Merge pull request #2 from MD-Studio/devel

Devel

Dockerfile

@@ -1,14 +1,14 @@
+
 # Install all the cheminformatic packages
-FROM mdstudio/mdstudio_docker_conda:0.0.1
+FROM mdstudio/mdstudio_docker_conda:0.0.2
 
-RUN apt-get update -y && apt-get install wget libopenbabel-dev openbabel -y 
+RUN apt-get update -y && apt-get install swig wget gcc g++ gfortran cmake libxrender-dev -y
 
 COPY . /home/mdstudio/lie_structures
 
 RUN chown mdstudio:mdstudio /home/mdstudio/lie_structures
 
-RUN conda install -c rdkit rdkit && \
-    conda install -c openbabel openbabel && \
+RUN conda install -c openbabel openbabel && \
     conda install -c bioconda java-jdk && \
     conda install -c conda-forge jpype1 && \
     conda install -c speleo3 indigo 
@@ -25,6 +25,7 @@ ENV CLASSPATH=/home/mdstudio/cdk-2.1.1.jar:/home/mdstudio/opsin-1.3.0-jar-with-d
 
 ENV JPYPE_JVM=/usr/local/jre/lib/amd64/server/libjvm.so
 
+
 RUN pip install "https://github.com/cinfony/cinfony/tarball/master#egg=cinfony-1.2"
 
 WORKDIR /home/mdstudio/lie_structures

lie_structures/__init__.py

@@ -3,18 +3,13 @@
 package:  lie_structures
 LIEStudio small molecule cheminformatics functions
 """
-
+# Pandas and Openbabel share a common json library name
+# Adding the pandas import here avoids a REALLY NASTY race condition
+# If you remove the pandas import all the HELL may break loose
+import pandas
 import os
 
-__module__ = 'lie_structures'
-__docformat__ = 'restructuredtext'
-__version__ = '{major:d}.{minor:d}'.format(major=0, minor=2)
-__author__ = 'Marc van Dijk'
-__status__ = 'pre-release beta1'
-__date__ = '5 august 2016'
 __licence__ = 'Apache Software License 2.0'
-__url__ = 'https://github.com/NLeSC/LIEStudio'
-__copyright__ = "Copyright (c) VU University, Amsterdam"
 __rootpath__ = os.path.dirname(__file__)
 
 from .cheminfo_pkgmanager import CinfonyPackageManager

lie_structures/wamp_services.py

@@ -5,7 +5,6 @@
 
 WAMP service methods the module exposes.
 """
-
 import os
 import tempfile
 

setup.py

@@ -41,7 +41,7 @@
     packages=find_packages(),
     py_modules=[distribution_name],
     install_requires=['biopython', 'cinfony==1.2', 'pandas',
-                      'pydpi', 'JPype1', 'Pillow', 'retrying', 'scipy'],
+                      'Pillow', 'retrying', 'scipy'],
     extras_require={
         'test': ['unittest2', 'coverage']},
     dependency_links=["https://github.com/cinfony/cinfony/tarball/master#egg=cinfony-1.2"],

tests/testall.py

@@ -316,7 +316,7 @@ def testRSgetprops(self):
 
 
 class TestRDKit(TestToolkit):
-    toolkit = rdk
+    toolkit = "rdk"
     tanimotoresult = 1/3.
     Natoms = 9
     tpsaname = "TPSA"
@@ -329,7 +329,7 @@ def testRSconversiontoMOL2(self):
 
 
 class TestIndigo(TestToolkit):
-    toolkit = indy
+    toolkit = "indy"
     tanimotoresult = 1/3.
     Natoms = 15
     tpsaname = "TPSA"
@@ -361,7 +361,7 @@ def testMake3D(self):
 
 
 class TestWebel(TestToolkit):
-    toolkit = webel
+    toolkit = "webel"
     tanimotoresult = 0.375
     Natoms = 9
     tpsaname = "TPSADescriptor_TopoPSA"
@@ -497,7 +497,7 @@ def testRSconversiontoMOL(self):
 
 
 class TestCDK(TestToolkit):
-    toolkit = cdk
+    toolkit = "cdk"
     tanimotoresult = 0.375
     Natoms = 15
     tpsaname = "tpsa"
@@ -522,7 +522,7 @@ def testRSgetprops(self):
 
 
 class TestJchem(TestToolkit):
-    toolkit = jchem
+    toolkit = "jchem"
     tanimotoresult = 0.444
     Natoms = 15
     tpsaname = "TPSA"
@@ -540,3 +540,7 @@ def testRSgetprops(self):
         self.assertAlmostEqual(self.mols[0].molwt, 58.12, 2)
         self.assertEqual(len(self.mols[0].atoms), 4)
         self.assertRaises(AttributeError, self.RSaccesstest)
+
+
+if __name__ == '__main__':
+    unittest2.main()