webchem v1.3.1

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.
• srs_query() broke because the URL was no longer working. We have updated the URL.
• is.inchikey(type = "chemspider") broke because the URL was no longer working. We have updated the URL but the function now requires an API key like all other ChemSpider functions.
• pc_prop() failed with properties = NULL because the list of accepted property names had changed. We have updated the list.

webchem v1.3.0

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 v1.2.0

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 v1.1.3

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 v1.1.2

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 v1.1.1

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 v1.1.0

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 v1.0.0

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. [PR #241, added by @andschar]
• 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 [PR #226, fixed by stitam]
• get_chebiid() and chebi_comp_entity() fixed for invalid queries [PR #225, fixed by stitam]
• get_cid() returned the PubChem ID of sodium when the query was NA [PR #223, fixed by stitam]
• aw_query() returned a list for successful queries, NA for unsuccessful queries [PR #222, fixed by stitam]

webchem v0.5.0

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 [contributed by @andschar].
• Retrieve retention indices from NIST (https://webbook.nist.gov) with nist_ri() [PR #154, contributed by @Aariq]
• Get record details from US EPA Substance Registry Services (https://cdxnodengn.epa.gov/cdx-srs-rest/) with srs_query() [PR #179]
• "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. [contributed by @Aariq]
• 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 [issue #148, reported and fixed by @stanstrup]
• pp_query() failed when compound present, but no properties [issue #151, reported and fixed by @stanstrup]
• ci_query() failed when missing table [issue #196, reported and fixed by @gjgetzinger]
• get_csid() failed because of a major change in the ChemSpider API [issue #149, PR #165, contributed by @stitam]
• multiple functions failed because of a major change in the ChemSpider API [issue #149, contributed by @stitam]
• cir_query() mistook NA for sodium [issue #158, reported and fixed by @Aariq]
• fixed functions that communicate with the ChemSpider API [issue #149, issue #160, fixed by @stitam]
• get_etoxid() printed incorrect results for certain match types [issue #201, fixed by @stitam]

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.

webchem v0. 4

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