NEWS.md

In ropensci/webchem: Chemical Information from the Web

dev

BUG FIXES

• pc_prop() returned NA without much further explanation if any of the queries were not positive integers. The updated function attempts to coerce queries to positive integers, only progresses valid queries, and prints informative messages along the way if verbose messages are enabled.

webchem 1.3.0

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

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

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

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.

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.

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

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

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

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

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. $Fluazinam$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().

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.

ropensci/webchem documentation built on Feb. 23, 2024, 6:28 p.m.