News

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

webchem 0.3

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 [isse #129, requested by @Aariq]
• cts_convert now returns NA if no matches are found.

BUG FIXES

• cs_prop() failed with some CSIDs [isse #127, reported by @Aariq]
• 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

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. [contributed by @Aariq]

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 (Issue #120, reported by @jranke)
• 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 0.0.5.0

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 predcitions (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 0.0.4.0

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() [contribution of @jranke]

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.

Reference manual