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Diffstat (limited to 'README.rmd')
| -rw-r--r-- | README.rmd | 39 |
1 files changed, 36 insertions, 3 deletions
@@ -20,14 +20,13 @@ provides a way to define and check the identity of chemically defined substances ("chemical entities") and to collect related information. - When first defining a chemical entity, some chemical information is retrieved from the [PubChem](https://pubchem.ncbi.nlm.nih.gov/) website using the [webchem](https://docs.ropensci.org/webchem/) package. ```{r} library(chents) -caffeine <- chent$new("caffeine") +caffeine <- chent$new("Caffeine") ``` If Python and [RDKit](https://rdkit.org) (> 2015.03) are installed and @@ -52,7 +51,7 @@ can use the 'pai' class derived from the 'chent' class, which starts with queryi the [BCPC compendium](http://www.bcpcpesticidecompendium.org/) first. ```{r fig.height = 3.5} -delta <- pai$new("deltamethrin") +delta <- pai$new("Deltamethrin") plot(delta) ``` @@ -96,3 +95,37 @@ location. Sys.setenv(RETICULATE_PYTHON="/usr/bin/python3") ``` +## Using R6 classes + +Note that the `chent` objects defined by this package are [R6](https://r6.r-lib.org/articles/Introduction.html) +classes. Therefore, if you think you make a copy by assigning them to a new name, the +objects will still be connected, because only the reference is copied. For +example, you can create a molecule without retrieving data from PubChem + +```{r} +but <- chent$new("Butane", smiles = "CCCC", pubchem = FALSE) +print(but) +``` + +If you then assign a new name and add PubChem information to the object with +the new name, the information will also be added to the original `chent` +object: + + +```{r} +but_pubchem <- but +but_pubchem$try_pubchem() +print(but) +``` + +You can create a derived, independent object using the `clone()` method +that will not be affectd by operations on the original object: + +```{r} +but_new <- chent$new("Butane", smiles = "CCCC", pubchem = FALSE) +but_clone <- but_new$clone() +but_new$try_pubchem() +but_clone +``` + + |