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authorJohannes Ranke <jranke@uni-bremen.de>2017-03-17 21:19:14 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2017-03-17 21:19:14 +0100
commitf5b36dc73e7778091a08eaed51fd9d4f8677fbc1 (patch)
treee13e0b5ae9a731e79e01d7883f39dbbb73ec9e01
parent13c59928390dd38073c7664ea1d2961d11ba60e2 (diff)
Support a common template for depictions
-rw-r--r--ChangeLog6
-rw-r--r--DESCRIPTION2
-rw-r--r--R/chent.R76
3 files changed, 49 insertions, 35 deletions
diff --git a/ChangeLog b/ChangeLog
index cccfa1a..767fc23 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -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
diff --git a/R/chent.R b/R/chent.R
index b901904..192c6df 100644
--- a/R/chent.R
+++ b/R/chent.R
@@ -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)
}

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