webchem - 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.

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Published by stitam over 2 years ago

webchem - 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.

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Published by stitam over 3 years ago

webchem - 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").

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Published by stitam over 3 years ago

webchem - 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 pingpubchempw() was incorrectly reporting that PUG VIEW was down. This has been fixed.
• is.cas() now catches whitespaces correctly.
• awquery() was renamed and adapted to bcpcquery, as the alanwood site has moved

MINOR IMPROVEMENTS

• webchem functions now default to global options regarding verbose messages.

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Published by stitam about 4 years ago

webchem - 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.

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Published by stitam about 5 years ago

webchem - 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.

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Published by stitam over 5 years ago

webchem - 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
• awidx.rda is no longer included in the package as a data set. Instead, it is built by buildaw_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]
• getchebiid() and chebicomp_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]

- R
Published by stitam over 5 years ago

webchem - webchem v0.5.0

NEW FEATURES

• Retrieve data from ChEBI (https://www.ebi.ac.uk/chebi/) webservice with getchebiid() and chebicomp_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 ctsconvert() and cirquery() 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.

- R
Published by stitam almost 6 years ago

webchem - 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

- R
Published by eduardszoecs almost 8 years ago

webchem - webchem v0.2

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

- R
Published by eduardszoecs almost 9 years ago

webchem - webchem v0.1.1

webchem 0.1.1

NEW FEATURES - added pingpubchem() to check whether pubchem is up & running - added csweb_ping () to check whether the chemspider webpage is functional

MINOR IMPROVEMENTS - updated allan wood index

BUG FIXES - pcprop() returned to many rows if last cid supplied was NA - Switched to https for NCBI, chemspider & chemid (Issue #120, reported by @jranke) - getwdid() 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

- R
Published by eduardszoecs over 9 years ago

webchem - webchem v0.1.0

webchem v0.1.0

NEW FEATURES - added ctsto() and ctsfrom() to retrieve possible ids that can be queried. - cts(), ppquery(), cirquery(), getcid(), getetoxid(), etox(), panquery() getwdid(), awquery(), getcsid(), csprop(), cscompinfo() and ciquery() can handle multiple inputs. - pcprop() 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 - panquery() did not return numeric values - getcid() failed with multiple results

DEPRECATED FUNCTIONS

DEFUNCT FUNCTIONS - ppdbquery() has been removed due to copyright issues. The new ppdbparse() parses only a html, but does not interact with the database - pan() - alanwood() - getcid() - cidcompinfo() - chemid() - physprop()

- R
Published by eduardszoecs almost 10 years ago

webchem - webchem v0.0.5

webchem 0.0.5.0

NEW FEATURES - is.smiles() checks SMILES strings, by parsing via (R)CDK. - getwdid() and wdindent() to retrieve information from wikidata. - getetoxid() can handle multi inputs (interactive mode, best match, first match, NA and all matches). - ciquery() 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 sourceurl for (micro-)attribution of sources - cscompinfo(): names of returned list changed. - csextcompinfo(): - names of returned list changed - result is numeric where appropriate - cir(): result is numeric where appropriate. - unified naming scheme of functions. - is.inchikeycs() 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. - ppdbidx returned duplicated CAS values, which caused ppdb() to fail. - ppdb() failed in some cases because of false encoding. - etox*() functions are more robust. - ciquery() failed if multi hits were found. Now returns first hit. - awfuery() failed if inchikey was not found.

DEPRECATED FUNCTIONS - panquery() replaces pan() - awquery() replaces alanwood() - getpcid() replaces getcid() - pccompinfo() replaces cidcompinfo() - ciquery() replaces chemid() - ppquery() replaces physprop()

DEFUNCT FUNCTIONS - csidcompinfo() - csidextcompinfo()

- R
Published by eduardszoecs about 10 years ago

webchem - webchem v0.0.4

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. - parsemol(): A simple molfile parser. - Functions to work with ChemSpider InChI API: - cscsidmol() : convert csid to mol - csinchikeycsid() : convert inchikey to csid - csinchikeyinchi() : convert inchikey to inchi - csinchikeymol() : convert inchikey to Molfile - csinchicsid() : convert inchi to csid - csinchiinchikey : convert inchi to inchikey - csinchimol() : convert inchi to molfile - csinchismiles() : convert inchi to smiles - cssmilesinchi() : convert smiles to inchi - These are all wrapped into csconvert() - is.inchikey_cs() : Check via ChemSpider if inchikey is valid - webchem has now a zenodo doi, please cite if you use it.

MINOR IMPROVEMENTS - ctscompinfo() checks if input is a inchikey (via exported function is.inchikey()). - ctscompinfo() 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 ppdbquery() and accepts individual index as created by ppdbbuildidx(). - cir() replaces cirquery(). - cscompinfo() replaces csidcompinfo() - csextcompinfo() replaces csid_extcompinfo()

DEFUNCT FUNCTIONS - allanwood()

- R
Published by eduardszoecs about 10 years ago

webchem - zenodo release

zenodo release

- R
Published by eduardszoecs over 10 years ago

webchem - webchem v0.0.0.4.alpha

zenodo init

- R
Published by eduardszoecs over 10 years ago

webchem - webchem v0.0.3

webchem version 0.0.3

- R
Published by eduardszoecs over 10 years ago

webchem - v0.0.2

webchem v0.0.2 on CRAN

- R
Published by eduardszoecs over 10 years ago

webchem - v0.0.1

webchem version 0.0.1 on CRAN.

- R
Published by eduardszoecs almost 11 years ago