diff options
| -rw-r--r-- | ChangeLog | 6 | ||||
| -rw-r--r-- | DESCRIPTION | 2 | ||||
| -rw-r--r-- | R/chent.R | 76 |
3 files changed, 49 insertions, 35 deletions
@@ -1,3 +1,9 @@ +commit 13c59928390dd38073c7664ea1d2961d11ba60e2 +Author: Johannes Ranke <jranke@uni-bremen.de> +Date: 2017-03-15 15:16:34 +0100 + + Rerun pkgdown + commit db711aaff2cbe3a620c497b1ef2cc3669d89b2b6 Author: Johannes Ranke <jranke@uni-bremen.de> Date: 2017-03-15 09:16:19 +0100 diff --git a/DESCRIPTION b/DESCRIPTION index 3fdb078..c311ded 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: chents Type: Package Title: Chemical Entities as R Objects Version: 0.2-6 -Date: 2017-03-15 +Date: 2017-03-17 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de")) Description: Utilities for dealing with chemical entities and associated @@ -16,7 +16,7 @@ # this program. If not, see <http://www.gnu.org/licenses/> #' An R6 class for chemical entities with associated data -#' +#' #' The class is initialised with an identifier. Chemical information is retrieved from #' the internet. Additionally, it can be generated using RDKit if RDKit and its #' python bindings are installed and configured for use with PythonInR. @@ -62,7 +62,7 @@ chent <- R6Class("chent", initialize = function(identifier, smiles = NULL, smiles_source = 'user', inchikey = NULL, inchikey_source = 'user', pubchem = TRUE, pubchem_from = c('name', 'smiles', 'inchikey'), - rdkit = TRUE, + rdkit = TRUE, template = NULL, chyaml = TRUE) { self$identifier <- identifier @@ -88,7 +88,7 @@ chent <- R6Class("chent", message("Trying to get chemical information from RDKit using ", names(self$smiles)[1], " SMILES\n", self$smiles[1]) - self$get_rdkit() + self$get_rdkit(template = template) self$mw <- self$rdkit$mw attr(self$mw, "source") <- "rdkit" } @@ -117,9 +117,9 @@ chent <- R6Class("chent", }, get_pubchem = function(pubchem_cid) { self$pubchem = as.list(webchem::pc_prop(pubchem_cid, from = "cid", - properties = c("MolecularFormula", "MolecularWeight", - "CanonicalSMILES", "IsomericSMILES", - "InChI", "InChIKey", "IUPACName", + properties = c("MolecularFormula", "MolecularWeight", + "CanonicalSMILES", "IsomericSMILES", + "InChI", "InChIKey", "IUPACName", "XLogP", "TPSA", "Complexity", "Charge", "HBondDonorCount", "HBondAcceptorCount"))) self$pubchem$synonyms = webchem::pc_synonyms(pubchem_cid, from ="cid")[[1]] @@ -139,7 +139,7 @@ chent <- R6Class("chent", } else { if (length(self$inchikey) > 1) { message("InChIKey ", self$inchikey, " retreived from ", - attr(self$inchikey, "source"), + attr(self$inchikey, "source"), " has length > 1, using PubChem InChIKey") self$inchikey <- self$pubchem$InChIKey attr(self$inchikey, "source") <- "pubchem" @@ -154,7 +154,7 @@ chent <- R6Class("chent", } } }, - get_rdkit = function() { + get_rdkit = function(template = NULL) { if (!requireNamespace("PythonInR")) stop("PythonInR can not be loaded") id <- names(self$identifier) @@ -181,6 +181,12 @@ chent <- R6Class("chent", PythonInR::pyImport("rdMolDraw2D", from = "rdkit.Chem.Draw") PythonInR::pyImport("rdDepictor", from = "rdkit.Chem") PythonInR::pyExec("rdDepictor.Compute2DCoords(mol)") + if (!is.null(template)) { + PythonInR::pyImport("AllChem", from = "rdkit.Chem") + PythonInR::pyExec(paste0("template = Chem.MolFromSmiles('", template, "')")) + PythonInR::pyExec("AllChem.Compute2DCoords(template)") + PythonInR::pyExec("AllChem.GenerateDepictionMatching2DStructure(mol, template)") + } PythonInR::pyExec("d2d = rdMolDraw2D.MolDraw2DSVG(400,500)") PythonInR::pyExec("d2d.DrawMolecule(mol)") PythonInR::pyExec("d2d.FinishDrawing()") @@ -203,15 +209,15 @@ chent <- R6Class("chent", unlink(c(xmlfile, psfile, svgfile)) } }, - get_chyaml = function(repo = c("wd", "local", "web"), + get_chyaml = function(repo = c("wd", "local", "web"), chyaml = paste0(URLencode(self$identifier), ".yaml")) { repo = match.arg(repo) - paths = c(wd = ".", + paths = c(wd = ".", local = file.path("~", "git/chyaml")) chyaml_handlers = list( expr = function(x) NULL, # To avoid security risks from reading chyaml files - dataframe = function(x) + dataframe = function(x) eval(parse(text = paste0("data.frame(", x, ", stringsAsFactors = FALSE)")))) if (repo %in% c("wd", "local")) { @@ -220,7 +226,7 @@ chent <- R6Class("chent", if (!file.exists(full)) { message("Did not find chyaml file ", full) } else { - if (is(try(self$chyaml <- yaml.load_file(chyaml, handlers = chyaml_handlers)), + if (is(try(self$chyaml <- yaml.load_file(chyaml, handlers = chyaml_handlers)), "try-error")) { message("Could not load ", full) } else { @@ -238,17 +244,17 @@ chent <- R6Class("chent", chent <- x } else { id <- make.names(x) - chent <- chent$new(x, smiles) + chent <- chent$new(x, smiles) } self$TPs[[id]] <- chent }, transformations = data.frame(study_type = character(0), - TP_identifier = character(0), - max_occurrence = numeric(0), - source = character(0), + TP_identifier = character(0), + max_occurrence = numeric(0), + source = character(0), pages = character(0), stringsAsFactors = FALSE), - add_transformation = function(study_type, TP_identifier, max_occurrence, + add_transformation = function(study_type, TP_identifier, max_occurrence, comment = "", source = NA, pages = NA) { TP_name = make.names(TP_identifier) if (!inherits(self$TPs[[TP_name]], "chent")) { @@ -257,16 +263,16 @@ chent <- R6Class("chent", TP_chent <- self$TPs[TP_name] if (is.numeric(pages)) pages <- paste(pages, collapse = ", ") cn <- colnames(self$transformations) - self$transformations <- rbind(self$transformations, - data.frame(study_type = study_type, - TP_identifier = TP_identifier, - max_occurrence = max_occurrence, - comment = comment, + self$transformations <- rbind(self$transformations, + data.frame(study_type = study_type, + TP_identifier = TP_identifier, + max_occurrence = max_occurrence, + comment = comment, source = source, pages = pages, stringsAsFactors = FALSE)) }, - soil_degradation_endpoints = data.frame(destination = character(0), + soil_degradation_endpoints = data.frame(destination = character(0), DT50 = numeric(0), comment = character(0), pages = character(0), @@ -275,7 +281,7 @@ chent <- R6Class("chent", comment = "", pages = NA) { if (length(pages) > 1) pages = paste(pages, collapse = ", ") i <- nrow(self$soil_degradation_endpoints) + 1 - self$soil_degradation_endpoints[i, c("destination", "comment", "pages")] <- + self$soil_degradation_endpoints[i, c("destination", "comment", "pages")] <- c(destination, comment, pages) self$soil_degradation_endpoints[i, "DT50"] <- DT50 }, @@ -290,7 +296,8 @@ chent <- R6Class("chent", if (!exists(to, self$TPs)) stop(to, " was not found in TPs") self$ff[i, ] <- c(from, to, ff, comment, pages) }, - pdf = function(file = paste0(self$identifier, ".pdf"), dir = "structures/pdf") { + pdf = function(file = paste0(self$identifier, ".pdf"), dir = "structures/pdf", + template = NULL) { if (!dir.exists(dir)) { message("Directory '", dir, "' does not exist") message("Trying to create directory '", dir, "'") @@ -365,7 +372,7 @@ draw_svg.chent = function(x, width = 300, height = 150, if (!dir.exists(subdir)) dir.create(subdir) PythonInR::pyExec(paste0("mol = Chem.MolFromSmiles('", x$smiles, "')")) PythonInR::pyImport("Draw", from = "rdkit.Chem") - cmd <- paste0("Draw.MolToFile(mol, '", file.path(subdir, filename), + cmd <- paste0("Draw.MolToFile(mol, '", file.path(subdir, filename), "', size = (", width, ", ", height, "))") PythonInR::pyExec(cmd) } @@ -383,9 +390,9 @@ plot.chent = function(x, ...) { } #' An R6 class for pesticidal active ingredients and associated data -#' +#' #' The class is initialised with an identifier which is generally an ISO common name. -#' Additional chemical information is retrieved from the internet if available. +#' Additional chemical information is retrieved from the internet if available. #' #' @docType class #' @importFrom R6 R6Class @@ -401,12 +408,13 @@ pai <- R6Class("pai", public <- list( iso = NULL, alanwood = NULL, - initialize = function(iso, identifier = iso, + initialize = function(iso, identifier = iso, smiles = NULL, smiles_source = 'user', inchikey = NULL, inchikey_source = 'user', - alanwood = TRUE, + alanwood = TRUE, pubchem = TRUE, pubchem_from = 'auto', - rdkit = TRUE, chyaml = TRUE) + rdkit = TRUE, template = NULL, + chyaml = TRUE) { if (!is.null(inchikey)) { @@ -440,7 +448,7 @@ pai <- R6Class("pai", } } } - } + } # Set pubchem_from if not specified if (pubchem_from == 'auto') { @@ -450,11 +458,11 @@ pai <- R6Class("pai", } } - super$initialize(identifier = identifier, + super$initialize(identifier = identifier, smiles = smiles, smiles_source = smiles_source, inchikey = self$inchikey, pubchem = pubchem, pubchem_from = pubchem_from, - rdkit = rdkit, chyaml = chyaml) + rdkit = rdkit, template = template, chyaml = chyaml) invisible(self) } |