Authors

"))&&h.css("position",a.css("position"));x=function(){var c,f,e;if(!G&&(I=A.height(),c=parseInt(g.css("border-top-width"),10),f=parseInt(g.css("padding-top"),10),d=parseInt(g.css("padding-bottom"),10),n=g.offset().top+c+f,C=g.height(),m&&(v=m=!1,null==p&&(a.insertAfter(h),h.detach()),a.css({position:"",top:"",width:"",bottom:""}).removeClass(t),e=!0),F=a.offset().top-(parseInt(a.css("margin-top"),10)||0)-q, +u=a.outerHeight(!0),r=a.css("float"),h&&h.css({width:a.outerWidth(!0),height:u,display:a.css("display"),"vertical-align":a.css("vertical-align"),"float":r}),e))return l()};x();if(u!==C)return D=void 0,c=q,z=E,l=function(){var b,l,e,k;if(!G&&(e=!1,null!=z&&(--z,0>=z&&(z=E,x(),e=!0)),e||A.height()===I||x(),e=f.scrollTop(),null!=D&&(l=e-D),D=e,m?(w&&(k=e+u+c>C+n,v&&!k&&(v=!1,a.css({position:"fixed",bottom:"",top:c}).trigger("sticky_kit:unbottom"))),eb&&!v&&(c-=l,c=Math.max(b-u,c),c=Math.min(q,c),m&&a.css({top:c+"px"})))):e>F&&(m=!0,b={position:"fixed",top:c},b.width="border-box"===a.css("box-sizing")?a.outerWidth()+"px":a.width()+"px",a.css(b).addClass(t),null==p&&(a.after(h),"left"!==r&&"right"!==r||h.append(a)),a.trigger("sticky_kit:stick")),m&&w&&(null==k&&(k=e+u+c>C+n),!v&&k)))return v=!0,"static"===g.css("position")&&g.css({position:"relative"}), +a.css({position:"absolute",bottom:d,top:"auto"}).trigger("sticky_kit:bottom")},y=function(){x();return l()},H=function(){G=!0;f.off("touchmove",l);f.off("scroll",l);f.off("resize",y);b(document.body).off("sticky_kit:recalc",y);a.off("sticky_kit:detach",H);a.removeData("sticky_kit");a.css({position:"",bottom:"",top:"",width:""});g.position("position","");if(m)return null==p&&("left"!==r&&"right"!==r||a.insertAfter(h),h.remove()),a.removeClass(t)},f.on("touchmove",l),f.on("scroll",l),f.on("resize", +y),b(document.body).on("sticky_kit:recalc",y),a.on("sticky_kit:detach",H),setTimeout(l,0)}};n=0;for(K=this.length;n + + diff --git a/docs/pkgdown.css b/docs/pkgdown.css new file mode 100644 index 0000000..fd7b0ba --- /dev/null +++ b/docs/pkgdown.css @@ -0,0 +1,113 @@ +/* Sticker footer */ +body > .container { + display: flex; + padding-top: 60px; + min-height: calc(100vh); + flex-direction: column; +} + +body > .container .row { + flex: 1; +} + +footer { + margin-top: 45px; + padding: 35px 0 36px; + border-top: 1px solid #e5e5e5; + color: #666; + display: flex; +} +footer p { + margin-bottom: 0; +} +footer div { + flex: 1; +} +footer .pkgdown { + text-align: right; +} +footer p { + margin-bottom: 0; +} + +img.icon { + float: right; +} + +/* Section anchors ---------------------------------*/ + +.hasAnchor { + margin-left: -30px; +} + +a.anchor { + display:inline-block; + width: 30px; + height: 30px; + visibility: hidden; + + background-image: url(./link.svg); + background-repeat: no-repeat; + background-size: 20px 20px; + background-position: center center; +} + +.hasAnchor:hover a.anchor { + visibility: visible; +} + +/* Fixes for fixed navbar --------------------------*/ + +.contents h1, .contents h2, .contents h3, .contents h4 { + padding-top: 60px; + margin-top: -60px; +} + +/* Sidebar --------------------------*/ + +#sidebar { + margin-top: 30px; +} +#sidebar h2 { + font-size: 1.5em; + margin-top: 1em; +} + +#sidebar h2:first-child { + margin-top: 0; +} + +#sidebar .list-unstyled li { + margin-bottom: 0.5em; +} + +/* Syntax highlighting ---------------------------------------------------- */ + +code { + background-color: #f7f7f7; + color: #333; +} +code a { + color: #375f84; +} + +.warning { color: red; } +.message { font-weight: bolder; } +.error { color: red; font-weight: bolder; } + +.fl,.number {color:rgb(21,20,181);} +.fu,.functioncall {color:#264D66 ;} +.ch,.st,.string {color:#375D81 ;} +.kw,.keyword {color:black;} +.argument {color:#264D66 ;} +.co,.comment {color: #777;} +.formalargs {color: #264D66;} +.eqformalargs {color:#264D66;} +.slot {font-style:italic;} +.symbol {color:black ;} +.prompt {color:black ;} + +pre img { + background-color: #fff; + display: block; +} diff --git a/docs/pkgdown.js b/docs/pkgdown.js new file mode 100644 index 0000000..c8b38c4 --- /dev/null +++ b/docs/pkgdown.js @@ -0,0 +1,8 @@ +$(function() { + $("#sidebar").stick_in_parent({offset_top: 40}); + $('body').scrollspy({ + target: '#sidebar', + offset: 60 + }); + +}); diff --git a/docs/reference/chent-22.png b/docs/reference/chent-22.png new file mode 100644 index 0000000..69b3b08 Binary files /dev/null and b/docs/reference/chent-22.png differ diff --git a/docs/reference/chent.html b/docs/reference/chent.html new file mode 100644 index 0000000..15c4d10 --- /dev/null +++ b/docs/reference/chent.html @@ -0,0 +1,160 @@ + + + + + + + + +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 and configured for use with PythonInR.

+ + +

chent

+ +

Format

+ +

An R6Class generator object

+ +

Fields

+ +

identifier: The identifier that was used to initiate the object, with attribute 'source'
inchikey: InChI Key, with attribute 'source'
smiles: SMILES code, with attribute 'source'
mw: Molecular weight, with attribute 'source'
pubchem: List of information retreived from PubChem
rdkit: List of information obtained with RDKit, if installed and +configured for use with PythonInR
svg: SVG code
Picture: Graph as a picture object obtained using grImport
Pict_font_size: Font size as extracted from the intermediate PostScript file
pdf_height: Height of the MediaBox in the pdf after cropping
chyaml: List of information obtained from a YAML file
degradation: List of degradation endpoints

+ + +

Examples

oct <- chent$new("1-octanol", smiles = "CCCCCCCCO")
#> PubChem:
#> https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON
#> https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount/JSON
#> https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON
#> 
+#> Initialize Python Version 3.4.2 (default, Oct  8 2014, 10:47:48) 
+#> [GCC 4.9.1]
#> 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 $mw: 130.2 
+#> PubChem synonyms (up to 10):
+#>  [1] "957"              "1-octanol"        "Octan-1-ol"       "octanol"         
+#>  [5] "Octyl alcohol"    "N-octanol"        "Capryl alcohol"   "n-Octyl alcohol" 
+#>  [9] "111-87-5"         "caprylic alcohol"
plot(oct)
caffeine <- chent$new("caffeine")
#> PubChem:
#> https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON
#> https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount/JSON
#> https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON
#> 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] "2519"                    "caffeine"               
+#>  [3] "Guaranine"               "1,3,7-Trimethylxanthine"
+#>  [5] "Methyltheobromine"       "Cafeina"                
+#>  [7] "Thein"                   "Koffein"                
+#>  [9] "Mateina"                 "Theine"                 
plot(caffeine)

+ +

+ + +

+ + + diff --git a/docs/reference/draw_svg.chent.html b/docs/reference/draw_svg.chent.html new file mode 100644 index 0000000..2cc3804 --- /dev/null +++ b/docs/reference/draw_svg.chent.html @@ -0,0 +1,117 @@ + + + + + + + + +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(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 new file mode 100644 index 0000000..e9dc7a8 --- /dev/null +++ b/docs/reference/index.html @@ -0,0 +1,137 @@ + + + + + + + + +Function reference • chents + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + +

+ +

+ + +

Class definitions

R6 classes and their methods

+ + +

An R6 class for chemical entities with associated data

chent

+ +

Draw SVG graph from a chent object using RDKit

draw_svg.chent

+ +

Plot method for chent objects

plot.chent

+ +

Printing method for chent objects

print.chent

+ +

An R6 class for pesticidal active ingredients and associated data

pai

+ +

Printing method for pai objects (pesticidal active ingredients)

print.pai

+ +

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

pp

+ +

+ + +

+ + + diff --git a/docs/reference/pai.html b/docs/reference/pai.html new file mode 100644 index 0000000..4c143a1 --- /dev/null +++ b/docs/reference/pai.html @@ -0,0 +1,133 @@ + + + + + + + + +An R6 class for pesticidal active ingredients and associated data — pai • chents + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

The class is initialised with an identifier which is generally an ISO common name. +Additional chemical information is retrieved from the internet if available.

+ + +

pai

+ +

Format

+ +

An R6Class generator object

+ +

Fields

+ +

iso: ISO common name according to ISO 1750 as retreived from www.alanwood.net/pesticides
alanwood: List of information retreived from www.alanwood.net/pesticides

+ + +

Examples

atr <- pai$new("atrazine")
#> alanwood.net:
#> Querying atrazine.html
#> PubChem:
#> https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/cids/JSON
#> https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount/JSON
#> https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON
#> 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
print(atr)
#> <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] "2256"         "atrazine"     "1912-24-9"    "Atranex"      "Fenatrol"    
+#>  [6] "Atred"        "Oleogesaprim" "Atazinax"     "Atrasine"     "Chromozin"

+ +

+ + +

+ + + diff --git a/docs/reference/plot.chent-11.png b/docs/reference/plot.chent-11.png new file mode 100644 index 0000000..69b3b08 Binary files /dev/null and b/docs/reference/plot.chent-11.png differ diff --git a/docs/reference/plot.chent.html b/docs/reference/plot.chent.html new file mode 100644 index 0000000..3cc23d9 --- /dev/null +++ b/docs/reference/plot.chent.html @@ -0,0 +1,128 @@ + + + + + + + + +Plot method for chent objects — plot.chent • chents + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

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:
#> https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON
#> https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount/JSON
#> https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON
#> 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] "2519"                    "caffeine"               
+#>  [3] "Guaranine"               "1,3,7-Trimethylxanthine"
+#>  [5] "Methyltheobromine"       "Cafeina"                
+#>  [7] "Thein"                   "Koffein"                
+#>  [9] "Mateina"                 "Theine"                 
plot(caffeine)

+ +

+ + +

+ + + diff --git a/docs/reference/pp.html b/docs/reference/pp.html new file mode 100644 index 0000000..4569a6f --- /dev/null +++ b/docs/reference/pp.html @@ -0,0 +1,119 @@ + + + + + + + + +R6 class for holding a product with at least one active ingredient — pp • chents + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

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

+ + +

pp

+ +

Format

+ +

An R6Class generator object.

+ +

Fields

+ +

name: The name of the product
ais: A list of active ingredients
concentrations: The concentration of the ais
concentration_units: Defaults to g/L

+ + +

+ +

+ + +

+ + + diff --git a/docs/reference/print.chent.html b/docs/reference/print.chent.html new file mode 100644 index 0000000..29b215a --- /dev/null +++ b/docs/reference/print.chent.html @@ -0,0 +1,111 @@ + + + + + + + + +Printing method for chent objects — print.chent • chents + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

Printing method for chent objects

+ + +

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

+ +

Arguments

x: The chent object to be printed
...: Further arguments for compatibility with the S3 method

+ + +

+ +

+ + +

+ + + diff --git a/docs/reference/print.pai.html b/docs/reference/print.pai.html new file mode 100644 index 0000000..d2da6b8 --- /dev/null +++ b/docs/reference/print.pai.html @@ -0,0 +1,111 @@ + + + + + + + + +Printing method for pai objects (pesticidal active ingredients) — print.pai • chents + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

Printing method for pai objects (pesticidal active ingredients)

+ + +

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

+ +

Arguments

x: The chent object to be printed
...: Further arguments for compatibility with the S3 method

+ + +

+ +

+ + +

+ + + -- cgit v1.2.1

Features

+ Features

chents

+ chents

License

Developers

Authors

An R6 class for chemical entities with associated data

Format

Fields

Examples

Contents

Draw SVG graph from a chent object using RDKit

Arguments

Contents

Function reference

version 0.2-5

Class definitions

Contents

An R6 class for pesticidal active ingredients and associated data

Format

Fields

Examples

Contents

Plot method for chent objects

Arguments

Examples

Contents

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

Format

Fields

Contents

Printing method for chent objects

Arguments

Contents

Printing method for pai objects (pesticidal active ingredients)

Arguments

Contents