Chemical Information from the Web

Chemical information from around the web. This package interacts with a suite of web APIs for chemical information.


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")

0.4.0 by Eduard Szöcs, a year ago


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, cre] , Daniel Muench [ctb] , Johannes Ranke [ctb] , Eric Scott [ctb] , Jan Stanstrup [ctb] , Robert Allaway [ctb]


Documentation:   PDF Manual  


Task views: Chemometrics and Computational Physics


MIT + file LICENSE license


Imports xml2, httr, rvest, RCurl, jsonlite, stringr, methods

Suggests testthat, rcdk


Imported by RAMClustR.


See at CRAN