diff --git a/DESCRIPTION b/DESCRIPTION index 2181f823..5df4a50e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -30,4 +30,4 @@ Imports: Suggests: testthat, rcdk -RoxygenNote: 5.0.1 +RoxygenNote: 6.0.1 diff --git a/NAMESPACE b/NAMESPACE index 9f6f25f8..34a94d94 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -50,6 +50,7 @@ export(etox_basic) export(etox_targets) export(etox_tests) export(extr_num) +export(fn_percept) export(get_cid) export(get_csid) export(get_etoxid) diff --git a/man/aw_idx.Rd b/man/aw_idx.Rd index ea6b196e..e43321f4 100644 --- a/man/aw_idx.Rd +++ b/man/aw_idx.Rd @@ -24,4 +24,3 @@ You can use the function \code{\link{build_aw_idx}} to rebuild the index. Date of build: 12. Feb. 2016 } \keyword{datasets} - diff --git a/man/aw_query.Rd b/man/aw_query.Rd index bc9c6cf8..66f4e24e 100644 --- a/man/aw_query.Rd +++ b/man/aw_query.Rd @@ -42,4 +42,3 @@ aw_query("79622-59-6", type = 'cas') \author{ Eduard Szoecs, \email{eduardszoecs@gmail.com} } - diff --git a/man/build_aw_idx.Rd b/man/build_aw_idx.Rd index 4fe4cb1e..8eb9942f 100644 --- a/man/build_aw_idx.Rd +++ b/man/build_aw_idx.Rd @@ -12,10 +12,9 @@ a data.frame with three columns: cas, url, and name \description{ Function to build index } -\author{ -Eduard Szoecs, \email{eduardszoecs@gmail.com} -} \seealso{ \code{\link{aw_query}}, \code{\link{aw_idx}} } - +\author{ +Eduard Szoecs, \email{eduardszoecs@gmail.com} +} diff --git a/man/ci_query.Rd b/man/ci_query.Rd index a5b42da0..852b05a8 100644 --- a/man/ci_query.Rd +++ b/man/ci_query.Rd @@ -56,4 +56,3 @@ sapply(y1, function(y){ }) } } - diff --git a/man/cir_query.Rd b/man/cir_query.Rd index 60b173fe..581b4908 100644 --- a/man/cir_query.Rd +++ b/man/cir_query.Rd @@ -116,9 +116,6 @@ cir_query(comp, 'cas', first = TRUE) } } -\author{ -Eduard Szoecs, \email{eduardszoecs@gmail.com} -} \references{ \code{cir} relies on the great CIR web service created by the CADD Group at NCI/NIH! \cr @@ -127,4 +124,6 @@ Group at NCI/NIH! \cr \url{http://cactus.nci.nih.gov/blog/?p=1386}, \cr \url{http://cactus.nci.nih.gov/blog/?p=1456}, \cr } - +\author{ +Eduard Szoecs, \email{eduardszoecs@gmail.com} +} diff --git a/man/cs_compinfo.Rd b/man/cs_compinfo.Rd index 85a6f65a..533912b5 100644 --- a/man/cs_compinfo.Rd +++ b/man/cs_compinfo.Rd @@ -40,11 +40,10 @@ csids <- get_csid(c('Aspirin', 'Triclosan'), token = token) cs_compinfo(csids, token = token) } } -\author{ -Eduard Szoecs, \email{eduardszoecs@gmail.com} -} \seealso{ \code{\link{get_csid}} to retrieve ChemSpider IDs, \code{\link{cs_extcompinfo}} for extended compound information. } - +\author{ +Eduard Szoecs, \email{eduardszoecs@gmail.com} +} diff --git a/man/cs_convert.Rd b/man/cs_convert.Rd index 82e81f89..d2501802 100644 --- a/man/cs_convert.Rd +++ b/man/cs_convert.Rd @@ -41,9 +41,6 @@ cs_convert('BQJCRHHNABKAKU-KBQPJGBKSA-N', from = 'inchikey', to = 'inchi') cs_convert('BQJCRHHNABKAKU-KBQPJGBKSA-N', from = 'inchikey', to = 'mol') } } -\author{ -Eduard Szoecs, \email{eduardszoecs@gmail.com} -} \seealso{ There are many low level functions underlying, which are exported from the package. The naming scheme is cs_from_to() here's a list and links to their manual pages: @@ -60,4 +57,6 @@ the package. The naming scheme is cs_from_to() here's a list and links to their } Check \code{\link{parse_mol}} for a description of the Mol R Object. } - +\author{ +Eduard Szoecs, \email{eduardszoecs@gmail.com} +} diff --git a/man/cs_csid_mol.Rd b/man/cs_csid_mol.Rd index 712672da..0e2734bc 100644 --- a/man/cs_csid_mol.Rd +++ b/man/cs_csid_mol.Rd @@ -40,10 +40,9 @@ tric_mol cs_csid_mol(5363, token = token, parse = FALSE) } } -\author{ -Eduard Szoecs, \email{eduardszoecs@gmail.com} -} \seealso{ This is a low level function. Please see \code{\link{cs_convert}} for the top level function. } - +\author{ +Eduard Szoecs, \email{eduardszoecs@gmail.com} +} diff --git a/man/cs_extcompinfo.Rd b/man/cs_extcompinfo.Rd index 018566a5..bea447f6 100644 --- a/man/cs_extcompinfo.Rd +++ b/man/cs_extcompinfo.Rd @@ -43,11 +43,10 @@ csids <- get_csid(c('Aspirin', 'Triclosan'), token = token) cs_compinfo(csids, token = token) } } -\author{ -Eduard Szoecs, \email{eduardszoecs@gmail.com} -} \seealso{ \code{\link{get_csid}} to retrieve ChemSpider IDs, \code{\link{cs_compinfo}} for extended compound information. } - +\author{ +Eduard Szoecs, \email{eduardszoecs@gmail.com} +} diff --git a/man/cs_inchi_csid.Rd b/man/cs_inchi_csid.Rd index a774b9f2..7e0d1aca 100644 --- a/man/cs_inchi_csid.Rd +++ b/man/cs_inchi_csid.Rd @@ -28,10 +28,9 @@ inchi <- "InChI=1S/C17H19NO3/c1-18-7-6-17-10-3-5-13(20)16(17)21-15-12(19)4- cs_inchi_csid(inchi) } } -\author{ -Eduard Szoecs, \email{eduardszoecs@gmail.com} -} \seealso{ This is a low level function. Please see \code{\link{cs_convert}} for the top level function. } - +\author{ +Eduard Szoecs, \email{eduardszoecs@gmail.com} +} diff --git a/man/cs_inchi_inchikey.Rd b/man/cs_inchi_inchikey.Rd index b7cf6e01..54b34e3f 100644 --- a/man/cs_inchi_inchikey.Rd +++ b/man/cs_inchi_inchikey.Rd @@ -28,10 +28,9 @@ inchi <- "InChI=1S/C17H19NO3/c1-18-7-6-17-10-3-5-13(20)16(17)21-15-12(19)4- cs_inchi_inchikey(inchi) } } -\author{ -Eduard Szoecs, \email{eduardszoecs@gmail.com} -} \seealso{ This is a low level function. Please see \code{\link{cs_convert}} for the top level function. } - +\author{ +Eduard Szoecs, \email{eduardszoecs@gmail.com} +} diff --git a/man/cs_inchi_mol.Rd b/man/cs_inchi_mol.Rd index e64df4b5..0e57b3f3 100644 --- a/man/cs_inchi_mol.Rd +++ b/man/cs_inchi_mol.Rd @@ -33,10 +33,9 @@ cs_inchi_mol(inchi) cs_inchi_mol(inchi, parse = FALSE) } } -\author{ -Eduard Szoecs, \email{eduardszoecs@gmail.com} -} \seealso{ This is a low level function. Please see \code{\link{cs_convert}} for the top level function. } - +\author{ +Eduard Szoecs, \email{eduardszoecs@gmail.com} +} diff --git a/man/cs_inchi_smiles.Rd b/man/cs_inchi_smiles.Rd index 0f17aaa5..6e269d82 100644 --- a/man/cs_inchi_smiles.Rd +++ b/man/cs_inchi_smiles.Rd @@ -28,10 +28,9 @@ inchi <- "InChI=1S/C17H19NO3/c1-18-7-6-17-10-3-5-13(20)16(17)21-15-12(19)4- cs_inchi_smiles(inchi) } } -\author{ -Eduard Szoecs, \email{eduardszoecs@gmail.com} -} \seealso{ This is a low level function. Please see \code{\link{cs_convert}} for the top level function. } - +\author{ +Eduard Szoecs, \email{eduardszoecs@gmail.com} +} diff --git a/man/cs_inchikey_csid.Rd b/man/cs_inchikey_csid.Rd index de47dd74..e2e66cfa 100644 --- a/man/cs_inchikey_csid.Rd +++ b/man/cs_inchikey_csid.Rd @@ -26,10 +26,9 @@ Convert a InChIKey to CSID cs_inchikey_csid('BQJCRHHNABKAKU-KBQPJGBKSA-N') } } -\author{ -Eduard Szoecs, \email{eduardszoecs@gmail.com} -} \seealso{ This is a low level function. Please see \code{\link{cs_convert}} for the top level function. } - +\author{ +Eduard Szoecs, \email{eduardszoecs@gmail.com} +} diff --git a/man/cs_inchikey_inchi.Rd b/man/cs_inchikey_inchi.Rd index e9ba2130..930abea2 100644 --- a/man/cs_inchikey_inchi.Rd +++ b/man/cs_inchikey_inchi.Rd @@ -25,10 +25,9 @@ Convert a InChIKey to InChI cs_inchikey_inchi('BQJCRHHNABKAKU-KBQPJGBKSA-N') } } -\author{ -Eduard Szoecs, \email{eduardszoecs@gmail.com} -} \seealso{ This is a low level function. Please see \code{\link{cs_convert}} for the top level function. } - +\author{ +Eduard Szoecs, \email{eduardszoecs@gmail.com} +} diff --git a/man/cs_inchikey_mol.Rd b/man/cs_inchikey_mol.Rd index 404b5a94..e2efab7d 100644 --- a/man/cs_inchikey_mol.Rd +++ b/man/cs_inchikey_mol.Rd @@ -31,10 +31,9 @@ tric_mol cs_inchikey_mol('BQJCRHHNABKAKU-KBQPJGBKSA-N',parse = FALSE) } } -\author{ -Eduard Szoecs, \email{eduardszoecs@gmail.com} -} \seealso{ This is a low level function. Please see \code{\link{cs_convert}} for the top level function. } - +\author{ +Eduard Szoecs, \email{eduardszoecs@gmail.com} +} diff --git a/man/cs_prop.Rd b/man/cs_prop.Rd index a8bf0347..8bba8118 100644 --- a/man/cs_prop.Rd +++ b/man/cs_prop.Rd @@ -35,11 +35,10 @@ sapply(out2, function(y){ }) } } -\author{ -Eduard Szoecs, \email{eduardszoecs@gmail.com} -} \seealso{ \code{\link{get_csid}} to retrieve ChemSpider IDs, \code{\link{cs_compinfo}} for extended compound information. } - +\author{ +Eduard Szoecs, \email{eduardszoecs@gmail.com} +} diff --git a/man/cs_smiles_inchi.Rd b/man/cs_smiles_inchi.Rd index bc00e43c..4bc33fd2 100644 --- a/man/cs_smiles_inchi.Rd +++ b/man/cs_smiles_inchi.Rd @@ -27,10 +27,9 @@ smiles <- "CN1CC[C@]23[C@H]4C=C[C@H]([C@H]3Oc3c(ccc(C[C@H]14)c23)O)O" cs_smiles_inchi(smiles) } } -\author{ -Eduard Szoecs, \email{eduardszoecs@gmail.com} -} \seealso{ This is a low level function. Please see \code{\link{cs_convert}} for the top level function. } - +\author{ +Eduard Szoecs, \email{eduardszoecs@gmail.com} +} diff --git a/man/cts_compinfo.Rd b/man/cts_compinfo.Rd index 7ba07b4a..fdbf081c 100644 --- a/man/cts_compinfo.Rd +++ b/man/cts_compinfo.Rd @@ -35,11 +35,10 @@ str(out2) sapply(out2, function(y) y$molweight) } } -\author{ -Eduard Szoecs, \email{eduardszoecs@gmail.com} -} \references{ Wohlgemuth, G., P. K. Haldiya, E. Willighagen, T. Kind, and O. Fiehn 2010The Chemical Translation Service -- a Web-Based Tool to Improve Standardization of Metabolomic Reports. Bioinformatics 26(20): 2647–2648. } - +\author{ +Eduard Szoecs, \email{eduardszoecs@gmail.com} +} diff --git a/man/cts_convert.Rd b/man/cts_convert.Rd index 7dc853b2..df2d90a8 100644 --- a/man/cts_convert.Rd +++ b/man/cts_convert.Rd @@ -40,9 +40,6 @@ comp <- c('XEFQLINVKFYRCS-UHFFFAOYSA-N', 'BSYNRYMUTXBXSQ-UHFFFAOYSA-N') cts_convert(comp, 'inchikey', 'Chemical Name') } } -\author{ -Eduard Szoecs, \email{eduardszoecs@gmail.com} -} \references{ Wohlgemuth, G., P. K. Haldiya, E. Willighagen, T. Kind, and O. Fiehn 2010The Chemical Translation Service -- a Web-Based Tool to Improve Standardization of Metabolomic Reports. Bioinformatics 26(20): 2647–2648. @@ -51,4 +48,6 @@ Wohlgemuth, G., P. K. Haldiya, E. Willighagen, T. Kind, and O. Fiehn 2010The Che \code{\link{cts_from}} for possible values in the 'from' argument and \code{\link{cts_to}} for possible values in the 'to' argument. } - +\author{ +Eduard Szoecs, \email{eduardszoecs@gmail.com} +} diff --git a/man/cts_from.Rd b/man/cts_from.Rd index 6ccb3c6d..eb30b9f5 100644 --- a/man/cts_from.Rd +++ b/man/cts_from.Rd @@ -23,9 +23,6 @@ See also \url{http://cts.fiehnlab.ucdavis.edu/moreServices/index#fromnames} cts_from() } } -\author{ -Eduard Szoecs, \email{eduardszoecs@gmail.com} -} \references{ Wohlgemuth, G., P. K. Haldiya, E. Willighagen, T. Kind, and O. Fiehn 2010The Chemical Translation Service -- a Web-Based Tool to Improve Standardization of Metabolomic Reports. Bioinformatics 26(20): 2647–2648. @@ -33,4 +30,6 @@ Wohlgemuth, G., P. K. Haldiya, E. Willighagen, T. Kind, and O. Fiehn 2010The Che \seealso{ \code{\link{cts_convert}} } - +\author{ +Eduard Szoecs, \email{eduardszoecs@gmail.com} +} diff --git a/man/cts_to.Rd b/man/cts_to.Rd index 07e06519..4d8c9c5e 100644 --- a/man/cts_to.Rd +++ b/man/cts_to.Rd @@ -23,9 +23,6 @@ See also \url{http://cts.fiehnlab.ucdavis.edu/moreServices/index#fromnames} cts_from() } } -\author{ -Eduard Szoecs, \email{eduardszoecs@gmail.com} -} \references{ Wohlgemuth, G., P. K. Haldiya, E. Willighagen, T. Kind, and O. Fiehn 2010The Chemical Translation Service -- a Web-Based Tool to Improve Standardization of Metabolomic Reports. Bioinformatics 26(20): 2647–2648. @@ -33,4 +30,6 @@ Wohlgemuth, G., P. K. Haldiya, E. Willighagen, T. Kind, and O. Fiehn 2010The Che \seealso{ \code{\link{cts_convert}} } - +\author{ +Eduard Szoecs, \email{eduardszoecs@gmail.com} +} diff --git a/man/etox_basic.Rd b/man/etox_basic.Rd index e398595e..526ee13b 100644 --- a/man/etox_basic.Rd +++ b/man/etox_basic.Rd @@ -37,11 +37,10 @@ out sapply(out, function(y) y$ec) } } -\author{ -Eduard Szoecs, \email{eduardszoecs@gmail.com} -} \seealso{ \code{\link{get_etoxid}} to retrieve ETOX IDs, \code{\link{etox_basic}} for basic information, \code{\link{etox_targets}} for quality targets and \code{\link{etox_tests}} for test results } - +\author{ +Eduard Szoecs, \email{eduardszoecs@gmail.com} +} diff --git a/man/etox_targets.Rd b/man/etox_targets.Rd index 8aebbd7b..70b036d6 100644 --- a/man/etox_targets.Rd +++ b/man/etox_targets.Rd @@ -32,11 +32,10 @@ etox_targets( c("20179", "9051")) } } -\author{ -Eduard Szoecs, \email{eduardszoecs@gmail.com} -} \seealso{ \code{\link{get_etoxid}} to retrieve ETOX IDs, \code{\link{etox_basic}} for basic information, \code{\link{etox_targets}} for quality targets and \code{\link{etox_tests}} for test results } - +\author{ +Eduard Szoecs, \email{eduardszoecs@gmail.com} +} diff --git a/man/etox_tests.Rd b/man/etox_tests.Rd index 998859ba..67897bf1 100644 --- a/man/etox_tests.Rd +++ b/man/etox_tests.Rd @@ -31,11 +31,10 @@ out[ , c('Organism', 'Effect', 'Duration', 'Time_Unit', etox_tests( c("20179", "9051")) } } -\author{ -Eduard Szoecs, \email{eduardszoecs@gmail.com} -} \seealso{ \code{\link{get_etoxid}} to retrieve ETOX IDs, \code{\link{etox_basic}} for basic information, \code{\link{etox_targets}} for quality targets and \code{\link{etox_tests}} for test results } - +\author{ +Eduard Szoecs, \email{eduardszoecs@gmail.com} +} diff --git a/man/extr_num.Rd b/man/extr_num.Rd index ec1a1e79..a7cf7ca4 100644 --- a/man/extr_num.Rd +++ b/man/extr_num.Rd @@ -18,4 +18,3 @@ Extract a number from a string \examples{ extr_num('aaaa -95') } - diff --git a/man/extractors.Rd b/man/extractors.Rd index c5207e94..569e1581 100644 --- a/man/extractors.Rd +++ b/man/extractors.Rd @@ -1,8 +1,8 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/extractors.R \name{extractors} -\alias{cas} \alias{extractors} +\alias{cas} \alias{inchikey} \alias{smiles} \title{Extract parts from webchem objects} @@ -24,4 +24,3 @@ a vector. \description{ Extract parts from webchem objects } - diff --git a/man/fn_percept.Rd b/man/fn_percept.Rd index 4fda4205..95959441 100644 --- a/man/fn_percept.Rd +++ b/man/fn_percept.Rd @@ -17,11 +17,12 @@ fn_percept(CAS, verbose = TRUE, ...) A named character vector containing flavor percepts or NA's in the case of CAS numbers that are not found } \description{ -Retreive flavor percepts from \url{http://www.flavornet.org}. Flavornet is a database of 738 compounds with odors +Retreive flavor percepts from \url{http://www.flavornet.org}. Flavornet is a database of 738 compounds with odors perceptible to humans detected using gas chromatography ofactometry (GCO). } \examples{ \donttest{ +# might fail if website is not available fn_percept("123-32-0") CASs <- c("75-07-0", "64-17-5", "109-66-0", "78-94-4", "78-93-3") diff --git a/man/get_cid.Rd b/man/get_cid.Rd index 458a55c7..764022da 100644 --- a/man/get_cid.Rd +++ b/man/get_cid.Rd @@ -41,9 +41,6 @@ get_cid(comp) } } -\author{ -Eduard Szoecs, \email{eduardszoecs@gmail.com} -} \references{ Wang, Y., J. Xiao, T. O. Suzek, et al. 2009 PubChem: A Public Information System for Analyzing Bioactivities of Small Molecules. Nucleic Acids Research 37: 623–633. @@ -54,4 +51,6 @@ PubChem Substance and Compound Databases. Nucleic Acids Research 44(D1): D1202 Kim, S., Thiessen, P. A., Bolton, E. E., & Bryant, S. H. (2015). PUG-SOAP and PUG-REST: web services for programmatic access to chemical information in PubChem. Nucleic acids research, gkv396. } - +\author{ +Eduard Szoecs, \email{eduardszoecs@gmail.com} +} diff --git a/man/get_csid.Rd b/man/get_csid.Rd index 7e078aaa..33a482ed 100644 --- a/man/get_csid.Rd +++ b/man/get_csid.Rd @@ -38,11 +38,10 @@ get_csid("Triclosan", token = token)[[1]] get_csid(c("Triclosan", "50-00-0"), token = token) } } -\author{ -Eduard Szoecs, \email{eduardszoecs@gmail.com} -} \seealso{ \code{\link{cs_compinfo}} and \code{\link{cs_extcompinfo}} to retrieve compound details from csid. } - +\author{ +Eduard Szoecs, \email{eduardszoecs@gmail.com} +} diff --git a/man/get_etoxid.Rd b/man/get_etoxid.Rd index 9ebc6edd..404e8221 100644 --- a/man/get_etoxid.Rd +++ b/man/get_etoxid.Rd @@ -37,11 +37,10 @@ get_etoxid(comps) get_etoxid(comps, match = 'all') } } -\author{ -Eduard Szoecs, \email{eduardszoecs@gmail.com} -} \seealso{ \code{\link{etox_basic}} for basic information, \code{\link{etox_targets}} for quality targets and \code{\link{etox_tests}} for test results. } - +\author{ +Eduard Szoecs, \email{eduardszoecs@gmail.com} +} diff --git a/man/get_wdid.Rd b/man/get_wdid.Rd index 25628603..a7dec6cf 100644 --- a/man/get_wdid.Rd +++ b/man/get_wdid.Rd @@ -42,4 +42,3 @@ get_wdid(comps) \author{ Eduard Szoecs, \email{eduardszoecs@gmail.com} } - diff --git a/man/is.cas.Rd b/man/is.cas.Rd index 08126498..211598e7 100644 --- a/man/is.cas.Rd +++ b/man/is.cas.Rd @@ -37,4 +37,3 @@ is.cas('64-17-6') \author{ Eduard Szoecs, \email{eduardszoecs@gmail.com} } - diff --git a/man/is.inchikey.Rd b/man/is.inchikey.Rd index 38d54c6d..ca89763d 100644 --- a/man/is.inchikey.Rd +++ b/man/is.inchikey.Rd @@ -37,10 +37,9 @@ is.inchikey('BQJCRHHNABKAKU/KBQPJGBKSA/N') is.inchikey('BQJCRHHNABKAKU-KBQPJGBKXA-N') is.inchikey('BQJCRHHNABKAKU-KBQPJGBKSB-N') } -\author{ -Eduard Szoecs, \email{eduardszoecs@gmail.com} -} \references{ Heller, Stephen R., et al. "InChI, the IUPAC International Chemical Identifier." Journal of Cheminformatics 7.1 (2015): 23. } - +\author{ +Eduard Szoecs, \email{eduardszoecs@gmail.com} +} diff --git a/man/is.inchikey_cs.Rd b/man/is.inchikey_cs.Rd index 9cfe3525..f18cf435 100644 --- a/man/is.inchikey_cs.Rd +++ b/man/is.inchikey_cs.Rd @@ -29,10 +29,9 @@ is.inchikey_cs('BQJCRHHNABKAKU-KBQPJGBKXA-N') is.inchikey_cs('BQJCRHHNABKAKU-KBQPJGBKSB-N') } } -\author{ -Eduard Szoecs, \email{eduardszoecs@gmail.com} -} \seealso{ \code{\link{is.inchikey}} for a pure-R implementation. } - +\author{ +Eduard Szoecs, \email{eduardszoecs@gmail.com} +} diff --git a/man/is.inchikey_format.Rd b/man/is.inchikey_format.Rd index 92289be9..60a0c854 100644 --- a/man/is.inchikey_format.Rd +++ b/man/is.inchikey_format.Rd @@ -34,10 +34,9 @@ is.inchikey_format('BQJCRHHNABKAKU-KBQPJGBKXA-N') is.inchikey_format('BQJCRHHNABKAKU-KBQPJGBKSB-N') } } -\author{ -Eduard Szoecs, \email{eduardszoecs@gmail.com} -} \seealso{ \code{\link{is.inchikey}} for a pure-R implementation. } - +\author{ +Eduard Szoecs, \email{eduardszoecs@gmail.com} +} diff --git a/man/is.smiles.Rd b/man/is.smiles.Rd index b1f6df1a..475fddbf 100644 --- a/man/is.smiles.Rd +++ b/man/is.smiles.Rd @@ -28,11 +28,10 @@ is.smiles('Clc(c(Cl)c(Cl)c1C(=O)O)c(Cl)c1Cl') is.smiles('Clc(c(Cl)c(Cl)c1C(=O)O)c(Cl)c1ClJ') } } -\author{ -Eduard Szoecs, \email{eduardszoecs@gmail.com} -} \references{ Egon Willighagen (2015). How to test SMILES strings in Supplementary Information. \url{https://chem-bla-ics.blogspot.nl/2015/10/how-to-test-smiles-strings-in.html} } - +\author{ +Eduard Szoecs, \email{eduardszoecs@gmail.com} +} diff --git a/man/jagst.Rd b/man/jagst.Rd index d095dd02..c1229740 100644 --- a/man/jagst.Rd +++ b/man/jagst.Rd @@ -28,4 +28,3 @@ on 13 sampling occasions. Values are given in ug/L. } \keyword{datasets} - diff --git a/man/lc50.Rd b/man/lc50.Rd index 9531b15c..f99b27ac 100644 --- a/man/lc50.Rd +++ b/man/lc50.Rd @@ -23,4 +23,3 @@ It comprises acute toxicity data (D. magna, 48h, Laboratory, 48h) and has been preprocessed (remove non-insecticides, aggregate multiple value, keep only numeric data etc). } \keyword{datasets} - diff --git a/man/opsin_query.Rd b/man/opsin_query.Rd index 331e0f3c..cc33849e 100644 --- a/man/opsin_query.Rd +++ b/man/opsin_query.Rd @@ -32,4 +32,3 @@ Lowe, D. M., Corbett, P. T., Murray-Rust, P., & Glen, R. C. (2011). Chemical Name to Structure: OPSIN, an Open Source Solution. Journal of Chemical Information and Modeling, 51(3), 739–753. http://doi.org/10.1021/ci100384d } - diff --git a/man/pan_query.Rd b/man/pan_query.Rd index 74ea5033..5746a5ea 100644 --- a/man/pan_query.Rd +++ b/man/pan_query.Rd @@ -79,4 +79,3 @@ Retrieve information from the PAN database (\url{http://www.pesticideinfo.org/}) \author{ Eduard Szoecs, \email{eduardszoecs@gmail.com} } - diff --git a/man/parse_mol.Rd b/man/parse_mol.Rd index fd2d757a..6d18bb5e 100644 --- a/man/parse_mol.Rd +++ b/man/parse_mol.Rd @@ -28,12 +28,11 @@ For more information see \url{infochim.u-strasbg.fr/recherche/Download/Fragment \description{ Parse Molfile (as returned by chemspider) into a R-object. } -\author{ -Eduard Szoecs, \email{eduardszoecs@gmail.com} -} \references{ Grabner, M., Varmuza, K., & Dehmer, M. (2012). RMol: a toolset for transforming SD/Molfile structure information into R objects. Source Code for Biology and Medicine, 7, 12. http://doi.org/10.1186/1751-0473-7-12 } - +\author{ +Eduard Szoecs, \email{eduardszoecs@gmail.com} +} diff --git a/man/pc_prop.Rd b/man/pc_prop.Rd index a2213032..c05a493a 100644 --- a/man/pc_prop.Rd +++ b/man/pc_prop.Rd @@ -35,9 +35,6 @@ cids <- unlist(get_cid(comp)) pc_prop(cids, properties = c('MolecularFormula', 'MolecularWeight', 'CanonicalSMILES')) } } -\author{ -Eduard Szoecs, \email{eduardszoecs@gmail.com} -} \references{ Wang, Y., J. Xiao, T. O. Suzek, et al. 2009 PubChem: A Public Information System for Analyzing Bioactivities of Small Molecules. Nucleic Acids Research 37: 623–633. @@ -51,4 +48,6 @@ PUG-SOAP and PUG-REST: web services for programmatic access to chemical informat \seealso{ \code{\link{get_cid}} to retrieve Pubchem IDs. } - +\author{ +Eduard Szoecs, \email{eduardszoecs@gmail.com} +} diff --git a/man/pc_synonyms.Rd b/man/pc_synonyms.Rd index e65f345a..5769e007 100644 --- a/man/pc_synonyms.Rd +++ b/man/pc_synonyms.Rd @@ -31,9 +31,6 @@ pc_synonyms(c('Aspirin', 'Triclosan')) pc_synonyms(5564, from = 'cid') } } -\author{ -Eduard Szoecs, \email{eduardszoecs@gmail.com} -} \references{ Wang, Y., J. Xiao, T. O. Suzek, et al. 2009 PubChem: A Public Information System for Analyzing Bioactivities of Small Molecules. Nucleic Acids Research 37: 623–633. @@ -44,4 +41,6 @@ PubChem Substance and Compound Databases. Nucleic Acids Research 44(D1): D1202 Kim, S., Thiessen, P. A., Bolton, E. E., & Bryant, S. H. (2015). PUG-SOAP and PUG-REST: web services for programmatic access to chemical information in PubChem. Nucleic acids research, gkv396. } - +\author{ +Eduard Szoecs, \email{eduardszoecs@gmail.com} +} diff --git a/man/ping.Rd b/man/ping.Rd index 77b8f6ec..7c73e52d 100644 --- a/man/ping.Rd +++ b/man/ping.Rd @@ -1,9 +1,9 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/ping.R \name{ping} -\alias{cs_web_ping} \alias{ping} \alias{pubchem_ping} +\alias{cs_web_ping} \title{Ping an API used in webchem to see if it's working.} \usage{ pubchem_ping(...) @@ -19,4 +19,3 @@ A logical, TRUE or FALSE \description{ Ping an API used in webchem to see if it's working. } - diff --git a/man/pp_query.Rd b/man/pp_query.Rd index 2e590717..6283aa66 100644 --- a/man/pp_query.Rd +++ b/man/pp_query.Rd @@ -45,4 +45,3 @@ sapply(out, function(y){ \author{ Eduard Szoecs, \email{eduardszoecs@gmail.com} } - diff --git a/man/ppdb_parse.Rd b/man/ppdb_parse.Rd index bb0b479e..9ec3581d 100644 --- a/man/ppdb_parse.Rd +++ b/man/ppdb_parse.Rd @@ -29,10 +29,9 @@ This function only parses a html. Saving (or downloading) substantial parts from the database is explicitly against the terms and conditions and copyright of use [link removed on request]. } -\author{ -Eduard Szoecs, \email{eduardszoecs@gmail.com} -} \references{ [Reference removed on request.] } - +\author{ +Eduard Szoecs, \email{eduardszoecs@gmail.com} +} diff --git a/man/wd_ident.Rd b/man/wd_ident.Rd index bbaddef9..738dd230 100644 --- a/man/wd_ident.Rd +++ b/man/wd_ident.Rd @@ -27,9 +27,6 @@ Only matches in labels are returned. wd_ident(id) } } -\author{ -Eduard Szoecs, \email{eduardszoecs@gmail.com} -} \references{ Willighagen, E., 2015. Getting CAS registry numbers out of WikiData. The Winnower. \url{http://dx.doi.org/10.15200/winn.142867.72538} @@ -40,4 +37,6 @@ Wikidata: A Platform for Data Integration and Dissemination for the Life Science \seealso{ \code{\link{get_wdid}} } - +\author{ +Eduard Szoecs, \email{eduardszoecs@gmail.com} +} diff --git a/man/webchem-defunct.Rd b/man/webchem-defunct.Rd index edac118e..107c9bc7 100644 --- a/man/webchem-defunct.Rd +++ b/man/webchem-defunct.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/webchem-defunct.R \name{webchem-defunct} -\alias{cir} -\alias{ppdb} -\alias{ppdb_query} \alias{webchem-defunct} +\alias{ppdb_query} +\alias{ppdb} +\alias{cir} \title{Defunct function(s) in the webchem package} \usage{ ppdb_query() @@ -24,4 +24,3 @@ Defunct functions are: \code{cir} \cr } } - diff --git a/man/webchem-deprecated.Rd b/man/webchem-deprecated.Rd index ab01e440..c1ef90b5 100644 --- a/man/webchem-deprecated.Rd +++ b/man/webchem-deprecated.Rd @@ -1,8 +1,8 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/webchem-deprecated.R \name{webchem-deprecated} -\alias{cid_compinfo} \alias{webchem-deprecated} +\alias{cid_compinfo} \title{Deprecated function(s) in the webchem package} \usage{ cid_compinfo(...) @@ -21,4 +21,3 @@ Deprecated functions are: \code{pc_compinfo} \tab is now a synonym for \code{\link{cid_compinfo}}\cr } } - diff --git a/man/webchem.Rd b/man/webchem.Rd index 4d897b00..7702e39e 100644 --- a/man/webchem.Rd +++ b/man/webchem.Rd @@ -8,4 +8,3 @@ \description{ webchem: An R package to retrieve chemical information from the web. } -