffeine$Picture)) { } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-get_pubchem}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-chent-get_pubchem}{}}} \subsection{Method \code{get_pubchem()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{chent$get_pubchem(pubchem_cid)}\if{html}{\out{
}} @@ -127,8 +127,8 @@ if (!is.null(caffeine$Picture)) { } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-get_rdkit}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-chent-get_rdkit}{}}} \subsection{Method \code{get_rdkit()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{chent$get_rdkit(template = NULL)}\if{html}{\out{
}} @@ -136,8 +136,8 @@ if (!is.null(caffeine$Picture)) { } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-get_chyaml}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-chent-get_chyaml}{}}} \subsection{Method \code{get_chyaml()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{chent$get_chyaml( @@ -148,8 +148,8 @@ if (!is.null(caffeine$Picture)) { } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-add_p0}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-chent-add_p0}{}}} \subsection{Method \code{add_p0()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{chent$add_p0(p0, T = NA, source = NA, page = NA, remark = "")}\if{html}{\out{
}} @@ -157,8 +157,8 @@ if (!is.null(caffeine$Picture)) { } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-add_cwsat}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-chent-add_cwsat}{}}} \subsection{Method \code{add_cwsat()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{chent$add_cwsat(cwsat, T = NA, pH = NA, source = NA, page = NA, remark = "")}\if{html}{\out{
}} @@ -166,8 +166,8 @@ if (!is.null(caffeine$Picture)) { } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-add_PUF}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-chent-add_PUF}{}}} \subsection{Method \code{add_PUF()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{chent$add_PUF( @@ -180,8 +180,8 @@ if (!is.null(caffeine$Picture)) { } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-add_TP}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-chent-add_TP}{}}} \subsection{Method \code{add_TP()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{chent$add_TP(x, smiles = NULL, pubchem = FALSE)}\if{html}{\out{
}} @@ -189,8 +189,8 @@ if (!is.null(caffeine$Picture)) { } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-add_transformation}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-chent-add_transformation}{}}} \subsection{Method \code{add_transformation()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{chent$add_transformation( @@ -205,8 +205,8 @@ if (!is.null(caffeine$Picture)) { } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-add_soil_degradation}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-chent-add_soil_degradation}{}}} \subsection{Method \code{add_soil_degradation()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{chent$add_soil_degradation( @@ -233,8 +233,8 @@ if (!is.null(caffeine$Picture)) { } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-add_soil_ff}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-chent-add_soil_ff}{}}} \subsection{Method \code{add_soil_ff()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{chent$add_soil_ff(target, soils, ff = 1, remark = "", source, page = NA)}\if{html}{\out{
}} @@ -242,8 +242,8 @@ if (!is.null(caffeine$Picture)) { } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-add_soil_sorption}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-chent-add_soil_sorption}{}}} \subsection{Method \code{add_soil_sorption()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{chent$add_soil_sorption( @@ -266,8 +266,8 @@ if (!is.null(caffeine$Picture)) { } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-pdf}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-chent-pdf}{}}} \subsection{Method \code{pdf()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{chent$pdf( @@ -279,8 +279,8 @@ if (!is.null(caffeine$Picture)) { } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-png}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-chent-png}{}}} \subsection{Method \code{png()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{chent$png( @@ -292,8 +292,8 @@ if (!is.null(caffeine$Picture)) { } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-emf}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-chent-emf}{}}} \subsection{Method \code{emf()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{chent$emf(file = paste0(self$identifier, ".emf"), dir = "structures/emf")}\if{html}{\out{
}} @@ -301,8 +301,8 @@ if (!is.null(caffeine$Picture)) { } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-clone}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-chent-clone}{}}} \subsection{Method \code{clone()}}{ The objects of this class are cloneable with this method. \subsection{Usage}{ diff --git a/man/pai.Rd b/man/pai.Rd index cec3015..088f5b9 100644 --- a/man/pai.Rd +++ b/man/pai.Rd @@ -41,34 +41,34 @@ if (!is.null(atr$Picture)) { \section{Methods}{ \subsection{Public methods}{ \itemize{ -\item \href{#method-new}{\code{pai$new()}} -\item \href{#method-clone}{\code{pai$clone()}} -} -} -\if{html}{ -\out{
Inherited methods} -\itemize{ -\item \out{}\href{../../chents/html/chent.html#method-add_PUF}{\code{chents::chent$add_PUF()}}\out{} -\item \out{}\href{../../chents/html/chent.html#method-add_TP}{\code{chents::chent$add_TP()}}\out{} -\item \out{}\href{../../chents/html/chent.html#method-add_cwsat}{\code{chents::chent$add_cwsat()}}\out{} -\item \out{}\href{../../chents/html/chent.html#method-add_p0}{\code{chents::chent$add_p0()}}\out{} -\item \out{}\href{../../chents/html/chent.html#method-add_soil_degradation}{\code{chents::chent$add_soil_degradation()}}\out{} -\item \out{}\href{../../chents/html/chent.html#method-add_soil_ff}{\code{chents::chent$add_soil_ff()}}\out{} -\item \out{}\href{../../chents/html/chent.html#method-add_soil_sorption}{\code{chents::chent$add_soil_sorption()}}\out{} -\item \out{}\href{../../chents/html/chent.html#method-add_transformation}{\code{chents::chent$add_transformation()}}\out{} -\item \out{}\href{../../chents/html/chent.html#method-emf}{\code{chents::chent$emf()}}\out{} -\item \out{}\href{../../chents/html/chent.html#method-get_chyaml}{\code{chents::chent$get_chyaml()}}\out{} -\item \out{}\href{../../chents/html/chent.html#method-get_pubchem}{\code{chents::chent$get_pubchem()}}\out{} -\item \out{}\href{../../chents/html/chent.html#method-get_rdkit}{\code{chents::chent$get_rdkit()}}\out{} -\item \out{}\href{../../chents/html/chent.html#method-pdf}{\code{chents::chent$pdf()}}\out{} -\item \out{}\href{../../chents/html/chent.html#method-png}{\code{chents::chent$png()}}\out{} -\item \out{}\href{../../chents/html/chent.html#method-try_pubchem}{\code{chents::chent$try_pubchem()}}\out{} -} -\out{
} -} +\item \href{#method-pai-new}{\code{pai$new()}} +\item \href{#method-pai-clone}{\code{pai$clone()}} +} +} +\if{html}{\out{ +
Inherited methods + +
+}} \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-new}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-pai-new}{}}} \subsection{Method \code{new()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{pai$new( @@ -89,8 +89,8 @@ if (!is.null(atr$Picture)) { } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-clone}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-pai-clone}{}}} \subsection{Method \code{clone()}}{ The objects of this class are cloneable with this method. \subsection{Usage}{ diff --git a/man/pp.Rd b/man/pp.Rd index cd950df..363f9ba 100644 --- a/man/pp.Rd +++ b/man/pp.Rd @@ -27,14 +27,14 @@ An R6 class for holding information about a product with at least one active ing \section{Methods}{ \subsection{Public methods}{ \itemize{ -\item \href{#method-new}{\code{pp$new()}} -\item \href{#method-print}{\code{pp$print()}} -\item \href{#method-clone}{\code{pp$clone()}} +\item \href{#method-pp-new}{\code{pp$new()}} +\item \href{#method-pp-print}{\code{pp$print()}} +\item \href{#method-pp-clone}{\code{pp$clone()}} } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-new}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-pp-new}{}}} \subsection{Method \code{new()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{pp$new( @@ -49,8 +49,8 @@ An R6 class for holding information about a product with at least one active ing } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-print}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-pp-print}{}}} \subsection{Method \code{print()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{pp$print()}\if{html}{\out{
}} @@ -58,8 +58,8 @@ An R6 class for holding information about a product with at least one active ing } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-clone}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-pp-clone}{}}} \subsection{Method \code{clone()}}{ The objects of this class are cloneable with this method. \subsection{Usage}{ -- cgit v1.2.1