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 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.