feat: SCHWED-3096 A working version including tests passing

docker/Dockerfile

 FROM ubuntu:16.04
 
-RUN apt-get update -y
-# basic packages
-
-RUN apt-get install -y cmake \
-                       sip-dev \
-                       libtiff-dev \
-                       libfftw3-dev \
-                       libeigen3-dev \
-                       libpng-dev \
-                       python-all \
-                       python2.7 \
-                       python-qt4 \
-                       libboost-all-dev \
-                       qt4-qtconfig \
-                       qt4-qmake \
-                       libqt4-dev \
-                       libpng-dev \
-                       wget \
-                       git \
-                       gfortran \
-                       libeigen3-dev \
-                       python-pip
-
-# Install miniconda - to get useful binaries
-RUN wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
-RUN bash Miniconda2-latest-Linux-x86_64.sh -p /opt/miniconda2 -b -f
-RUN rm Miniconda2-latest-Linux-x86_64.sh
-
-# Install ClustalW and MSMS
-RUN /opt/miniconda2/bin/conda install -y -c bioconda clustalw=2.1 msms=2.6.1
+RUN apt-get update -y && apt-get install -y cmake \
+                                            sip-dev \
+                                            libtiff-dev \
+                                            libfftw3-dev \
+                                            libeigen3-dev \
+                                            libboost-all-dev \
+                                            libpng-dev \
+                                            python-all \
+                                            python2.7 \
+                                            python-qt4 \
+                                            qt4-qtconfig \
+                                            qt4-qmake \
+                                            libqt4-dev \
+                                            libpng-dev \
+                                            wget \
+                                            git \
+                                            gfortran \
+                                            libeigen3-dev \
+                                            python-pip \
+                                            tar \
+                                            libbz2-dev \
+                                            doxygen \
+                                            swig \
+                                            clustalw
+
+
+# Install MSMS
+WORKDIR /
+RUN mkdir -p /msms
+WORKDIR /msms
+RUN wget http://mgltools.scripps.edu/downloads/tars/releases/MSMSRELEASE/REL2.6.1/msms_i86_64Linux2_2.6.1.tar.gz
+RUN tar -xvzf msms_i86_64Linux2_2.6.1.tar.gz
+RUN ln -s /msms/msms.x86_64Linux2.2.6.1 /usr/bin/msms
+RUN ln -s /msms/pdb_to_xyzr /usr/bin/pdb_to_xyzr
+RUN ln -s /msms/pdb_to_xyzrn /usr/bin/pdb_to_xyzrn
+
 
 # Install OpenMM
-RUN /opt/miniconda2/bin/conda install -y -c omnia openmm=7.1.1=py27_0
+WORKDIR /
+RUN git clone https://github.com/pandegroup/openmm
+WORKDIR /openmm
+RUN git checkout -b 7.1.1 tags/7.1.1
+RUN cmake .
+RUN make -j4
+RUN make install
 
 # Install DSSP
-RUN /opt/miniconda2/bin/conda install -y -c salilab dssp=3.0.0
+WORKDIR /
+RUN wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.2.1.tgz
+RUN tar -xvzf dssp-2.2.1.tgz
+WORKDIR /dssp-2.2.1
+RUN make
+RUN ln -s /dssp-2.2.1/mkdssp /usr/bin/mkdssp
 
 # Install some python packages
-RUN pip install --upgrade pip && pip install numpy==1.14.0 \
+WORKDIR /
+RUN pip install --upgrade pip && pip install numpy==1.10.4 \
                                              scipy==1.0.0 \
                                              pandas==0.22.0 \
                                              jupyter==1.0.0
@@ -54,9 +72,9 @@ RUN cmake . -DPYTHON_LIBRARIES=/usr/lib/x86_64-linux-gnu/libpython2.7.so \
             -DENABLE_MM=ON \
             -DCOMPILE_TMTOOLS=1 \
             -DUSE_NUMPY=1 \
-            -DOPEN_MM_LIBRARY=/opt/miniconda2/pkgs/openmm-7.1.1-py27_0/lib/libOpenMM.so \
-            -DOPEN_MM_INCLUDE_DIR=/opt/miniconda2/pkgs/openmm-7.1.1-py27_0/include/ \
-            -DOPEN_MM_PLUGIN_DIR=/opt/miniconda2/pkgs/openmm-7.1.1-py27_0/lib/plugins
+            -DOPEN_MM_LIBRARY=/usr/local/openmm/lib/libOpenMM.so \
+            -DOPEN_MM_INCLUDE_DIR=/usr/local/openmm/include \
+            -DOPEN_MM_PLUGIN_DIR=/usr/local/openmm/lib/plugins
 
 # Build chemdict_tool
 RUN make -j4 chemdict_tool
@@ -70,21 +88,18 @@ RUN stage/bin/chemdict_tool update modules/conop/data/charmm.cif compounds.cheml
 RUN cmake . -DPYTHON_LIBRARIES=/usr/lib/x86_64-linux-gnu/libpython2.7.so \
             -DOPTIMIZE=ON \
             -DENABLE_MM=ON \
-            -DOPEN_MM_LIBRARY=/opt/miniconda2/pkgs/openmm-7.1.1-py27_0/lib/libOpenMM.so \
-            -DOPEN_MM_INCLUDE_DIR=/opt/miniconda2/pkgs/openmm-7.1.1-py27_0/include/ \
-            -DOPEN_MM_PLUGIN_DIR=/opt/miniconda2/pkgs/openmm-7.1.1-py27_0/lib/plugins \
+            -DOPEN_MM_LIBRARY=/usr/local/openmm/lib/libOpenMM.so \
+            -DOPEN_MM_INCLUDE_DIR=/usr/local/openmm/include \
+            -DOPEN_MM_PLUGIN_DIR=/usr/local/openmm/lib/plugins \
             -DCOMPOUND_LIB=/opt/ost/compounds.chemlib
 
 # Build OST
 RUN make -j4
-#RUN make check
+RUN make check
 
 # go back home
 WORKDIR /home
 
-# Get the example
-RUN wget https://files.rcsb.org/view/5X28.pdb
-
 # Set the environment
 # - for GUI
 ENV QT_X11_NO_MITSHM 1
@@ -93,11 +108,6 @@ ENV PYTHONPATH="/opt/ost/stage/lib64/python2.7/site-packages:${PYTHONPATH}"
 # - for PATH
 ENV PATH="/opt/ost/stage/bin:${PATH}"
 
-# Link binaries
-RUN ln -s /opt/miniconda2/pkgs/clustalw*/bin/* /usr/bin
-RUN ln -s /opt/miniconda2/pkgs/dssp*/bin/* /usr/bin
-RUN ln -s /opt/miniconda2/pkgs/msms*/bin/* /usr/bin
-
 ENTRYPOINT ["ost"]
 CMD ["-i"]