diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/chent.R | 122 |
1 files changed, 68 insertions, 54 deletions
@@ -1,4 +1,4 @@ -# Copyright (C) 2016,2017,2018 Johannes Ranke +# Copyright (C) 2016-2019 Johannes Ranke # Contact: jranke@uni-bremen.de # This file is part of the R package chents @@ -88,7 +88,7 @@ chent <- R6Class("chent", } if (rdkit) { - if(requireNamespace("PythonInR", quietly = TRUE)) { + if(rdkit_available()) { if (is.null(self$smiles)) { message("RDKit would need a SMILES code") } else { @@ -99,6 +99,8 @@ chent <- R6Class("chent", self$mw <- self$rdkit$mw attr(self$mw, "source") <- "rdkit" } + } else { + message("RDKit is not available via PythonInR") } } @@ -162,62 +164,54 @@ chent <- R6Class("chent", } }, get_rdkit = function(template = NULL) { - if (!requireNamespace("PythonInR")) - stop("PythonInR can not be loaded") - id <- names(self$identifier) - if (!PythonInR::pyIsConnected()) { - PythonInR::pyConnect() + if(!rdkit_available()) { + stop("RDKit is not available via PythonInR") } - try_rdkit <- try(PythonInR::pyImport("Chem", from = "rdkit")) - if (inherits(try_rdkit, "try-error")) { - message("Could not import RDKit in Python session") - } else { - self$rdkit <- list() - PythonInR::pyImport("Descriptors", from = "rdkit.Chem") - PythonInR::pyExec(paste0("mol = Chem.MolFromSmiles('", self$smiles[1], "')")) - self$rdkit$mw <- PythonInR::pyExecg("mw = Descriptors.MolWt(mol)", "mw") - if (!is.null(self$mw)) { - if (round(self$rdkit$mw, 1) != round(self$mw, 1)) { - message("RDKit mw is ", self$rdkit$mw) - message("mw is ", self$mw) - } + self$rdkit <- list() + PythonInR::pyImport("Descriptors", from = "rdkit.Chem") + PythonInR::pyExec(paste0("mol = Chem.MolFromSmiles('", self$smiles[1], "')")) + self$rdkit$mw <- PythonInR::pyExecg("mw = Descriptors.MolWt(mol)", "mw") + if (!is.null(self$mw)) { + if (round(self$rdkit$mw, 1) != round(self$mw, 1)) { + message("RDKit mw is ", self$rdkit$mw) + message("mw is ", self$mw) } + } - # Create an SVG representation - PythonInR::pyImport("Draw", from = "rdkit.Chem") - 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()") - self$svg <- PythonInR::pyGet("d2d.GetDrawingText()") + # Create an SVG representation + PythonInR::pyImport("Draw", from = "rdkit.Chem") + PythonInR::pyImport("rdMolDraw2D", from = "rdkit.Chem.Draw") + PythonInR::pyImport("rdDepictor", from = "rdkit.Chem") + PythonInR::pyExec("rdDepictor.Compute2DCoords(mol)") + if (!is.null(template)) { + PythonInR::pyImport("AllChem", from = "rdkit.Chem") + PythonInR::pyExec(paste0("template = Chem.MolFromSmiles('", template, "')")) + PythonInR::pyExec("AllChem.Compute2DCoords(template)") + PythonInR::pyExec("AllChem.GenerateDepictionMatching2DStructure(mol, template)") + } + PythonInR::pyExec("d2d = rdMolDraw2D.MolDraw2DSVG(400,500)") + PythonInR::pyExec("d2d.DrawMolecule(mol)") + PythonInR::pyExec("d2d.FinishDrawing()") + self$svg <- PythonInR::pyGet("d2d.GetDrawingText()") - if (!requireNamespace("grConvert")) { - stop("grConvert is not available, self$Picture will not be created") - } else { - # Convert to PostScript, remembering size properties - svgfile <- tempfile(fileext = ".svg") - writeLines(self$svg, svgfile) - psfile <- tempfile(fileext = ".ps") - suppressMessages(grConvert::convertPicture(svgfile, psfile)) - ps_font_line <- grep("Tm$", readLines(psfile), value = TRUE)[1] - ps_font_size <- gsub(" .*$", "", ps_font_line) - self$Pict_font_size = as.numeric(ps_font_size) - - # Read in to create Picture - xmlfile <- tempfile(fileext = ".xml") - PostScriptTrace(psfile, outfilename = xmlfile) - unlink(paste0("capture", basename(psfile))) - self$Picture <- readPicture(xmlfile) - unlink(c(xmlfile, psfile, svgfile)) - } + if (!requireNamespace("grConvert")) { + stop("grConvert is not available, self$Picture will not be created") + } else { + # Convert to PostScript, remembering size properties + svgfile <- tempfile(fileext = ".svg") + writeLines(self$svg, svgfile) + psfile <- tempfile(fileext = ".ps") + suppressMessages(grConvert::convertPicture(svgfile, psfile)) + ps_font_line <- grep("Tm$", readLines(psfile), value = TRUE)[1] + ps_font_size <- gsub(" .*$", "", ps_font_line) + self$Pict_font_size = as.numeric(ps_font_size) + + # Read in to create Picture + xmlfile <- tempfile(fileext = ".xml") + PostScriptTrace(psfile, outfilename = xmlfile) + unlink(paste0("capture", basename(psfile))) + self$Picture <- readPicture(xmlfile) + unlink(c(xmlfile, psfile, svgfile)) } }, get_chyaml = function(repo = c("wd", "local", "web"), @@ -607,4 +601,24 @@ pp <- R6Class("pp", } ) ) + +rdkit_available <- function() +{ + if(requireNamespace("PythonInR", quietly = TRUE)) { + if (!PythonInR::pyIsConnected()) { + PythonInR::pyConnect() + } + sink(tempfile()) + try_rdkit <- try(PythonInR::pyImport("Chem", from = "rdkit"), + silent = TRUE) + sink() + if (inherits(try_rdkit, "try-error")) { + return(FALSE) + } else { + return(TRUE) + } + } else { + return(FALSE) + } +} # vim: set ts=2 sw=2 expandtab: |