Chemical Entities as R Objects

Public fields

@@ -55,83 +55,83 @@ generated using RDKit if RDKit and its python bindings are installed.

The identifier that was used to initiate the object, with attribute 'source'

inchikey

(character(1))
InChI Key, with attribute 'source'

smiles

(character())
SMILES code(s), with attribute 'source'

mw

(numeric(1))
Molecular weight, with attribute 'source'

pubchem

(list())
List of information retrieved from PubChem

rdkit

List of information obtained with RDKit

mol

<rdkit.Chem.rdchem.Mol> object

svg

SVG code

Picture

Graph as a grImport::Picture object obtained using the grImport package

Pict_font_size

Font size as extracted from the intermediate PostScript file

pdf_height

Height of the MediaBox in the pdf after cropping

p0

Vapour pressure in Pa

cwsat

Water solubility in mg/L

PUF

Plant uptake factor

chyaml

List of information obtained from a YAML file

TPs

List of transformation products as chent objects

transformations

Data frame of observed transformations

soil_degradation

Dataframe of modelling DT50 values

soil_ff

Dataframe of formation fractions

soil_sorption

Dataframe of soil sorption data

@@ -142,8 +142,7 @@ List of information retrieved from PubChem

Public methods

- -

chent$new()

chent$new()
chent$try_pubchem()
chent$get_pubchem()
chent$get_rdkit()

chent$png()
chent$emf()
chent$clone()

Method `new()`

`chent$new()`

Creates a new instance of this R6 class.

Usage

chent$new(
@@ -174,43 +173,34 @@ List of information retrieved from PubChem
   template = NULL,
   chyaml = FALSE
 )

- -

Arguments

identifier: Identifier to be stored in the object
smiles
smiles: Optional user provided SMILES code
inchikey
inchikey: Optional user provided InChI Key
pubchem
pubchem: Should an attempt be made to retrieve chemical information from PubChem via the webchem package?
pubchem_from
pubchem_from: Possibility to select the argument that is used to query pubchem
rdkit
rdkit: Should an attempt be made to retrieve chemical information from a local rdkit installation via python and the reticulate package?
template
template: An optional SMILES code to be used as template for RDKit
chyaml
chyaml: Should we look for a identifier.yaml file in the working directory?

Method `try_pubchem()`

+ +

`chent$try_pubchem()`

Try to get chemical information from PubChem

Usage

chent$try_pubchem(query = self$identifier, from = "name")

- -

Arguments

query: Query string to be passed to get_cid
from
from: Passed to get_cid

Method `get_pubchem()`

+ +

`chent$get_pubchem()`

Get chemical information from PubChem for a known PubChem CID

Usage

chent$get_pubchem(pubchem_cid)

- -

Arguments

pubchem_cid: CID

Method `get_rdkit()`

+ +

`chent$get_rdkit()`

Get chemical information from RDKit if available

Usage

chent$get_rdkit(template = NULL)

- -

Arguments

template: An optional SMILES code to be used as template for RDKit

Method `get_chyaml()`

+ +

`chent$get_chyaml()`

Obtain information from a YAML file

Usage

chent$get_chyaml(
   repo = c("wd", "local", "web"),
   chyaml = paste0(URLencode(self$identifier), ".yaml")
 )

- -

Arguments

repo: Should the file be looked for in the current working directory, a local git repository under ~/git/chyaml, or from the web (not implemented).
chyaml
chyaml: The filename to be looked for

Method `add_p0()`

+ +

`chent$add_p0()`

Add a vapour pressure

Usage

chent$add_p0(p0, T = NA, source = NA, page = NA, remark = "")

- -

Arguments

p0: The vapour pressure in Pa
T
T: Temperature
source
source: An acronym specifying the source of the information
page
page: The page from which the information was taken
remark
remark: A remark

Method `add_cwsat()`

+ +

`chent$add_cwsat()`

Add a water solubility

Usage

chent$add_cwsat(cwsat, T = NA, pH = NA, source = NA, page = NA, remark = "")

- -

Arguments

cwsat: The water solubility in mg/L
T
T: Temperature
pH
pH: pH value
source
source: An acronym specifying the source of the information
page
page: The page from which the information was taken
remark
remark: A remark

Method `add_PUF()`

+ +

`chent$add_PUF()`

Add a plant uptake factor

Usage

chent$add_PUF(
@@ -373,55 +354,50 @@ the web (not implemented).
   page = 41,
   remark = "Conservative default value"
 )

- -

Arguments

PUF: The plant uptake factor, a number between 0 and 1
source
source: An acronym specifying the source of the information
page
page: The page from which the information was taken
remark
remark: A remark

Method `add_TP()`

+ +

`chent$add_TP()`

Add a transformation product to the internal list

Usage

chent$add_TP(x, smiles = NULL, pubchem = FALSE)

- -

Arguments

x: A chent object, or an identifier to generate a chent object
smiles
smiles: Optional user provided SMILES code
pubchem
pubchem: Should chemical information be obtained from PubChem?

Method `add_transformation()`

+ +

`chent$add_transformation()`

Add a line in the internal dataframe holding observed transformations

Usage

chent$add_transformation(
@@ -432,42 +408,37 @@ the web (not implemented).
   source = NA,
   pages = NA
 )

- -

Arguments

study_type: A characterisation of the study type
TP_identifier
TP_identifier: An identifier of one of the transformation products in self$TPs
max_occurrence
max_occurrence: The maximum observed occurrence of the transformation product, expressed as a fraction of the amount that would result from stochiometric transformation
remark
remark: A remark
source
source: An acronym specifying the source of the information
pages
pages: The pages from which the information was taken

Method `add_soil_degradation()`

+ +

`chent$add_soil_degradation()`

Add a line in the internal dataframe holding modelling DT50 values

Usage

chent$add_soil_degradation(
@@ -490,126 +461,104 @@ result from stochiometric transformation
   source,
   page = NA
 )

- -

Arguments

soils: Names of the soils
DT50_mod
DT50_mod: The modelling DT50 in the sense of regulatory pesticide fate modelling
DT50_mod_ref
DT50_mod_ref: The normalised modelling DT50 in the sense of regulatory pesticide fate modelling
type
type: The soil type
country
country: The country (mainly for field studies)
pH_orig
pH_orig: The pH stated in the study
pH_medium
pH_medium: The medium in which this pH was measured
pH_H2O
pH_H2O: The pH extrapolated to pure water
perc_OC
perc_OC: The percentage of organic carbon in the soil
temperature
temperature: The temperature during the study in degrees Celsius
moisture
moisture: The moisture during the study
category
category: Is it a laboratory ('lab') or field study ('field')
formulation
formulation: Name of the formulation applied, if it was not the technical active ingredient
model
model: The degradation model used for deriving DT50_mod
chi2
chi2: The relative error as defined in FOCUS kinetics
remark
remark: A remark
source
source: An acronym specifying the source of the information
page
page: The page from which the information was taken

Method `add_soil_ff()`

+ +

`chent$add_soil_ff()`

Add one or more formation fractions for degradation in soil

Usage

chent$add_soil_ff(target, soils, ff = 1, remark = "", source, page = NA)

- -

Arguments

target: The identifier(s) of the transformation product
soils
soils: The soil name(s) in which the transformation was observed
ff
ff: The formation fraction(s)
remark
remark: A remark
source
source: An acronym specifying the source of the information
page
page: The page from which the information was taken

Method `add_soil_sorption()`

+ +

`chent$add_soil_sorption()`

Add soil sorption data

Usage

chent$add_soil_sorption(
@@ -628,72 +577,59 @@ the technical active ingredient
   source,
   page = NA
 )

- -

Arguments

soils: Names of the soils
Kf
Kf: The sorption constant in L/kg, either linear (then N is 1) or according to Freundlich
Kfoc
Kfoc: The constant from above, normalised to soil organic carbon
N
N: The Freundlich exponent
type
type: The soil type
pH_orig
pH_orig: The pH stated in the study
pH_medium
pH_medium: The medium in which this pH was measured
pH_H2O
pH_H2O: The pH extrapolated to pure water
perc_OC
perc_OC: The percentage of organic carbon in the soil
perc_clay
perc_clay: The percentage of clay in the soil
CEC
CEC: The cation exchange capacity
remark
remark: A remark
source
source: An acronym specifying the source of the information
page
page: The page from which the information was taken

Method `pdf()`

+ +

`chent$pdf()`

Write a PDF image of the structure

Usage

chent$pdf(
@@ -701,27 +637,25 @@ or according to Freundlich
   dir = "structures/pdf",
   template = NULL
 )

- -

Arguments

file: The file to write to
dir
dir: The directory to write the file to
template
template: An optional SMILES code to be used as template for RDKit

Method `png()`

+ +

`chent$png()`

Write a PNG image of the structure

Usage

chent$png(
@@ -729,53 +663,48 @@ or according to Freundlich
   dir = "structures/png",
   antialias = "gray"
 )

- -

Arguments

file: The file to write to
dir
dir: The directory to write the file to
antialias
antialias: Passed to png

Method `emf()`

+ +

`chent$emf()`

Write an EMF image of the structure using emf

Usage

chent$emf(file = paste0(self$identifier, ".emf"), dir = "structures/emf")

- -

Arguments

file: The file to write to
dir
dir: The directory to write the file to

Method `clone()`

+ +

`chent$clone()`

The objects of this class are cloneable with this method.

Usage

chent$clone(deep = FALSE)

- -

Arguments

deep: Whether to make a deep clone.

diff --git a/docs/reference/chent.md b/docs/reference/chent.md index 40716ce..aeaac75 100644 --- a/docs/reference/chent.md +++ b/docs/reference/chent.md @@ -6,7 +6,7 @@ RDKit if RDKit and its python bindings are installed. ## Format -An [R6::R6Class](https://r6.r-lib.org/reference/R6Class.html) generator +An [R6Class](https://r6.r-lib.org/reference/R6Class.html) generator object ## Public fields @@ -103,7 +103,7 @@ object ### Public methods -- [`chent$new()`](#method-chent-new) +- [`chent$new()`](#method-chent-initialize) - [`chent$try_pubchem()`](#method-chent-try_pubchem) @@ -139,7 +139,7 @@ object ------------------------------------------------------------------------ -### Method `new()` +### `chent$new()` Creates a new instance of this [R6](https://r6.r-lib.org/reference/R6Class.html) class. @@ -195,7 +195,7 @@ Creates a new instance of this ------------------------------------------------------------------------ -### Method `try_pubchem()` +### `chent$try_pubchem()` Try to get chemical information from PubChem @@ -217,7 +217,7 @@ Try to get chemical information from PubChem ------------------------------------------------------------------------ -### Method `get_pubchem()` +### `chent$get_pubchem()` Get chemical information from PubChem for a known PubChem CID @@ -233,7 +233,7 @@ Get chemical information from PubChem for a known PubChem CID ------------------------------------------------------------------------ -### Method `get_rdkit()` +### `chent$get_rdkit()` Get chemical information from RDKit if available @@ -249,7 +249,7 @@ Get chemical information from RDKit if available ------------------------------------------------------------------------ -### Method `get_chyaml()` +### `chent$get_chyaml()` Obtain information from a YAML file @@ -274,7 +274,7 @@ Obtain information from a YAML file ------------------------------------------------------------------------ -### Method `add_p0()` +### `chent$add_p0()` Add a vapour pressure @@ -306,7 +306,7 @@ Add a vapour pressure ------------------------------------------------------------------------ -### Method `add_cwsat()` +### `chent$add_cwsat()` Add a water solubility @@ -342,7 +342,7 @@ Add a water solubility ------------------------------------------------------------------------ -### Method `add_PUF()` +### `chent$add_PUF()` Add a plant uptake factor @@ -375,7 +375,7 @@ Add a plant uptake factor ------------------------------------------------------------------------ -### Method `add_TP()` +### `chent$add_TP()` Add a transformation product to the internal list @@ -399,7 +399,7 @@ Add a transformation product to the internal list ------------------------------------------------------------------------ -### Method `add_transformation()` +### `chent$add_transformation()` Add a line in the internal dataframe holding observed transformations @@ -444,7 +444,7 @@ Add a line in the internal dataframe holding observed transformations ------------------------------------------------------------------------ -### Method `add_soil_degradation()` +### `chent$add_soil_degradation()` Add a line in the internal dataframe holding modelling DT50 values @@ -549,7 +549,7 @@ Add a line in the internal dataframe holding modelling DT50 values ------------------------------------------------------------------------ -### Method `add_soil_ff()` +### `chent$add_soil_ff()` Add one or more formation fractions for degradation in soil @@ -585,7 +585,7 @@ Add one or more formation fractions for degradation in soil ------------------------------------------------------------------------ -### Method `add_soil_sorption()` +### `chent$add_soil_sorption()` Add soil sorption data @@ -669,7 +669,7 @@ Add soil sorption data ------------------------------------------------------------------------ -### Method [`pdf()`](https://rdrr.io/r/grDevices/pdf.html) +### `chent$pdf()` Write a PDF image of the structure @@ -697,7 +697,7 @@ Write a PDF image of the structure ------------------------------------------------------------------------ -### Method [`png()`](https://rdrr.io/r/grDevices/png.html) +### `chent$png()` Write a PNG image of the structure @@ -725,7 +725,7 @@ Write a PNG image of the structure ------------------------------------------------------------------------ -### Method `emf()` +### `chent$emf()` Write an EMF image of the structure using [emf](https://rdrr.io/pkg/devEMF/man/emf.html) @@ -746,7 +746,7 @@ Write an EMF image of the structure using ------------------------------------------------------------------------ -### Method `clone()` +### `chent$clone()` The objects of this class are cloneable with this method. diff --git a/docs/reference/draw_svg.chent.html b/docs/reference/draw_svg.chent.html index dd50cd9..8bea16c 100644 --- a/docs/reference/draw_svg.chent.html +++ b/docs/reference/draw_svg.chent.html @@ -7,7 +7,7 @@ - 0.4.0 + 0.4.2

chents

Usage +

Installation

Format

Public fields

Public methods

Method new()

chent$new()

Usage

Arguments

Method try_pubchem()

chent$try_pubchem()

Usage

Arguments

Method get_pubchem()

chent$get_pubchem()

Usage

Arguments

Method get_rdkit()

chent$get_rdkit()

Usage

Arguments

Method get_chyaml()

chent$get_chyaml()

Usage

Arguments

Method add_p0()

chent$add_p0()

Usage

Arguments

Method add_cwsat()

chent$add_cwsat()

Usage

Arguments

Method add_PUF()

chent$add_PUF()

Usage

Arguments

Method add_TP()

chent$add_TP()

Usage

Arguments

Method add_transformation()

chent$add_transformation()

Usage

Arguments

Method add_soil_degradation()

chent$add_soil_degradation()

Usage

Arguments

Method add_soil_ff()

chent$add_soil_ff()

Usage

Arguments

Method add_soil_sorption()

chent$add_soil_sorption()

Usage

Arguments

Method pdf()

chent$pdf()

Usage

Arguments

Method png()

chent$png()

Usage

Arguments

Method emf()

chent$emf()

Usage

Arguments

Method clone()

chent$clone()

Usage

Arguments

Super class

Public fields

Public methods

Method new()

pai$new()

Usage

Method `new()`

`chent$new()`

Method `try_pubchem()`

`chent$try_pubchem()`

Method `get_pubchem()`

`chent$get_pubchem()`

Method `get_rdkit()`

`chent$get_rdkit()`

Method `get_chyaml()`

`chent$get_chyaml()`

Method `add_p0()`

`chent$add_p0()`

Method `add_cwsat()`

`chent$add_cwsat()`

Method `add_PUF()`

`chent$add_PUF()`

Method `add_TP()`

`chent$add_TP()`

Method `add_transformation()`

`chent$add_transformation()`

Method `add_soil_degradation()`

`chent$add_soil_degradation()`

Method `add_soil_ff()`

`chent$add_soil_ff()`

Method `add_soil_sorption()`

`chent$add_soil_sorption()`

Method `pdf()`

`chent$pdf()`

Method `png()`

`chent$png()`

Method `emf()`

`chent$emf()`

Method `clone()`

`chent$clone()`

Method `new()`

`pai$new()`

Method `clone()`

`pai$clone()`

Method `new()`

`ppp$new()`

Method `clone()`

`ppp$clone()`