diff options
Diffstat (limited to 'man')
| -rw-r--r-- | man/chent.Rd | 145 | ||||
| -rw-r--r-- | man/pai.Rd | 3 |
2 files changed, 130 insertions, 18 deletions
diff --git a/man/chent.Rd b/man/chent.Rd index 15fbc54..e069938 100644 --- a/man/chent.Rd +++ b/man/chent.Rd @@ -7,12 +7,12 @@ An \code{\link{R6Class}} generator object } \description{ -The class is initialised with an identifier. Chemical information is retrieved from -the internet. Additionally, it can be generated using RDKit if RDKit and its -python bindings are installed. +The class is initialised with an identifier. Chemical +information is retrieved from the internet. Additionally, it can be +generated using RDKit if RDKit and its python bindings are installed. } \examples{ -oct <- chent$new("1-octanol", smiles = "CCCCCCCCO") +oct <- chent$new("1-octanol", smiles = "CCCCCCCCO", pubchem = FALSE) print(oct) if (!is.null(oct$Picture)) { plot(oct) @@ -24,19 +24,23 @@ if (!is.null(caffeine$Picture)) { plot(caffeine) } } -\keyword{data} \section{Public fields}{ \if{html}{\out{<div class="r6-fields">}} \describe{ -\item{\code{identifier}}{The identifier that was used to initiate the object, with attribute 'source'} +\item{\code{identifier}}{(\code{character(1)})\cr +The identifier that was used to initiate the object, with attribute 'source'} -\item{\code{inchikey}}{InChI Key, with attribute 'source'} +\item{\code{inchikey}}{(\code{character(1)})\cr +InChI Key, with attribute 'source'} -\item{\code{smiles}}{SMILES code, with attribute 'source'} +\item{\code{smiles}}{(\code{character()})\cr +SMILES code(s), with attribute 'source'} -\item{\code{mw}}{Molecular weight, with attribute 'source'} +\item{\code{mw}}{(\code{numeric(1)})\cr +Molecular weight, with attribute 'source'} -\item{\code{pubchem}}{List of information retreived from PubChem} +\item{\code{pubchem}}{(\code{list()})\cr +List of information retrieved from PubChem} \item{\code{rdkit}}{List of information obtained with RDKit} @@ -54,15 +58,22 @@ if (!is.null(caffeine$Picture)) { \item{\code{cwsat}}{Water solubility in mg/L} +\item{\code{PUF}}{Plant uptake factor} + \item{\code{chyaml}}{List of information obtained from a YAML file} -\item{\code{soil_degradation}}{Dataframe of modelling DT50 values} +\item{\code{TPs}}{List of transformation products as chent objects +Add a transformation product to the internal list} + +\item{\code{transformations}}{Data frame of observed transformations +Add a line in the internal dataframe holding observed transformations} + +\item{\code{soil_degradation}}{Dataframe of modelling DT50 values +Add a line in the internal dataframe holding modelling DT50 values} \item{\code{soil_ff}}{Dataframe of formation fractions} \item{\code{soil_sorption}}{Dataframe of soil sorption data} - -\item{\code{PUF}}{Plant uptake factor} } \if{html}{\out{</div>}} } @@ -92,13 +103,12 @@ if (!is.null(caffeine$Picture)) { \if{html}{\out{<a id="method-chent-new"></a>}} \if{latex}{\out{\hypertarget{method-chent-new}{}}} \subsection{Method \code{new()}}{ +Creates a new instance of this \link[R6:R6Class]{R6} class. \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$new( identifier, smiles = NULL, - smiles_source = "user", inchikey = NULL, - inchikey_source = "user", pubchem = TRUE, pubchem_from = c("name", "smiles", "inchikey"), rdkit = TRUE, @@ -107,6 +117,33 @@ if (!is.null(caffeine$Picture)) { )}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{identifier}}{Identifier to be stored in the object} + +\item{\code{smiles}}{Optional user provided SMILES code} + +\item{\code{inchikey}}{Optional user provided InChI Key} + +\item{\code{pubchem}}{Should an attempt be made to retrieve chemical +information from PubChem via the webchem package?} + +\item{\code{pubchem_from}}{Possibility to select the argument +that is used to query pubchem} + +\item{\code{rdkit}}{Should an attempt be made to retrieve chemical +information from a local rdkit installation via python +and the reticulate package?} + +\item{\code{template}}{An optional SMILES code to be used as template for RDKit} + +\item{\code{chyaml}}{Should we look for a identifier.yaml file in the working +directory? +Try to get chemical information from PubChem} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-chent-try_pubchem"></a>}} @@ -116,6 +153,16 @@ if (!is.null(caffeine$Picture)) { \if{html}{\out{<div class="r">}}\preformatted{chent$try_pubchem(query, from = "name")}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{query}}{Query string to be passed to \link[webchem:get_cid]{get_cid}} + +\item{\code{from}}{Passed to \link[webchem:get_cid]{get_cid} +Get chemical information from PubChem for a known PubChem CID} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-chent-get_pubchem"></a>}} @@ -125,6 +172,14 @@ if (!is.null(caffeine$Picture)) { \if{html}{\out{<div class="r">}}\preformatted{chent$get_pubchem(pubchem_cid)}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{pubchem_cid}}{CID +Get chemical information from RDKit if available} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-chent-get_rdkit"></a>}} @@ -134,6 +189,14 @@ if (!is.null(caffeine$Picture)) { \if{html}{\out{<div class="r">}}\preformatted{chent$get_rdkit(template = NULL)}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{template}}{Optional template specified as a SMILES code +Obtain information from a YAML file} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-chent-get_chyaml"></a>}} @@ -146,6 +209,16 @@ if (!is.null(caffeine$Picture)) { )}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{repo}}{Should the file be looked for in the current working +directory, a local git repository under \verb{~/git/chyaml}, or from +the web (not implemented). +Add a vapour pressure} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-chent-add_p0"></a>}} @@ -155,6 +228,22 @@ if (!is.null(caffeine$Picture)) { \if{html}{\out{<div class="r">}}\preformatted{chent$add_p0(p0, T = NA, source = NA, page = NA, remark = "")}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{p0}}{The vapour pressure in Pa} + +\item{\code{T}}{Temperature} + +\item{\code{source}}{An acronym specifying the source of the information} + +\item{\code{page}}{The page from which the information was taken} + +\item{\code{remark}}{A remark +Add a water solubility} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-chent-add_cwsat"></a>}} @@ -164,6 +253,14 @@ if (!is.null(caffeine$Picture)) { \if{html}{\out{<div class="r">}}\preformatted{chent$add_cwsat(cwsat, T = NA, pH = NA, source = NA, page = NA, remark = "")}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{p0}}{The water solubility in mg/L +Add a plant uptake factor} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-chent-add_PUF"></a>}} @@ -178,6 +275,13 @@ if (!is.null(caffeine$Picture)) { )}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{PUF}}{The plant uptake factor, a number between 0 and 1} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-chent-add_TP"></a>}} @@ -187,6 +291,17 @@ if (!is.null(caffeine$Picture)) { \if{html}{\out{<div class="r">}}\preformatted{chent$add_TP(x, smiles = NULL, pubchem = FALSE)}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{x}}{A \link{chent} object, or an identifier to generate a \link{chent} object} + +\item{\code{smiles}}{A SMILES code for defining a \link{chent} object} + +\item{\code{pubchem}}{Should chemical information be obtained from PubChem?} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-chent-add_transformation"></a>}} @@ -25,7 +25,6 @@ if (!is.null(atr$Picture)) { } } -\keyword{data} \section{Super class}{ \code{\link[chents:chent]{chents::chent}} -> \code{pai} } @@ -75,9 +74,7 @@ if (!is.null(atr$Picture)) { iso, identifier = iso, smiles = NULL, - smiles_source = "user", inchikey = NULL, - inchikey_source = "user", bcpc = TRUE, pubchem = TRUE, pubchem_from = "auto", |