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NEWS
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NEWS
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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]
* is.smiles() failed because of changes in rcdk [PR #140, reported and fixed by @allaway]
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.