Jixing Liu: Build block data clean

Jixing Liu

library(tidyverse)
data_path_ACEMOL <- here::here("analysis/data/raw_data/Build_block_ACEMOL.csv")

ACEMOL

df <- read_csv(data_path_ACEMOL)

df %>% head()

#> # A tibble: 6 × 9
#>   标题   标题链接  CatalogNo. CasNo. Name  ReaxyNo. CNName `cards-box`
#>   <chr>  <chr>     <chr>      <chr>  <chr> <chr>    <chr>  <chr>      
#> 1 >(2S)… http://w… Catalog N… Cas N… >(2S… Reaxy N… CN Na… 216237-52-4
#> 2 >1-Am… http://w… Catalog N… Cas N… >1-A… Reaxy N… CN Na… 22059-21-8 
#> 3 >1-(B… http://w… Catalog N… Cas N… >1-(… Reaxy N… CN Na… 88950-64-5 
#> 4 >Meth… http://w… Catalog N… Cas N… >Met… Reaxy N… CN Na… 72784-43-1 
#> 5 >Meth… http://w… Catalog N… Cas N… >Met… Reaxy N… CN Na… 72784-42-0 
#> 6 >ethy… http://w… Catalog N… Cas N… >eth… Reaxy N… CN Na… 42303-42-4 
#> # … with 1 more variable: cards-box-desc1 <chr>

df %>% colnames()

#> [1] "标题"            "标题链接"        "CatalogNo."     
#> [4] "CasNo."          "Name"            "ReaxyNo."       
#> [7] "CNName"          "cards-box"       "cards-box-desc1"


df_clean <- 
df %>%
  select(name = Name,
         name_zh = CNName,
         SMILES = `cards-box-desc1`) %>%
  mutate(name_zh = str_remove(name_zh, "CN Name:"),
         name = str_remove(name, "^>"))



library(docking)
docking::init_py()

df_clean %>% 
  pull(SMILES) %>% 
  map_chr(~ py$smiles_to_canonical(.x))

is.na(.Last.value) %>% sum()



# df_clean %>% 
#   py$df_add_ROMol() %>% 
#   rename(ID = name) %>% 
#   open_in_DataWarrior()

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Citation

For attribution, please cite this work as

Liu (2021, Feb. 3). Jixing Liu: Build block data clean. Retrieved from https://jixing.org/posts/2022-02-04-buildblock/

BibTeX citation

@misc{liu2021build,
  author = {Liu, Jixing},
  title = {Jixing Liu: Build block data clean},
  url = {https://jixing.org/posts/2022-02-04-buildblock/},
  year = {2021}
}