Chemical Information from the Web

Chemical information from around the web. This package interacts with a suite of web services for chemical information. Sources include: Alan Wood's Compendium of Pesticide Common Names, Chemical Identifier Resolver, ChEBI, Chemical Translation Service, ChemIDplus, ChemSpider, ETOX, Flavornet, NIST Chemistry WebBook, OPSIN, PAN Pesticide Database, PubChem, SRS, Wikidata.


News

webchem 0.4

NEW FEATURES

MINOR IMPROVEMENTS

BUG FIXES

  • extr_num() did not work properly with decimal numbers [issue #136, reported and fixed by @stanstrup]
  • cs_prop() failed when epi-suite data was not available [issue #139, reported and fixed by @stanstrup]
  • cs_prop() failed with invalid html [issue #138, reported and fixed by @stanstrup]
  • cs_prop() gave incorrect answer, if entries were not available [issue #142, reported and fixed by @stanstrup]
  • cs_prop() did not parse scientific number correctly [issue #143, reported by @stanstrup, fixed by @EDiLD]
  • is.smiles() failed because of changes in rcdk [PR #140, reported and fixed by @allaway]
  • cir_query() failed with identifiers containing spaces (e.g. 'acetic acid') [issue #146, reported by Lars Nielsen]
  • several other functions failed with identifiers containing spaces & returned wrong distance.

DEPRECATED FUNCTIONS

DEFUNCT FUNCTIONS

webchem 0.3

NEW FEATURES

MINOR IMPROVEMENTS

  • cs_prop() now also return experimental data for Boiling and Melting Points.
  • pc_synonyms gained an argument 'interactive' to enter an interactive mode for selecting synonyms [isse #129, requested by @Aariq]
  • cts_convert now returns NA if no matches are found.

BUG FIXES

  • cs_prop() failed with some CSIDs [isse #127, reported by @Aariq]
  • wd_ident() failed if multiple entries where found. Now returns the first hit only.
  • ci_query() did not return fully cleaned smiles and inchi

DEPRECATED FUNCTIONS

DEFUNCT FUNCTIONS

webchem 0.2

NEW FEATURES

  • fn_percept() extracts flavor percepts using CAS numbers from www.flavornet.org. Flavornet is a database of 738 compounds with human-detectible odors. [contributed by @Aariq]

MINOR IMPROVEMENTS

BUG FIXES

DEPRECATED FUNCTIONS

DEFUNCT FUNCTIONS

webchem 0.1.1

NEW FEATURES

  • added ping_pubchem() to check whether pubchem is up & running
  • added cs_web_ping () to check whether the chemspider webpage is functional

MINOR IMPROVEMENTS

  • updated allan wood index

BUG FIXES

  • pc_prop() returned to many rows if last cid supplied was NA
  • Switched to https for NCBI, chemspider & chemid (Issue #120, reported by @jranke)
  • get_wdid() failed if non-ascii characters where returned by wikipedia
  • rcdk:parse.smiles() now returns NA if a SMILES string could not be parsed. => broke is.smiles

DEPRECATED FUNCTIONS

DEFUNCT FUNCTIONS

webchem 0.1.0

NEW FEATURES

  • added cts_to() and cts_from() to retrieve possible ids that can be queried.
  • cts_(), pp_query(), cir_query(), get_cid(), get_etoxid(), etox_(), pan_query() get_wdid(), aw_query(), get_csid(), cs_prop(), cs_compinfo() and ci_query() can handle multiple inputs.
  • pc_prop() queries properties and pc_synonmy() synonyms from PUG-REST.
  • added extractors for webchem objects: cas(), inchikey() and smiles().

MINOR IMPROVEMENTS

  • rewrite of pubchem functions using PUG-REST
  • chemspider: better use of NA in input (=return NA)
  • more robust matching in get_etoxid

BUG FIXES

  • pan_query() did not return numeric values
  • get_cid() failed with multiple results

DEPRECATED FUNCTIONS

DEFUNCT FUNCTIONS

  • ppdb_query() has been removed due to copyright issues. The new ppdb_parse() parses only a html, but does not interact with the database
  • pan()
  • alanwood()
  • get_cid()
  • cid_compinfo()
  • chemid()
  • physprop()

webchem 0.0.5.0

NEW FEATURES

  • is.smiles() checks SMILES strings, by parsing via (R)CDK.
  • get_wdid() and wd_indent() to retrieve information from wikidata.
  • get_etoxid() can handle multi inputs (interactive mode, best match, first match, NA and all matches).
  • ci_query() can handle multi inputs (interactive mode, best match, first match and NA).
  • cs_prop() queries predcitions (ACD and EPiSuite) from ChemSpider

MINOR IMPROVEMENTS

  • webchem uses exclusively xml2 (instead of XML).
  • All function return source_url for (micro-)attribution of sources
  • cs_compinfo(): names of returned list changed.
  • cs_extcompinfo():
    • names of returned list changed
    • result is numeric where appropriate
  • cir(): result is numeric where appropriate.
  • unified naming scheme of functions.
  • is.inchikey_cs() has been integrated into is.inchikey().
  • aw_query() returns multiple inchikey if found.
  • pan() now returns chemical name and matched synonym.

BUG FIXES

  • utility functions are not vectorized and throw an error.
  • chemid() did mot work with inchikey as input.
  • ppdb_idx returned duplicated CAS values, which caused ppdb() to fail.
  • ppdb() failed in some cases because of false encoding.
  • etox_*() functions are more robust.
  • ci_query() failed if multi hits were found. Now returns first hit.
  • aw_fuery() failed if inchikey was not found.

DEPRECATED FUNCTIONS

  • pan_query() replaces pan()
  • aw_query() replaces alanwood()
  • get_pcid() replaces get_cid()
  • pc_compinfo() replaces cid_compinfo()
  • ci_query() replaces chemid()
  • pp_query() replaces physprop()

DEFUNCT FUNCTIONS

  • csid_compinfo()
  • csid_extcompinfo()

webchem 0.0.4.0

NEW FEATURES

  • chemid() to query ChemIDplus http://chem.sis.nlm.nih.gov/chemidplus/.
  • is.inchikey() and is.cas() to check if a string is valid inchikey or CAS registry number.
  • parse_mol(): A simple molfile parser.
  • Functions to work with ChemSpider InChI API:
    • cs_csid_mol() : convert csid to mol
    • cs_inchikey_csid() : convert inchikey to csid
    • cs_inchikey_inchi() : convert inchikey to inchi
    • cs_inchikey_mol() : convert inchikey to Molfile
    • cs_inchi_csid() : convert inchi to csid
    • cs_inchi_inchikey : convert inchi to inchikey
    • cs_inchi_mol() : convert inchi to molfile
    • cs_inchi_smiles() : convert inchi to smiles
    • cs_smiles_inchi() : convert smiles to inchi
    • These are all wrapped into cs_convert()
    • is.inchikey_cs() : Check via ChemSpider if inchikey is valid
  • webchem has now a zenodo doi, please cite if you use it.

MINOR IMPROVEMENTS

  • cts_compinfo() checks if input is a inchikey (via exported function is.inchikey()).
  • cts_compinfo() is now more robust and verbose, if problems are encountered
  • alanwood() returns separate inchi and ichikeys in case of isomers.
  • alanwood() returns also subactvity (e.g. $Fluazinam$activity [1] "fungicides" and $Fluazinam$subactivity [1] "pyridine fungicides").
  • physprop() also returns boiling and melting points. Moreover, values are now numeric.

BUG FIXES

  • alanwood() returns only results for first match in case of multiple links found
  • physprop() stopped working after change of SRC to https, fixed now.
  • changed etox_* functions to https

DEPRECATED FUNCTIONS

  • ppdb() replaces ppdb_query() and accepts individual index as created by ppdb_buildidx().
  • cir() replaces cir_query().
  • cs_compinfo() replaces csid_compinfo()
  • cs_extcompinfo() replaces csid_extcompinfo()

DEFUNCT FUNCTIONS

  • allanwood()

webchem 0.0.3

NEW FEATURES

  • Query SRC PHYSPROP Database with physprop().
  • Query the ETOX ID with get_etoxid(); query basic information with etox_basic(); quality targets with etox_targets() and test results with etox_tests().
  • Query PPDB with ppdb_query()

MINOR IMPROVEMENTS

  • added exceptions/checks to tests
  • improved robustness of cir_query()

BUG FIXES

  • Correct the spelling of Alan Wood and rename function allanwood() to alanwood() [contribution of @jranke]

webchem 0.0.2

NEW FEATURES

  • Query the PAN Pesticides Database with pan().
  • Query Allan Woods Compendium of Pesticide Common Names with allanwood().

MINOR IMPROVEMENTS

  • Added checks for user input.
  • Fixed documentation, added example for bulk processing.
  • cts_convert() returns NA if no result was found.
  • Set 'verbose = TRUE' as default for all functions.
  • Added unit tests.
  • All functions return silently NA, if API is not reachable.

BUG FIXES

  • cts_convert() does not ignore 'first' argument.
  • get_csid() did not return NA, if there was a problem with the API.
  • Many functions returned 'NA2+' if NA was given - now return NA by default.
  • Many fixes in NA handling, e.g. when no hit was found.

Reference manual

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install.packages("webchem")

1.0.0 by Tamás Stirling, 4 months ago


https://docs.ropensci.org/webchem, https://github.com/ropensci/webchem


Report a bug at https://github.com/ropensci/webchem/issues


Browse source code at https://github.com/cran/webchem


Authors: Eduard Szöcs [aut] , Robert Allaway [ctb] , Daniel Muench [ctb] , Johannes Ranke [ctb] , Andreas Scharmüller [ctb] , Eric R Scott [ctb] , Jan Stanstrup [ctb] , Gordon Getzinger [ctb] , Tamás Stirling [ctb, cre]


Documentation:   PDF Manual  


Task views: Chemometrics and Computational Physics


MIT + file LICENSE license


Imports xml2, httr, rvest, RCurl, jsonlite, stringr, methods, dplyr, purrr, data.tree, tibble

Suggests testthat, rcdk, covr, robotstxt, knitr, rmarkdown


Imported by MetaDBparse.


See at CRAN