ropensci / webchem Goto Github PK

> ci_query('Tetracyclin', type = 'name')
http://chem.sis.nlm.nih.gov/chemidplus/name/Tetracyclin
Error in html_table(xml_find_all(ttt, "//h2[contains(., 'Toxicity')]/following-sibling::div//table"))[[1]] : 
  subscript out of bounds

> alanwood("S-Metolachlor", type = "commonname")$inchikey

# More then one link found! Returning first.
# 
# Querying s-metolachlor.html
# [1] "major component (S)-isomer:WVQBLGZPHOPPFO-LBPRGKRZSA-Nminor component (R)-isomer:WVQBLGZPHOPPFO-GFCCVEGCSA-N"

> alanwood("S-Metolachlor", type = "commonname")$inchikey

# More then one link found! Returning first.
# 
# Querying s-metolachlor.html
# [1] "major component (S)-isomer" - WVQBLGZPHOPPFO-LBPRGKRZSA-N
[2] "minor component (R)-isomer" - WVQBLGZPHOPPFO-GFCCVEGCSA-N

  h <- try(GET(qurl, timeout(2)))
  if (inherits(h, "try-error")) {
    warning('Problem with web service encountered... Returning NA.')
    return(NA)
  } else {
    tt <- read_xml(content(h, as = 'raw'))
  }

cs_inchikey_csid(inchi = 'KYOUEHWYDNYHAL-IOORBXIBSA-N')
http://www.chemspider.com/InChI.asmx/InChIKeyToCSID?inchi_key=KYOUEHWYDNYHAL-IOORBXIBSA-N
[1] ""

> alanwood("S-Metolachlor", type = "commonname")$activity
[1] "herbicides (chloroacetanilide herbicides)"

$activity  [1] "herbicides"
$activity_subgroup [1] "chloroacetanilide herbicides"

BFPGVJIMBRLFIR-GUCBCRIZSA-Nidentifier for no stereochemistry:ZXQYGBMAQZUVMI-UHFFFAOYSA-N

## Querying s-metolachlor.htmls-metolachlor.html

## [1] "major component (S)-isomer:WVQBLGZPHOPPFO-LBPRGKRZSA-Nminor component (R)-isomer:WVQBLGZPHOPPFO-GFCCVEGCSA-N"
## [2] "major component (S)-isomer:WVQBLGZPHOPPFO-LBPRGKRZSA-Nminor component (R)-isomer:WVQBLGZPHOPPFO-GFCCVEGCSA-N"

isinchikey=function(s) {      
    (s==toupper(s))&(nchar(s) == 27)&(substr(s,15,15)=="-")&(substr(s,26,26)=="-")
}

Hi Rajarshi or Eduard,
I just figured out how to download Kovats retention indices from Pubchem - in case you would be interested to include something like this in rpubchem or webchem :

library("xml2")
library("data.table")
compound.retention.index <- function(file=NULL) {
  pubchemid <- sub(".*/([0-9]+)/?.*", "\\1", file)
  compound <- read_xml(file)
  ns <- xml_ns(compound)
  information <- xml_find_all(compound, paste0(
    "//d1:TOCHeading[text()='Kovats Retention Index']",
    "/following-sibling::d1:Information"
  ), ns)
  indexes <- lapply(information, function(x) {
    name <- xml_text(xml_find_one(x, "./d1:Name", ns))
    values <- as.numeric(sapply(
      xml_find_all(x, "./*[contains(name(), 'NumValue')]", ns),
      xml_text))

    data.frame(pubchemid=pubchemid,
               column_class=name,
               kovats_ri=values)
  })

  return( do.call("rbind", indexes) )
}

cids <- c("5282108", "5282148", "91754124") # example pubchem cids
compounds <- paste0("https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/",cids,"/XML/?response_type=display")

# Kovats retention indices
rti <- do.call("rbind",
               lapply(compounds, compound.retention.index))
names(rti)
rti

Some time ago I also wrote some code to retrieve detailed retention index information, compound properties and EI mass spectra from the NIST Chemistry Webbook.
@Eduard - would you be interested by any chance to have some functions to interact with the NIST Chemistry Webbook in your webchem package?

best regards,
Tom

PS using the xml2 package in R tends to work better than the XML package, as the latter is known to have memory leaks, which can be really annoying for large annotation jobs

PS2 @Rajarshi - could be nice perhaps in your package if you could query also by inchikey, and that it would automatically recognize the input, and convert from inchikey to cid if desired:
library(webchem)
get_cid('GLZPCOQZEFWAFX-JXMROGBWSA-N')

"637566"

Hi Eduard,
Ha that's great! And yes I know how to use github - only thing is that I got quite a lot of teaching to do shortly, so it may be a little while then before I get to it then... I'll dig into my NIST functions too then.
Ha and to access all the info available in Pherobase (e.g. http://www.pherobase.com/database/nmr/nmr-detail-geraniol.php, http://www.pherobase.com/database/kovats/kovats-detail-geraniol.php, http://www.pherobase.com/database/compound/compounds-detail-geraniol.php, http://www.pherobase.com/database/floral-compounds/floral-taxa-compounds-detail-geraniol.php) I also have some functions - only thing is that for that one to enable generic queries (e.g. based on structure/InChiKey or name) I created a file with the relevant pointers and conversion from a given name or structure to a particular Pherobase page with retention index info, natural occurrece and behavioural function. 
(As pherobase itself does not implement a generic search function, it just uses Google for that)

best regards,
Tom

aw_query('12071-83-9', type = 'cas')
Querying propineb.html
Error in if (grepl("isomer", inchikey)) { : argument is of length zero

1. Failure (at test-physprop.R#8): physprop returns correct results ------------
fl$cas not equal to "50-00-0"
1 string mismatches:
x[1]: "50-00-0"
y[1]: "�000050-00-0"