From 7517eb0ed1a66488b937c039d4bcadefeff6b479 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Sat, 8 Oct 2016 03:07:50 +0200
Subject: Add a method to write cropped pdf files

---
 ChangeLog   | 36 ++++++++++++++++++++++++++++++++++++
 DESCRIPTION |  2 +-
 R/chent.R   | 14 ++++++++++++++
 3 files changed, 51 insertions(+), 1 deletion(-)

diff --git a/ChangeLog b/ChangeLog
index 257e4cc..38c401e 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,39 @@
+commit d22214d9f1b17bd3ab2febe810ab996bebb01410
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2016-09-28 08:56:57 +0200
+
+    Add drat target
+
+commit cc5ba9d7cf9435bc6243222691b76d35c866aea5
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2016-09-27 19:31:04 +0200
+
+    Update .Rbuildignore
+
+commit 7915ca3a209a052902893cb583e15cee85854821
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2016-09-27 17:48:38 +0200
+
+    Make the new README
+
+commit 2985771a8fad29e2ebeef533adcf81d621fb5a35
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2016-09-27 17:46:59 +0200
+
+    Remove header with metadata, misrendered on github
+
+commit e23da46d572df2636d68572710b1f2ffbf27b7bd
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2016-09-27 17:39:28 +0200
+
+    Remove mathjax from README
+
+commit 5bec469048899cfd785dec4f91ec3840cff18adb
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2016-09-27 16:43:15 +0200
+
+    Add a bit of info to README
+
 commit b3e6adc8da99f895fa9d289133de60ce1d5bd889
 Author: Johannes Ranke <jranke@uni-bremen.de>
 Date:   2016-09-27 16:43:15 +0200
diff --git a/DESCRIPTION b/DESCRIPTION
index 639cfe2..11a63f8 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: chents
 Type: Package
 Title: Chemical Entities as R Objects
 Version: 0.2-3
-Date: 2016-09-27
+Date: 2016-10-07
 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 dd51798..b2a1da6 100644
--- a/R/chent.R
+++ b/R/chent.R
@@ -241,6 +241,20 @@ 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") {
+      if (!dir.exists("structures")) {
+        message("Directory '", dir, "' does not exist")
+        message("Creating directory '", dir, "'")
+        dir.create(dir)
+      }
+      path = file.path(dir, file)
+      message("Creating file '", path, "'")
+      pdf(path)
+      plot(self)
+      dev.off()
+      message("Cropping file '", path, "' using pdfcrop")
+      system(paste("pdfcrop --margin 10", path, path, "> /dev/null"))
     }
   )
 )
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