CRAN release: 2023-06-09
nist_rifunction now returns a column with the CAS number to facilitate querying of multiple retention index tables.
nist_rifunction can now take multiple arguments for
- CAS numbers are automatically reformatted using
as.casfunction now has a
CRAN release: 2022-11-02
- 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.
- 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.
CRAN release: 2022-06-15
- 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.
CRAN release: 2021-12-06
- 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.
CRAN release: 2021-02-07
CRAN release: 2020-10-02
- Download images of substances from Chemical Identifier Resolver (CIR) with
- Download images of substances from ChemSpider with
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.
- Most functions now use httr::RETRY() to access webservices.
- Verbose messages are now harmonized.
aw_query()has been changed to
"from"for consistency with other functions.
"from"arguments for consistency with other functions.
- Possible values for
"from"have been made more consistent across functions.
cir_query()have been changed to use the
matchargument instead of
choicesfor 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.
CRAN release: 2020-05-28
- 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
- nist_ri() now can search by name, InChI, InChIKey, or CAS. The
casargument is deprecated. Use
from = "cas".
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().
- 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.
CRAN release: 2020-03-02
- 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.
- as.cas() added.
- Removed documentation files for non-exported functions that were only used internally.
- 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.
- cs_extcompinfo() cannot be fixed as there is no equivalent in the new ChemSpider API yet.
CRAN release: 2018-04-07
- 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.
CRAN release: 2017-10-20
- 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.
- 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.
- fn_percept() extracts flavor percepts using CAS numbers from www.flavornet.org. Flavornet is a database of 738 compounds with human-detectible odors.
- Added ping_pubchem() to check whether pubchem is up & running.
- Added cs_web_ping () to check whether the chemspider webpage is functional.
- 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
- 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().
- Rewrite of pubchem functions using PUG-REST.
- ChemSpider: better use of NA in input (=return NA).
- More robust matching in get_etoxid.
- 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.
- webchem uses exclusively xml2 (instead of XML).
- All function return source_url for (micro-)attribution of sources.
- cs_compinfo(): names of returned list changed.
- 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.
- 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.
- 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().
- 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.
- 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  “fungicides” and Fluazinamsubactivity  “pyridine fungicides”).
- physprop() also returns boiling and melting points. Moreover, values are now numeric.
- 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.
- 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().
CRAN release: 2015-09-25
- 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().
CRAN release: 2015-08-15
- Query the PAN Pesticides Database with pan().
- Query Allan Woods Compendium of Pesticide Common Names with allanwood().
- 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.