knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
ClassyFire 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) Classification <- get_classification('BRMWTNUJHUMWMS-LURJTMIESA-N') Classification
The result of each classification is stored in a single S4 (ClassyFire) object. To retrieve multiple classification, simply iterate over a vector of InChI Keys'
InChI_Keys <- c('BRMWTNUJHUMWMS-LURJTMIESA-N', 'MDHYEMXUFSJLGV-UHFFFAOYSA-N', 'MYYIAHXIVFADCU-QMMMGPOBSA-N') Classification_List <- purrr::map(InChI_Keys, get_classification)
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) meta(Classification) chebi(Classification)
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.
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.