compound_classyfireR.R

library(classyfireR)

## Loading required package: magrittr

Classification <- get_classification('BRMWTNUJHUMWMS-LURJTMIESA-N')

## ✔ BRMWTNUJHUMWMS-LURJTMIESA-N

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

Classification@meta

## $inchikey
## [1] "InChIKey=BRMWTNUJHUMWMS-LURJTMIESA-N"
## 
## $smiles
## [1] "[H][C@](N)(CC1=CN(C)C=N1)C(O)=O"
## 
## $version
## [1] "2.1"

Classification@direct_parent

## $name
## [1] "Histidine and derivatives"
## 
## $description
## [1] "Compounds containing cysteine or a derivative thereof resulting from reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom."
## 
## $chemont_id
## [1] "CHEMONTID:0004311"
## 
## $url
## [1] "http://classyfire.wishartlab.com/tax_nodes/C0004311"

class(Classification@classification)

## [1] "tbl_df"     "tbl"        "data.frame"

data_1 <- data.frame(Classification@classification)
data_1$inchikey <- Classification@meta$inchikey
data_1$smiles <- Classification@meta$smiles
data_1

##        Level                       Classification           CHEMONT
## 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
##                               inchikey                          smiles
## 1 InChIKey=BRMWTNUJHUMWMS-LURJTMIESA-N [H][C@](N)(CC1=CN(C)C=N1)C(O)=O
## 2 InChIKey=BRMWTNUJHUMWMS-LURJTMIESA-N [H][C@](N)(CC1=CN(C)C=N1)C(O)=O
## 3 InChIKey=BRMWTNUJHUMWMS-LURJTMIESA-N [H][C@](N)(CC1=CN(C)C=N1)C(O)=O
## 4 InChIKey=BRMWTNUJHUMWMS-LURJTMIESA-N [H][C@](N)(CC1=CN(C)C=N1)C(O)=O
## 5 InChIKey=BRMWTNUJHUMWMS-LURJTMIESA-N [H][C@](N)(CC1=CN(C)C=N1)C(O)=O
## 6 InChIKey=BRMWTNUJHUMWMS-LURJTMIESA-N [H][C@](N)(CC1=CN(C)C=N1)C(O)=O
## 7 InChIKey=BRMWTNUJHUMWMS-LURJTMIESA-N [H][C@](N)(CC1=CN(C)C=N1)C(O)=O

InChI_Keys <-
  c('BRMWTNUJHUMWMS-LURJTMIESA-N',
    'MDHYEMXUFSJLGV-UHFFFAOYSA-N',
    'MYYIAHXIVFADCU-QMMMGPOBSA-N')


Classification_List <- purrr::map(InChI_Keys, get_classification)

## ✔ BRMWTNUJHUMWMS-LURJTMIESA-N

## ✔ MDHYEMXUFSJLGV-UHFFFAOYSA-N

## ✔ MYYIAHXIVFADCU-QMMMGPOBSA-N

Classification_List 

## [[1]]
## ── 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 derivatives
## 
## [[2]]
## ── ClassyFire Object ───────────────────────────────────── classyfireR v0.3.8 ── 
## Object Size: 11.2 Kb 
##  
## Info: 
## • InChIKey=MDHYEMXUFSJLGV-UHFFFAOYSA-N
##   
## • CC(=O)OCCC1=CC=CC=C1
##   
## • Classification Version: 2.1
##   
## kingdom : Organic compounds
## └─superclass : Benzenoids
##   └─class : Benzene and substituted derivatives
## 
## [[3]]
## ── ClassyFire Object ───────────────────────────────────── classyfireR v0.3.8 ── 
## Object Size: 18.3 Kb 
##  
## Info: 
## • InChIKey=MYYIAHXIVFADCU-QMMMGPOBSA-N
##   
## • [H][C@@](CC1=CN=CN1C)(N=C(O)CCN)C(O)=O
##   
## • Classification Version: 2.1
##   
## kingdom : Organic compounds
## └─superclass : Organic acids and derivatives
##   └─class : Peptidomimetics
##     └─subclass : Hybrid peptides

input <- c(MOL1 = 'CCCOCC', MOL2 = 'COCC=CCC', MOL3 = 'CXN')
submit_query(label = 'query_test', input = input, type = 'STRUCTURE')

## No encoding supplied: defaulting to UTF-8.

## ── ClassyFire Query Object ─────────────────────────────── classyfireR v0.3.8 ── 
## Object Size: 19.5 Kb 
##  
## 2 structures classified 
## • MOL1 : InChIKey=NVJUHMXYKCUMQA-UHFFFAOYSA-N
## • MOL2 : InChIKey=YCVHIAQANWEUFE-UHFFFAOYSA-N
## 
## 1 structures not classified 
## • MOL3 : CXN

#ref https://rdrr.io/cran/classyfireR/f/vignettes/Getting-Started.Rmd