vignettes/Getting-Started.Rmd
Getting-Started.RmdClassyFire is a web-based application for automated structural classification of chemical compounds.
The classyfireR R package provides access to the ClassyFire RESTful API for retrieving existing compound classifications and submitted structures to the web-server for classification.
classyfireR can be installed from CRAN or, for the latest development version, directly from GitHub using the remotes package.
install.packages('classyfireR')
remotes::install_github('aberHRML/classyfireR')To retrieve classifications that are already available simply provide an InChI key to the get_classification function.
library(classyfireR)
#> Loading required package: magrittr
Classification <- get_classification('BRMWTNUJHUMWMS-LURJTMIESA-N')
#> ✔ BRMWTNUJHUMWMS-LURJTMIESA-N
Classification
#> ── ClassyFire Object ───────────────────────────────────── classyfireR v0.3.8 ──
#> Object Size: 18.2 Kb
#>
#> Info:
#> • InChIKey=BRMWTNUJHUMWMS-LURJTMIESA-N
#>
#> • [H][C@](N)(CC1=CN(C)C=N1)C(O)=O
#>
#> • Classification Version: 2.1
#>
#> kingdom : Organic compounds
#> └─superclass : Organic acids and derivatives
#> └─class : Carboxylic acids and derivatives
#> └─subclass : Amino acids, peptides, and analogues
#> └─level 5 : Amino acids and derivatives
#> └─level 6 : Alpha amino acids and derivatives
#> └─level 7 : Histidine and derivativesThe result of each classification is stored in a single S4 (ClassyFire) object. To retrieve multiple classification, simply iterate over a vector of InChI Keys’
For classification submission using SMILES, this can be performed by supplying multiple SMILES to the submit_query function. The results from all of the inputs, will be returned to a single S4 Query class.
If any of the inputs are not successfully classified, then these will be stored in the unclassified slot and can be accessed using the unclassified accessor method.
Input <- c(MOL1 = 'CCCOCC', MOL2 = 'CNC(CC1=CN=CN1)C(=O)O', MOL3 = 'CXN')
Query <-
submit_query(label = 'query_test',
input = Input,
type = 'STRUCTURE')
Query
── ClassyFire Query Object ──────────────────────────────── classyfireR v0.3.7 ──
Object Size: 27.6 Kb
2 structures classified
• MOL1 : InChIKey=NVJUHMXYKCUMQA-UHFFFAOYSA-N
• MOL2 : InChIKey=CYZKJBZEIFWZSR-UHFFFAOYSA-N
1 structures not classified
• MOL3 : CXN
unclassified(Query)
MOL3
"CXN" There are a series of accessor methods which will work with either object type to return results from a specific slot in the object.
classification(Classification)
#> # A tibble: 7 × 3
#> Level Classification CHEMONT
#> <chr> <chr> <chr>
#> 1 kingdom Organic compounds CHEMONTID:0000000
#> 2 superclass Organic acids and derivatives CHEMONTID:0000264
#> 3 class Carboxylic acids and derivatives CHEMONTID:0000265
#> 4 subclass Amino acids, peptides, and analogues CHEMONTID:0000013
#> 5 level 5 Amino acids and derivatives CHEMONTID:0000347
#> 6 level 6 Alpha amino acids and derivatives CHEMONTID:0000060
#> 7 level 7 Histidine and derivatives CHEMONTID:0004311
meta(Classification)
#> $inchikey
#> [1] "InChIKey=BRMWTNUJHUMWMS-LURJTMIESA-N"
#>
#> $smiles
#> [1] "[H][C@](N)(CC1=CN(C)C=N1)C(O)=O"
#>
#> $version
#> [1] "2.1"
chebi(Classification)
#> [1] "L-alpha-amino acid (CHEBI:15705)"
#> [2] "imidazolyl carboxylic acid (CHEBI:38307)"
#> [3] "aralkylamine (CHEBI:18000)"
#> [4] "imidazoles (CHEBI:24780)"
#> [5] "organic aromatic compound (CHEBI:33659)"
#> [6] "amino acid (CHEBI:33709)"
#> [7] "carbonyl compound (CHEBI:36586)"
#> [8] "carboxylic acid (CHEBI:33575)"
#> [9] "carboxylic acid anion (CHEBI:29067)"
#> [10] "organonitrogen heterocyclic compound (CHEBI:38101)"
#> [11] "pnictogen molecular entity (CHEBI:33302)"
#> [12] "organic molecular entity (CHEBI:50860)"
#> [13] "organic oxide (CHEBI:25701)"
#> [14] "alkylamine (CHEBI:13759)"
#> [15] "organic molecule (CHEBI:72695)"
#> [16] "histidine derivative (CHEBI:24599)"
#> [17] "chemical entity (CHEBI:24431)"
#> [18] "organooxygen compound (CHEBI:36963)"
#> [19] "peptide (CHEBI:16670)"
#> [20] "organonitrogen compound (CHEBI:35352)"
#> [21] "alpha-amino acid (CHEBI:33704)"
#> [22] "organic heterocyclic compound (CHEBI:24532)"
#> [23] "azole (CHEBI:68452)"
#> [24] "nitrogen molecular entity (CHEBI:51143)"
#> [25] "amine (CHEBI:32952)"
#> [26] "oxygen molecular entity (CHEBI:25806)"
#> [27] "primary amine (CHEBI:32877)"A local cache can be used to save queries too, which will speed up workflows where large numbers of entities are being classified each time, and will mean that the API only queries the server, when absolutely necessary.
A local cache can easily be created using the following command
ClassyFireDB <- RSQLite::dbConnect(RSQLite::SQLite(), 'ClassyFireCache.db')Before running the get_classifcation function, a connection to the cache needs to be created.
ClassyFireCache <- open_cache(dbname = 'ClassyFireCache.db')Then pass the cache variable as the conn argument in the get_classification function.
get_classification('BRMWTNUJHUMWMS-LURJTMIESA-N', conn = ClassyFireCache)If you use classyfireR you should cite the ClassyFire publication
Djoumbou Feunang Y, Eisner R, Knox C, Chepelev L, Hastings J, Owen G, Fahy E, Steinbeck C, Subramanian S, Bolton E, Greiner R, and Wishart DS. ClassyFire: Automated Chemical Classification With A Comprehensive, Computable Taxonomy. Journal of Cheminformatics, 2016, 8:61.