diff options
Diffstat (limited to 'R/chent.R')
| -rw-r--r-- | R/chent.R | 15 |
1 files changed, 7 insertions, 8 deletions
@@ -155,13 +155,13 @@ chent <- R6Class("chent", #' Try to get chemical information from PubChem #' @param query Query string to be passed to [get_cid][webchem::get_cid] #' @param from Passed to [get_cid][webchem::get_cid] - try_pubchem = function(query, from = 'name') { - message("PubChem:") + try_pubchem = function(query = self$identifier, from = 'name') { + message("Querying PubChem for ", from , " ", query, " ...") if (missing(query)) query <- self$identifier pubchem_result = webchem::get_cid(query, from = from, match = "first") if (is.na(pubchem_result[[1, "cid"]])) { - message("Query ", query, " did not give results at PubChem") + message("Querying for ", query, " as ", from, " did not give results at PubChem") } else { self$get_pubchem(pubchem_result[[1, "cid"]]) } @@ -228,16 +228,15 @@ chent <- R6Class("chent", smiles_preferred_i <- min(match(available_smiles, smiles_preference)) smiles_preferred <- smiles_preference[smiles_preferred_i] - message("Trying to get chemical information from RDKit using ", + message("Get chemical information from RDKit using ", smiles_preferred, " SMILES\n", self$smiles[smiles_preferred]) self$rdkit <- list() self$mol <- rdkit_module$Chem$MolFromSmiles(self$smiles[1]) self$rdkit$mw <- rdkit_module$Chem$Descriptors$MolWt(self$mol) - if (!is.na(self$mw)) { + if (!is.null(self$mw) && !is.na(self$mw)) { if (round(self$rdkit$mw, 1) != round(self$mw, 1)) { - message("RDKit mw is ", self$rdkit$mw) - message("mw is ", self$mw) + warning("RDKit mw is ", self$rdkit$mw, " while mw is ", self$mw) } } else { self$mw <- self$rdkit$mw @@ -705,7 +704,7 @@ pai <- R6Class("pai", } if (!missing(iso) & bcpc) { - message("BCPC:") + message("Querying BCPC for ", identifier, " ...") bcpc_result = webchem::bcpc_query(identifier, from = "name") # Use first element of list, as we passed a query of length one |