From 81dd5ed73a48ba811304ab9211d501b973eb640c Mon Sep 17 00:00:00 2001 From: Ranke Johannes Date: Thu, 20 Jun 2024 14:57:23 +0200 Subject: Fix rdkit availability, prefer user/isomeric SMILES In cases that the user specifies an isomeric SMILES, we want to use that with rdkit. If the user does not specify a SMILES, we prefer the isomeric one from PubChem over the canonical one, where stereochemistry is not defined. --- .Rhistory | 16 + DESCRIPTION | 2 +- R/chent.R | 11 +- R/zzz.R | 2 +- docs/404.html | 16 +- docs/authors.html | 18 +- docs/deps/bootstrap-5.3.1/bootstrap.bundle.min.js | 7 + .../bootstrap-5.3.1/bootstrap.bundle.min.js.map | 1 + docs/deps/bootstrap-5.3.1/bootstrap.min.css | 5 + docs/deps/bootstrap-5.3.1/font.css | 400 +++++++++++++++++++++ .../fonts/07d40e985ad7c747025dabb9f22142c4.woff2 | Bin 0 -> 16456 bytes .../fonts/1Ptug8zYS_SKggPNyC0ITw.woff2 | Bin 0 -> 48208 bytes .../fonts/1Ptug8zYS_SKggPNyCAIT5lu.woff2 | Bin 0 -> 26788 bytes .../fonts/1Ptug8zYS_SKggPNyCIIT5lu.woff2 | Bin 0 -> 11176 bytes .../fonts/1Ptug8zYS_SKggPNyCMIT5lu.woff2 | Bin 0 -> 30744 bytes .../fonts/1Ptug8zYS_SKggPNyCkIT5lu.woff2 | Bin 0 -> 25828 bytes .../fonts/1f5e011d6aae0d98fc0518e1a303e99a.woff2 | Bin 0 -> 10332 bytes .../fonts/4iCs6KVjbNBYlgoKcQ72j00.woff2 | Bin 0 -> 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1a9e67f..ca272cf 100644 --- a/.Rhistory +++ b/.Rhistory @@ -2,3 +2,19 @@ library(chents) ?chent library(chents) ?chent +conf <- reticulate::py_discover_config("rdkit") +conf$available +str(conf) +rdkit_module <- try( +reticulate::import("rdkit"), +silent = TRUE) +install.packages("reticulate") +Sys.getenv("PYTHONPATH") +conf <- reticulate::py_discover_config("rdkit") +conf$available +str(conf) +py_config() +reticulate::py_config() +reticulate::py_discover_config +rdkit_available <- reticulate::py_module_available("rdkit") +quit() diff --git a/DESCRIPTION b/DESCRIPTION index 116d485..1895fb9 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -28,4 +28,4 @@ LazyData: yes Encoding: UTF-8 URL: https://pkgdown.jrwb.de/chents, https://github.com/jranke/chents Roxygen: list(markdown = TRUE, r6 = TRUE) -RoxygenNote: 7.3.1 +RoxygenNote: 7.3.1.9000 diff --git a/R/chent.R b/R/chent.R index 4375305..aee95f0 100644 --- a/R/chent.R +++ b/R/chent.R @@ -118,9 +118,14 @@ chent <- R6Class("chent", if (is.null(self$smiles)) { message("RDKit would need a SMILES code") } else { + available_smiles <- names(self$smiles) + smiles_preference <- c("user", "PubChem_Isomeric", "PubChem_Canonical") + 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 ", - names(self$smiles)[1], " SMILES\n", - self$smiles[1]) + smiles_preferred, " SMILES\n", + self$smiles[smiles_preferred]) self$get_rdkit(template = template) self$mw <- self$rdkit$mw attr(self$mw, "source") <- "rdkit" @@ -196,7 +201,7 @@ chent <- R6Class("chent", #' Get chemical information from RDKit if available #' @param template Optional template specified as a SMILES code get_rdkit = function(template = NULL) { - if(!rdkit_available) { + if (!rdkit_available) { stop("RDKit is not available") } self$rdkit <- list() diff --git a/R/zzz.R b/R/zzz.R index f18e559..fc39fbf 100644 --- a/R/zzz.R +++ b/R/zzz.R @@ -1,6 +1,6 @@ .onLoad = function(libname, pkgname) { conf <- reticulate::py_discover_config("rdkit") - rdkit_available <- conf$available + rdkit_available <- reticulate::py_module_available("rdkit") rdkit_module <- try( reticulate::import("rdkit"), silent = TRUE) diff --git a/docs/404.html b/docs/404.html index 00dc371..dee85af 100644 --- a/docs/404.html +++ b/docs/404.html @@ -7,10 +7,10 @@ Page not found (404) • chents - - + + - + Authors and Citation • chentsAuthors and Citation • chents Skip to contents -