From 291337e920cc95510fce3c0cdcc62b4443cd3bc4 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Thu, 13 Oct 2016 14:03:19 +0200
Subject: Fix retrieving pubchem infos for ambiguous names

---
 ChangeLog                 | 12 ++++++++++++
 DESCRIPTION               |  4 ++--
 GNUmakefile               |  2 ++
 R/chent.R                 |  2 +-
 test.log                  | 11 +++++------
 tests/testthat/test_pai.R |  8 ++++----
 6 files changed, 26 insertions(+), 13 deletions(-)

diff --git a/ChangeLog b/ChangeLog
index 38c401e..5fe2f05 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,15 @@
+commit 65c481910d65f6935b7f52450ea809586e71d384
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2016-10-13 10:08:32 +0200
+
+    Do not fail if PythonInR is not installed
+
+commit 7517eb0ed1a66488b937c039d4bcadefeff6b479
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2016-10-08 03:07:50 +0200
+
+    Add a method to write cropped pdf files
+
 commit d22214d9f1b17bd3ab2febe810ab996bebb01410
 Author: Johannes Ranke <jranke@uni-bremen.de>
 Date:   2016-09-28 08:56:57 +0200
diff --git a/DESCRIPTION b/DESCRIPTION
index 11a63f8..bc02e64 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: chents
 Type: Package
 Title: Chemical Entities as R Objects
-Version: 0.2-3
-Date: 2016-10-07
+Version: 0.2-4
+Date: 2016-10-13
 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/GNUmakefile b/GNUmakefile
index 76339e7..c22ff44 100644
--- a/GNUmakefile
+++ b/GNUmakefile
@@ -5,6 +5,8 @@ TGZ     := $(PKGNAME)_$(PKGVERS).tar.gz
 R_HOME  ?= $(shell R RHOME)
 DATE    := $(shell date +%Y-%m-%d)
 
+all: install
+
 .PHONEY: usage check clean roxygen sd
 
 usage:
diff --git a/R/chent.R b/R/chent.R
index e170307..fe87d5e 100644
--- a/R/chent.R
+++ b/R/chent.R
@@ -89,7 +89,7 @@ chent <- R6Class("chent",
     try_pubchem = function(identifier) {
       message("PubChem:")
       if (missing(identifier)) identifier <- self$identifier
-      pubchem_cids = webchem::get_cid(identifier)
+      pubchem_cids = webchem::get_cid(identifier)[[identifier]]
 
       if (is.na(pubchem_cids[1])) {
         message("Query ", identifier, " did not give results at PubChem")
diff --git a/test.log b/test.log
index e2dbdd5..158cb5a 100644
--- a/test.log
+++ b/test.log
@@ -1,23 +1,22 @@
 Loading chents
 Loading required package: testthat
-
+Testing chents
+Generation of chent objects: 
 Initialize Python Version 2.7.9 (default, Jun 29 2016, 13:11:10) 
 [GCC 4.9.2]
 
-Testing chents
-Generation of chent objects: Trying to get chemical information from RDKit using user SMILES
+Trying to get chemical information from RDKit using user SMILES
 CCCCCCCCO
 ......
 Generation of pai objects: alanwood.net:
 Querying glyphosate.html
 PubChem:
-http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/glyphosate/cids/JSON
-No encoding supplied: defaulting to UTF-8.
+http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON
 Found 1 entries in PubChem, using the first one.
 http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,ExactMass,MonoisotopicMass,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount,RotatableBondCount,HeavyAtomCount,IsotopeAtomCount,AtomStereoCount,DefinedAtomStereoCount,UndefinedAtomStereoCount,BondStereoCount,DefinedBondStereoCount,UndefinedBondStereoCount,CovalentUnitCount,Volume3D,XStericQuadrupole3D,YStericQuadrupole3D,ZStericQuadrupole3D,FeatureCount3D,FeatureAcceptorCount3D,FeatureDonorCount3D,FeatureAnionCount3D,FeatureCationCount3D,FeatureRingCount3D,FeatureHydrophobeCount3D,ConformerModelRMSD3D,EffectiveRotorCount3D,ConformerCount3D,Fingerprint2D/JSON
 http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON
 Trying to get chemical information from RDKit using PubChem_Canonical SMILES
 C(C(=O)O)NCP(=O)(O)O
-........
+.......
 
 DONE ===========================================================================
diff --git a/tests/testthat/test_pai.R b/tests/testthat/test_pai.R
index 944ad04..1718a9a 100644
--- a/tests/testthat/test_pai.R
+++ b/tests/testthat/test_pai.R
@@ -1,8 +1,8 @@
 context("Generation of pai objects")
 
 glyphosate <- pai$new("glyphosate", chyaml = FALSE)
-
-test_that("We can generate a pai object from its ISO common name", {
+ 
+test_that("a pai object is generated from its ISO common name", {
   expect_equivalent(glyphosate$alanwood$cas, "1071-83-6")
   expect_equivalent(glyphosate$alanwood$formula, "C3H8NO5P")
   expect_equivalent(glyphosate$alanwood$iupac_name, "N-(phosphonomethyl)glycine")
@@ -12,8 +12,8 @@ test_that("We can generate a pai object from its ISO common name", {
   expect_equal(glyphosate$inchikey, ik)
 })
 
-test_that("RDKit information was added", {
-  expect_equivalent(glyphosate$rdkit$mw, 169.073)
+test_that("a pai object is generated from an ambiguous name", {
+  deltamethrin <- pai$new("deltamethrin", chyaml = FALSE)
 })
 
 test_that("PubChem information was added via webchem", {
-- 
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