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Changelog

Source: NEWS.md

webchem 1.3.0

CRAN release: 2023-06-09

NEW FEATURES

  • The nist_ri function now returns a column with the CAS number to facilitate querying of multiple retention index tables.
  • The nist_ri function can now take multiple arguments for type, polarity and temp_prog.
  • CAS numbers are automatically reformatted using as.cas in bcpc_query, cts_convert, get_etoxid, fn_percept, get_cid, and srs_query.
  • The as.cas function now has a verbose argument.

DEFUNCT FUNCTIONS

  • ci_query() has been removed from the package because NLM had retired ChemIDplus.
  • pan_query() has been removed from the package because PAN no longer supports programmatic access.

BUG FIXES

  • nist_ri() failed because the behaviour of a dependency had changed. This has been fixed.
  • pc_sect() failed when query response was valid but the content was NA. This has been fixed.

webchem 1.2.0

CRAN release: 2022-11-02

NEW FEATURES

  • webchem can now access ChEMBL (https://www.ebi.ac.uk/chembl/) with chembl_*() functions. ChEMBL is a manually curated database of bioactive molecules with drug-like properties.

BUG FIXES

  • ChemSpider functions did not include time delays between queries. This has been fixed.
  • Multiple ChemSpider functions failed when the API key was provided during function call. This has been fixed.
  • Minor change in NIST retention index tables was causing nist_ri() to fail. This has been fixed.

webchem 1.1.3

CRAN release: 2022-06-15

NEW FEATURES

  • cir_query() now returns a tibble instead of a list to be consistent with other translator functions. This is a potentially breaking change for users.

BUG FIXES

  • cts_convert() now accepts numeric input as well e.g. PubChem CID.
  • get_cid() became more robust to smiles queries with special characters.
  • bcpc_query now correctly parses the activity in cases that two activities are given (e.g. “herbicides” and “plant growth regulators”).

webchem 1.1.2

CRAN release: 2021-12-06

NEW FEATURES

  • Export chemical structures in Mol format with write_mol().

BUG FIXES

  • ci_query() can no longer query chemicals by name.
  • Non-exported function ping_pubchem_pw() was incorrectly reporting that PUG VIEW was down. This has been fixed.
  • is.cas() now catches whitespaces correctly.
  • aw_query() was renamed and adapted to bcpc_query, as the alanwood site has moved.

MINOR IMPROVEMENTS

  • webchem functions now default to global options regarding verbose messages.

webchem 1.1.1.

CRAN release: 2021-02-07

NEW FEATURES

  • Fetch LIPID MAPS and SwissLipids identifiers from Wikidata.

BUG FIXES

  • Fix get_csid() so it doesn’t break when a query is invalid.

webchem 1.1.0.

CRAN release: 2020-10-02

NEW FEATURES

  • Download images of substances from Chemical Identifier Resolver (CIR) with cir_img().
  • Download images of substances from ChemSpider with cs_img().
  • find_db() checks if a query gets a hit in most databases integrated in webchem. Useful for deciding which of several databases to focus on given a set of chemicals.

MINOR IMPROVEMENTS

  • Most functions now use httr::RETRY() to access webservices.
  • Verbose messages are now harmonized.
  • The "type" argument in ci_query() and aw_query() has been changed to "from" for consistency with other functions.
  • fn_percept() and cts_compinfo() now have "query" and "from" arguments for consistency with other functions.
  • Possible values for "from" have been made more consistent across functions.
  • pc_synonyms(), cts_convert(), cir_query() have been changed to use the match argument instead of choices for consistency with other functions.
  • get_etoxid() output changed slightly so that the matched chemical name string no longer includes the etoxid in parentheses.
  • is.cas() is now vectorized.

BUG FIXES

  • Fix URL encoding so SMILES queries don’t fail on some special characters.

webchem 1.0.0

CRAN release: 2020-05-28

NEW FEATURES

  • get_cid() now can search by registry IDs (e.g. CAS RN), and can handle more complex requests like searching for similar compounds.
  • Retrieve chemical data from PubChem content pages with pc_sect().
  • get_etoxid() now can search by CAS, EC, GSBL and RTECS numbers. Added from = argument.
  • nist_ri() now can search by name, InChI, InChIKey, or CAS. The cas argument is deprecated. Use query instead with from = "cas".

MINOR IMPROVEMENTS

  • All get_*() functions now output tibbles with a column for the query and a column for the retrieved ID.
  • Changes to arguments in get_*() functions to make them more consistent.
  • aw_idx.rda is no longer included in the package as a data set. Instead, it is built by build_aw_idx() to tempdir().

BUG FIXES

  • nist_ri() returned malformed tables or errored if there was only one entry for a query.
  • get_csid() now returns all csids when queried from formula.
  • get_csid() returned an error when query was NA.
  • get_chebiid() and chebi_comp_entity() fixed for invalid queries.
  • get_cid() returned the PubChem ID of sodium when the query was NA.
  • aw_query() returned a list for successful queries, NA for unsuccessful queries.

DEPRECATED FUNCTIONS

DEFUNCT FUNCTIONS

webchem 0.5.0

CRAN release: 2020-03-02

NEW FEATURES

  • Retrieve data from ChEBI (https://www.ebi.ac.uk/chebi/) webservice with get_chebiid() and chebi_comp_entity(). ChEBI comprises a rich data base on chemicals with bilogical interest.
  • Retrieve retention indices from NIST (https://webbook.nist.gov) with nist_ri().
  • Get record details from US EPA Substance Registry Services (https://cdxnodengn.epa.gov/cdx-srs-rest/) with srs_query().
  • “first” argument in cts_convert() and cir_query() and “interactive” argument in pc_synonyms() deprecated. Use “choices” instead to return either a list of all results, only the first result, or an interactive menu to choose a result to return.
  • ChemSpider functions now look for an API token stored in .Renviron or .Rprofile by default so you can keep them hidden more easily.

MINOR IMPROVEMENTS

  • as.cas() added.
  • Removed documentation files for non-exported functions that were only used internally.

BUG FIXES

  • cs_prop() failed with duplicated return values.
  • pp_query() failed when compound present, but no properties.
  • ci_query() failed when missing table.
  • get_csid() failed because of a major change in the ChemSpider API.
  • multiple functions failed because of a major change in the ChemSpider API.
  • cir_query() mistook NA for sodium.
  • fixed functions that communicate with the ChemSpider API.
  • get_etoxid() printed incorrect results for certain match types.

DEPRECATED FUNCTIONS

  • cs_extcompinfo() cannot be fixed as there is no equivalent in the new ChemSpider API yet.

DEFUNCT FUNCTIONS

  • ppdb_parse() has been removed. webchem no longer offers any support for PPDB.
  • pp_query() has been removed. Physprop API is no longer active.
  • cs_prop() has been removed.

webchem 0.4.0

CRAN release: 2018-04-07

NEW FEATURES

MINOR IMPROVEMENTS

BUG FIXES

  • extr_num() did not work properly with decimal numbers.
  • cs_prop() failed when epi-suite data was not available.
  • cs_prop() failed with invalid html.
  • cs_prop() gave incorrect answer, if entries were not available.
  • cs_prop() did not parse scientific number correctly.
  • is.smiles() failed because of changes in rcdk.
  • cir_query() failed with identifiers containing spaces (e.g. ‘acetic acid’).
  • Aeveral other functions failed with identifiers containing spaces & returned wrong distance.

DEPRECATED FUNCTIONS

DEFUNCT FUNCTIONS

webchem 0.3.0

CRAN release: 2017-10-20

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.
  • cts_convert now returns NA if no matches are found.

BUG FIXES

  • cs_prop() failed with some CSIDs.
  • 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 0.2.0

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.

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.
  • 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

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 predictions (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

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. Fluazinamactivity [1] “fungicides” and Fluazinamsubactivity [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

CRAN release: 2015-09-25

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().

webchem 0.0.2

CRAN release: 2015-08-15

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.