From 816de01ce642c1c3d633ffb1cbcf960036d27114 Mon Sep 17 00:00:00 2001 From: Ranke Johannes Date: Fri, 10 Nov 2023 18:40:34 +0100 Subject: Make an RStudio project and improve the docs --- docs/reference/Rplot001.png | Bin 19923 -> 20712 bytes docs/reference/chent-1.png | Bin 46431 -> 46730 bytes docs/reference/chent.html | 807 +++++++++++++++++++++---------------- docs/reference/draw_svg.chent.html | 173 +++----- docs/reference/index.html | 160 ++------ docs/reference/pai-1.png | Bin 33683 -> 34388 bytes docs/reference/pai.html | 315 ++++++--------- docs/reference/plot.chent-1.png | Bin 46149 -> 46142 bytes docs/reference/plot.chent.html | 190 +++------ docs/reference/pp.html | 208 ++++------ docs/reference/print.chent.html | 137 ++----- docs/reference/print.pai.html | 137 ++----- 12 files changed, 863 insertions(+), 1264 deletions(-) (limited to 'docs/reference') diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png index 377b927..d92e93f 100644 Binary files a/docs/reference/Rplot001.png and b/docs/reference/Rplot001.png differ diff --git a/docs/reference/chent-1.png b/docs/reference/chent-1.png index 7229a66..acab3e6 100644 Binary files a/docs/reference/chent-1.png and b/docs/reference/chent-1.png differ diff --git a/docs/reference/chent.html b/docs/reference/chent.html index 941eabb..a6b8dde 100644 --- a/docs/reference/chent.html +++ b/docs/reference/chent.html @@ -1,69 +1,14 @@ - - - - - - - -An R6 class for chemical entities with associated data — chent • chents - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -An R6 class for chemical entities with associated data — chent • chents - - - - + + -
-
- -
- -
+
-

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.

+
+

Format

+

An R6Class generator object

+
+
+

Public fields

+

identifier
+

(character(1))
+The identifier that was used to initiate the object, with attribute 'source'

-

Format

-

An R6Class generator object

-

Public fields

+
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

+ -

-
identifier

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

+
rdkit
+

List of information obtained with RDKit

-
inchikey

InChI Key, with attribute 'source'

-
smiles

SMILES code, with attribute 'source'

+
mol
+

<rdkit.Chem.rdchem.Mol> object

-
mw

Molecular weight, with attribute 'source'

-
pubchem

List of information retreived from PubChem

+
svg
+

SVG code

-
rdkit

List of information obtained with RDKit

-
mol

<rdkit.Chem.rdchem.Mol> object

+
Picture
+

Graph as a picture object obtained using grImport

-
svg

SVG code

-
Picture

Graph as a picture object obtained using grImport

+
Pict_font_size
+

Font size as extracted from the intermediate PostScript file

-
Pict_font_size

Font size as extracted from the intermediate PostScript file

-
pdf_height

Height of the MediaBox in the pdf after cropping

+
pdf_height
+

Height of the MediaBox in the pdf after cropping

-
p0

Vapour pressure in Pa

-
cwsat

Water solubility in mg/L

+
p0
+

Vapour pressure in Pa

-
chyaml

List of information obtained from a YAML file

-
soil_degradation

Dataframe of modelling DT50 values

+
cwsat
+

Water solubility in mg/L

-
soil_ff

Dataframe of formation fractions

-
soil_sorption

Dataframe of soil sorption data

+
PUF
+

Plant uptake factor

-
PUF

Plant uptake factor

-

-

Methods

+
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

+ + +

+
+
+

Methods

-

Public methods

- - -


-

Method new()

- -

Usage

-

chent$new(
-  identifier,
-  smiles = NULL,
-  smiles_source = "user",
-  inchikey = NULL,
-  inchikey_source = "user",
-  pubchem = TRUE,
-  pubchem_from = c("name", "smiles", "inchikey"),
-  rdkit = TRUE,
-  template = NULL,
-  chyaml = TRUE
-)

- -


-

Method try_pubchem()

- -

Usage

-

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

- -


-

Method get_pubchem()

- -

Usage

-

chent$get_pubchem(pubchem_cid)

- -


-

Method get_rdkit()

- -

Usage

-

chent$get_rdkit(template = NULL)

- -


-

Method get_chyaml()

- -

Usage

-

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

- -


-

Method add_p0()

- -

Usage

-

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

- -


-

Method add_cwsat()

- -

Usage

-

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

- -


-

Method add_PUF()

- -

Usage

-

chent$add_PUF(
-  PUF = 0,
-  source = "focus_generic_gw_2014",
-  page = 41,
-  remark = "Conservative default value"
-)

- -


-

Method add_TP()

- -

Usage

-

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

- -


-

Method add_transformation()

- -

Usage

-

chent$add_transformation(
-  study_type,
-  TP_identifier,
-  max_occurrence,
-  remark = "",
-  source = NA,
-  pages = NA
-)

- -


-

Method add_soil_degradation()

- -

Usage

-

chent$add_soil_degradation(
-  soils,
-  DT50_mod,
-  DT50_mod_ref,
-  type = NA,
-  country = NA,
-  pH_orig = NA,
-  pH_medium = NA,
-  pH_H2O = NA,
-  perc_OC = NA,
-  temperature = NA,
-  moisture = NA,
-  category = "lab",
-  formulation = NA,
-  model = NA,
-  chi2 = NA,
-  remark = "",
-  source,
-  page = NA
-)

- -


-

Method add_soil_ff()

- -

Usage

-

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

- -


-

Method add_soil_sorption()

- -

Usage

-

chent$add_soil_sorption(
-  soils,
-  Kf,
-  Kfoc,
-  N,
-  type = NA,
-  pH_orig = NA,
-  pH_medium = NA,
-  pH_H2O = NA,
-  perc_OC = NA,
-  perc_clay = NA,
-  CEC = NA,
-  remark = "",
-  source,
-  page = NA
-)

- -


-

Method pdf()

- -

Usage

-

chent$pdf(
-  file = paste0(self$identifier, ".pdf"),
-  dir = "structures/pdf",
-  template = NULL
-)

- -


-

Method png()

- -

Usage

-

chent$png(
-  file = paste0(self$identifier, ".png"),
-  dir = "structures/png",
-  antialias = "gray"
-)

- -


-

Method emf()

- -

Usage

-

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

- -


-

Method clone()

-

The objects of this class are cloneable with this method.

Usage

-

chent$clone(deep = FALSE)

- -

Arguments

-

-
deep

Whether to make a deep clone.

- -

- - - -

Examples

-
oct <- chent$new("1-octanol", smiles = "CCCCCCCCO") -
#> PubChem:
#> Trying to get chemical information from RDKit using user SMILES -#> CCCCCCCCO
#> Did not find chyaml file ./1-octanol.yaml
print(oct) -
#> <chent> -#> Identifier $identifier 1-octanol -#> InChI Key $inchikey KBPLFHHGFOOTCA-UHFFFAOYSA-N -#> SMILES string $smiles: -#> user PubChem_Canonical -#> "CCCCCCCCO" "CCCCCCCCO" -#> Molecular weight $mw: 130.2 -#> PubChem synonyms (up to 10): -#> [1] "1-octanol" "Octan-1-ol" "octanol" "111-87-5" -#> [5] "N-octanol" "Octyl alcohol" "Capryl alcohol" "caprylic alcohol" -#> [9] "n-Octyl alcohol" "Heptyl carbinol"
if (!is.null(oct$Picture)) { - plot(oct) -} -
-caffeine <- chent$new("caffeine") -
#> PubChem:
#> Trying to get chemical information from RDKit using PubChem_Canonical SMILES -#> CN1C=NC2=C1C(=O)N(C(=O)N2C)C
#> Did not find chyaml file ./caffeine.yaml
print(caffeine) -
#> <chent> -#> Identifier $identifier caffeine -#> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N -#> SMILES string $smiles: -#> PubChem_Canonical -#> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" -#> Molecular weight $mw: 194.2 -#> PubChem synonyms (up to 10): -#> [1] "caffeine" "58-08-2" -#> [3] "1,3,7-Trimethylxanthine" "Guaranine" -#> [5] "Thein" "Methyltheobromine" -#> [7] "Cafeina" "Theine" -#> [9] "Koffein" "Mateina"
if (!is.null(caffeine$Picture)) { - plot(caffeine) -} -
+


+

Method new()

+

Creates a new instance of this R6 class.

+

Usage

+

chent$new(
+  identifier,
+  smiles = NULL,
+  inchikey = NULL,
+  pubchem = TRUE,
+  pubchem_from = c("name", "smiles", "inchikey"),
+  rdkit = TRUE,
+  template = NULL,
+  chyaml = TRUE
+)

+
+ +
+

Arguments

+

identifier
+

Identifier to be stored in the object

+ + +
smiles
+

Optional user provided SMILES code

+ + +
inchikey
+

Optional user provided InChI Key

+ + +
pubchem
+

Should an attempt be made to retrieve chemical +information from PubChem via the webchem package?

+ + +
pubchem_from
+

Possibility to select the argument +that is used to query pubchem

+ + +
rdkit
+

Should an attempt be made to retrieve chemical +information from a local rdkit installation via python +and the reticulate package?

+ + +
template
+

An optional SMILES code to be used as template for RDKit

+ + +
chyaml
+

Should we look for a identifier.yaml file in the working +directory? +Try to get chemical information from PubChem

+ + +

+
+ +


+

Method try_pubchem()

+ +
+

Usage

+

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

+
+ +
+

Arguments

+

query
+

Query string to be passed to get_cid

+ + +
from
+

Passed to get_cid +Get chemical information from PubChem for a known PubChem CID

+ + +

+
+ +


+

Method get_pubchem()

+ +
+

Usage

+

chent$get_pubchem(pubchem_cid)

+
+ +
+

Arguments

+

pubchem_cid
+

CID

+ + +

+
+ +


+

Method get_rdkit()

+ +
+

Usage

+

chent$get_rdkit(template = NULL)

+
+ + +


+

Method get_chyaml()

+ +
+

Usage

+

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

+
+ + +


+

Method add_p0()

+ +
+

Usage

+

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

+
+ + +


+

Method add_cwsat()

+ +
+

Usage

+

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

+
+ + +


+

Method add_PUF()

+ +
+

Usage

+

chent$add_PUF(
+  PUF = 0,
+  source = "focus_generic_gw_2014",
+  page = 41,
+  remark = "Conservative default value"
+)

+
+ + +


+

Method add_TP()

+ +
+

Usage

+

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

+
+ + +


+

Method add_transformation()

+ +
+

Usage

+

chent$add_transformation(
+  study_type,
+  TP_identifier,
+  max_occurrence,
+  remark = "",
+  source = NA,
+  pages = NA
+)

+
+ + +


+

Method add_soil_degradation()

+ +
+

Usage

+

chent$add_soil_degradation(
+  soils,
+  DT50_mod,
+  DT50_mod_ref,
+  type = NA,
+  country = NA,
+  pH_orig = NA,
+  pH_medium = NA,
+  pH_H2O = NA,
+  perc_OC = NA,
+  temperature = NA,
+  moisture = NA,
+  category = "lab",
+  formulation = NA,
+  model = NA,
+  chi2 = NA,
+  remark = "",
+  source,
+  page = NA
+)

+
+ + +


+

Method add_soil_ff()

+ +
+

Usage

+

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

+
+ + +


+

Method add_soil_sorption()

+ +
+

Usage

+

chent$add_soil_sorption(
+  soils,
+  Kf,
+  Kfoc,
+  N,
+  type = NA,
+  pH_orig = NA,
+  pH_medium = NA,
+  pH_H2O = NA,
+  perc_OC = NA,
+  perc_clay = NA,
+  CEC = NA,
+  remark = "",
+  source,
+  page = NA
+)

+
+ + +


+

Method pdf()

+ +
+

Usage

+

chent$pdf(
+  file = paste0(self$identifier, ".pdf"),
+  dir = "structures/pdf",
+  template = NULL
+)

+
+ + +


+

Method png()

+ +
+

Usage

+

chent$png(
+  file = paste0(self$identifier, ".png"),
+  dir = "structures/png",
+  antialias = "gray"
+)

+
+ + +


+

Method emf()

+ +
+

Usage

+

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

+
+ + +


+

Method clone()

+

The objects of this class are cloneable with this method.

+

Usage

+

chent$clone(deep = FALSE)

+
+ +
+

Arguments

+

deep
+

Whether to make a deep clone.

+ + +

+
+ +
+ +
+ +
+

Examples

+
oct <- chent$new("1-octanol", smiles = "CCCCCCCCO", pubchem = FALSE)
+#> Trying to get chemical information from RDKit using user SMILES
+#> CCCCCCCCO
+#> Did not find chyaml file ./1-octanol.yaml
+print(oct)
+#> <chent>
+#> Identifier $identifier 1-octanol 
+#> InChI Key $inchikey 
+#> SMILES string $smiles:
+#>        user 
+#> "CCCCCCCCO" 
+#> Molecular weight $mw: 130.2 
+if (!is.null(oct$Picture)) {
+  plot(oct)
+}
+
+caffeine <- chent$new("caffeine")
+#> PubChem:
+#> Trying to get chemical information from RDKit using PubChem_Canonical SMILES
+#> CN1C=NC2=C1C(=O)N(C(=O)N2C)C
+#> Did not find chyaml file ./caffeine.yaml
+print(caffeine)
+#> <chent>
+#> Identifier $identifier caffeine 
+#> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N 
+#> SMILES string $smiles:
+#>              PubChem_Canonical 
+#> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" 
+#> Molecular weight $mw: 194.2 
+#> PubChem synonyms (up to 10):
+#>  [1] "caffeine"                "58-08-2"                
+#>  [3] "Guaranine"               "1,3,7-Trimethylxanthine"
+#>  [5] "Methyltheobromine"       "Theine"                 
+#>  [7] "Thein"                   "Cafeina"                
+#>  [9] "Koffein"                 "Mateina"                
+if (!is.null(caffeine$Picture)) {
+  plot(caffeine)
+}
+
+
+
+
-
- +
- - + + diff --git a/docs/reference/draw_svg.chent.html b/docs/reference/draw_svg.chent.html index 1805ff1..cae8c0b 100644 --- a/docs/reference/draw_svg.chent.html +++ b/docs/reference/draw_svg.chent.html @@ -1,67 +1,12 @@ - - - - - - - -Draw SVG graph from a chent object using RDKit — draw_svg.chent • chents - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Draw SVG graph from a chent object using RDKit — draw_svg.chent • chents - + + - - - -
-
- -
- -
+
@@ -117,65 +49,60 @@

Draw SVG graph from a chent object using RDKit

-
draw_svg.chent(
-  x,
-  width = 300,
-  height = 150,
-  filename = paste0(names(x$identifier), ".svg"),
-  subdir = "svg"
-)
- -

Arguments

- - - - - - - - - - - - - - - - - - - - - - -
x

The chent object to be plotted

width

The desired width in pixels

height

The desired height in pixels

filename

The filename

subdir

The path to which the file should be written

+
+
draw_svg.chent(
+  x,
+  width = 300,
+  height = 150,
+  filename = paste0(names(x$identifier), ".svg"),
+  subdir = "svg"
+)
+
+ +
+

Arguments

+
x
+

The chent object to be plotted

+ +
width
+

The desired width in pixels

+ + +
height
+

The desired height in pixels

+ + +
filename
+

The filename

+ + +
subdir
+

The path to which the file should be written

+ +
+
- - - + + diff --git a/docs/reference/index.html b/docs/reference/index.html index 9de4a87..d9eb797 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,66 +1,12 @@ - - - - - - - -Function reference • chents - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Function reference • chents - - + + - - -
-
- -
- -
+
- - - - - - - - - - -
-

R6 Class definitions and methods

+ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+

R6 Class definitions and methods

+

chent

An R6 class for chemical entities with associated data

+

draw_svg.chent()

Draw SVG graph from a chent object using RDKit

+

plot(<chent>)

Plot method for chent objects

+

print(<chent>)

Printing method for chent objects

+

pai

An R6 class for pesticidal active ingredients and associated data

+

print(<pai>)

Printing method for pai objects (pesticidal active ingredients)

+

pp

R6 class for holding a product with at least one active ingredient

- +
+
-
- +
- - + + diff --git a/docs/reference/pai-1.png b/docs/reference/pai-1.png index c235304..802fd50 100644 Binary files a/docs/reference/pai-1.png and b/docs/reference/pai-1.png differ diff --git a/docs/reference/pai.html b/docs/reference/pai.html index 0bb3399..636007f 100644 --- a/docs/reference/pai.html +++ b/docs/reference/pai.html @@ -1,68 +1,13 @@ - - - - - - - -An R6 class for pesticidal active ingredients and associated data — pai • chents - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -An R6 class for pesticidal active ingredients and associated data — pai • chents - - - - + + -
-
- -
- -
+
@@ -120,132 +52,143 @@ Additional chemical information is retrieved from the internet if available.

+
+

Format

+

An R6Class generator object

+
+
+

Super class

+

chents::chent -> pai

+
+
+

Public fields

+

iso
+

ISO common name according to ISO 1750 as retreived from pesticidecompendium.bcpc.org

+ + +
bcpc
+

List of information retrieved from pesticidecompendium.bcpc.org

-

Format

-

An R6Class generator object

-

Super class

+

+
+
+

Methods

+ +
+

Public methods

+ +

Inherited methods


+

Method new()

+ +
+

Usage

+

pai$new(
+  iso,
+  identifier = iso,
+  smiles = NULL,
+  inchikey = NULL,
+  bcpc = TRUE,
+  pubchem = TRUE,
+  pubchem_from = "auto",
+  rdkit = TRUE,
+  template = NULL,
+  chyaml = TRUE
+)

+
-

chents::chent -> pai

-

Public fields

-

-
iso

ISO common name according to ISO 1750 as retreived from pesticidecompendium.bcpc.org

+


+

Method clone()

+

The objects of this class are cloneable with this method.

+

Usage

+

pai$clone(deep = FALSE)

+
-
bcpc

List of information retrieved from pesticidecompendium.bcpc.org

+
+

Arguments

+

deep
+

Whether to make a deep clone.

-

-

Methods

- -

Public methods

- - -

Inherited methods - -
- -
-

Method new()

- -

Usage

-

pai$new(
-  iso,
-  identifier = iso,
-  smiles = NULL,
-  smiles_source = "user",
-  inchikey = NULL,
-  inchikey_source = "user",
-  bcpc = TRUE,
-  pubchem = TRUE,
-  pubchem_from = "auto",
-  rdkit = TRUE,
-  template = NULL,
-  chyaml = TRUE
-)

- -


-

Method clone()

-

The objects of this class are cloneable with this method.

Usage

-

pai$clone(deep = FALSE)

- -

Arguments

-

-
deep

Whether to make a deep clone.

- -

- - - -

Examples

-
# On Travis, we get a certificate validation error, -# likely because the system (xenial) is so old, -# therefore don't run this example on Travis -if (Sys.getenv("TRAVIS") == "") { - -atr <- pai$new("atrazine") -print(atr) -if (!is.null(atr$Picture)) { - plot(atr) -} - -} -
#> BCPC:
#> PubChem:
#> Trying to get chemical information from RDKit using PubChem_Canonical SMILES -#> CCNC1=NC(=NC(=N1)Cl)NC(C)C
#> Did not find chyaml file ./atrazine.yaml
#> <pai> with ISO common name $iso atrazine -#> <chent> -#> Identifier $identifier atrazine -#> InChI Key $inchikey MXWJVTOOROXGIU-UHFFFAOYSA-N -#> SMILES string $smiles: -#> PubChem_Canonical -#> "CCNC1=NC(=NC(=N1)Cl)NC(C)C" -#> Molecular weight $mw: 215.7 -#> PubChem synonyms (up to 10): -#> [1] "atrazine" "1912-24-9" "Gesaprim" "Oleogesaprim" "Chromozin" -#> [6] "Aktikon" "Atrazin" "Argezin" "Atazinax" "Atranex"
+

+
+ +
+ +
+ +
+

Examples

+
# On Travis, we get a certificate validation error,
+# likely because the system (xenial) is so old,
+# therefore don't run this example on Travis
+if (Sys.getenv("TRAVIS") == "") {
+
+atr <- pai$new("atrazine")
+print(atr)
+if (!is.null(atr$Picture)) {
+  plot(atr)
+}
+
+}
+#> BCPC:
+#> PubChem:
+#> Trying to get chemical information from RDKit using PubChem_Canonical SMILES
+#> CCNC1=NC(=NC(=N1)Cl)NC(C)C
+#> Did not find chyaml file ./atrazine.yaml
+
+#> <pai> with ISO common name $iso atrazine 
+#> <chent>
+#> Identifier $identifier atrazine 
+#> InChI Key $inchikey MXWJVTOOROXGIU-UHFFFAOYSA-N 
+#> SMILES string $smiles:
+#>            PubChem_Canonical 
+#> "CCNC1=NC(=NC(=N1)Cl)NC(C)C" 
+#> Molecular weight $mw: 215.7 
+#> PubChem synonyms (up to 10):
+#>  [1] "atrazine"     "1912-24-9"    "Gesaprim"     "Oleogesaprim" "Aktikon"     
+#>  [6] "Atranex"      "Chromozin"    "Atazinax"     "Atrasine"     "Gesoprim"    
+
+
+
- - - + + diff --git a/docs/reference/plot.chent-1.png b/docs/reference/plot.chent-1.png index 330f0a5..1e8885d 100644 Binary files a/docs/reference/plot.chent-1.png and b/docs/reference/plot.chent-1.png differ diff --git a/docs/reference/plot.chent.html b/docs/reference/plot.chent.html index 62bf38f..470ce79 100644 --- a/docs/reference/plot.chent.html +++ b/docs/reference/plot.chent.html @@ -1,67 +1,12 @@ - - - - - - - -Plot method for chent objects — plot.chent • chents - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Plot method for chent objects — plot.chent • chents - + + - - - -
-
- -
- -
+
@@ -117,68 +49,70 @@

Plot method for chent objects

-
# S3 method for chent
-plot(x, ...)
- -

Arguments

- - - - - - - - - - -
x

The chent object to be plotted

...

Further arguments passed to grid.picture

- - -

Examples

-
caffeine <- chent$new("caffeine") -
#> PubChem:
#> Trying to get chemical information from RDKit using PubChem_Canonical SMILES -#> CN1C=NC2=C1C(=O)N(C(=O)N2C)C
#> Did not find chyaml file ./caffeine.yaml
print(caffeine) -
#> <chent> -#> Identifier $identifier caffeine -#> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N -#> SMILES string $smiles: -#> PubChem_Canonical -#> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" -#> Molecular weight $mw: 194.2 -#> PubChem synonyms (up to 10): -#> [1] "caffeine" "58-08-2" -#> [3] "1,3,7-Trimethylxanthine" "Guaranine" -#> [5] "Thein" "Methyltheobromine" -#> [7] "Cafeina" "Theine" -#> [9] "Koffein" "Mateina"
if (!is.null(caffeine$Picture)) { - plot(caffeine) -} -
+
+
# S3 method for chent
+plot(x, ...)
+
+ +
+

Arguments

+
x
+

The chent object to be plotted

+ + +
...
+

Further arguments passed to grid.picture

+ +
+ +
+

Examples

+
caffeine <- chent$new("caffeine")
+#> PubChem:
+#> Trying to get chemical information from RDKit using PubChem_Canonical SMILES
+#> CN1C=NC2=C1C(=O)N(C(=O)N2C)C
+#> Did not find chyaml file ./caffeine.yaml
+print(caffeine)
+#> <chent>
+#> Identifier $identifier caffeine 
+#> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N 
+#> SMILES string $smiles:
+#>              PubChem_Canonical 
+#> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" 
+#> Molecular weight $mw: 194.2 
+#> PubChem synonyms (up to 10):
+#>  [1] "caffeine"                "58-08-2"                
+#>  [3] "Guaranine"               "1,3,7-Trimethylxanthine"
+#>  [5] "Methyltheobromine"       "Theine"                 
+#>  [7] "Thein"                   "Cafeina"                
+#>  [9] "Koffein"                 "Mateina"                
+if (!is.null(caffeine$Picture)) {
+  plot(caffeine)
+}
+
+
+
+
- - - + + diff --git a/docs/reference/pp.html b/docs/reference/pp.html index c4e4a01..2607035 100644 --- a/docs/reference/pp.html +++ b/docs/reference/pp.html @@ -1,67 +1,12 @@ - - - - - - - -R6 class for holding a product with at least one active ingredient — pp • chents - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -R6 class for holding a product with at least one active ingredient — pp • chents - - - - + + -
-
- -
- -
+
@@ -118,89 +50,105 @@
+
+

Format

+

An R6Class generator object.

+
+
+

Public fields

+

name
+

The name of the product

-

Format

-

An R6Class generator object.

-

Public fields

+
ais
+

A list of active ingredients

-

-
name

The name of the product

-
ais

A list of active ingredients

+
concentrations
+

The concentration of the ais

-
concentrations

The concentration of the ais

-
concentration_units

Defaults to g/L

+
concentration_units
+

Defaults to g/L

-

-

Methods

+

+
+
+

Methods

-

Public methods

+
+

Public methods

+ +


+

Method new()

+ +
+

Usage

+

pp$new(
+  name,
+  ...,
+  concentrations,
+  concentration_units = "g/L",
+  density = 1000,
+  density_units = "g/L"
+)

+
- -


-

Method new()

-

Usage

-

pp$new(
-  name,
-  ...,
-  concentrations,
-  concentration_units = "g/L",
-  density = 1000,
-  density_units = "g/L"
-)

+


+

Method print()

-


-

Method print()

+
+

Usage

+

pp$print()

+
-

Usage

-

pp$print()

-


-

Method clone()

-

The objects of this class are cloneable with this method.

Usage

-

pp$clone(deep = FALSE)

+


+

Method clone()

+

The objects of this class are cloneable with this method.

+

Usage

+

pp$clone(deep = FALSE)

+
+ +
+

Arguments

+

deep
+

Whether to make a deep clone.

-

Arguments

-

-
deep

Whether to make a deep clone.

-

+

+
+
+
+
- - - + + diff --git a/docs/reference/print.chent.html b/docs/reference/print.chent.html index b188ed9..08497dd 100644 --- a/docs/reference/print.chent.html +++ b/docs/reference/print.chent.html @@ -1,67 +1,12 @@ - - - - - - - -Printing method for chent objects — print.chent • chents - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Printing method for chent objects — print.chent • chents - + + - - - -
-
- -
- -
+
@@ -117,48 +49,43 @@

Printing method for chent objects

-
# S3 method for chent
-print(x, ...)
+
+
# S3 method for chent
+print(x, ...)
+
+ +
+

Arguments

+
x
+

The chent object to be printed

+ -

Arguments

- - - - - - - - - - -
x

The chent object to be printed

...

Further arguments for compatibility with the S3 method

+
...
+

Further arguments for compatibility with the S3 method

+
+
- - - + + diff --git a/docs/reference/print.pai.html b/docs/reference/print.pai.html index 284792f..3faa5f7 100644 --- a/docs/reference/print.pai.html +++ b/docs/reference/print.pai.html @@ -1,67 +1,12 @@ - - - - - - - -Printing method for pai objects (pesticidal active ingredients) — print.pai • chents - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Printing method for pai objects (pesticidal active ingredients) — print.pai • chents - + + - - - -
-
- -
- -
+
@@ -117,48 +49,43 @@

Printing method for pai objects (pesticidal active ingredients)

-
# S3 method for pai
-print(x, ...)
+
+
# S3 method for pai
+print(x, ...)
+
+ +
+

Arguments

+
x
+

The chent object to be printed

+ -

Arguments

- - - - - - - - - - -
x

The chent object to be printed

...

Further arguments for compatibility with the S3 method

+
...
+

Further arguments for compatibility with the S3 method

+
+
- - - + + -- cgit v1.2.1