diff --git a/docker/Dockerfile b/docker/Dockerfile
index 12c3fd65249ea915d7aa75aae238933e2dde8052..a02301453bc4c02b5cbb0de4a2948d64f2d15d0e 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -1,16 +1,9 @@
-FROM ubuntu:16.04
+FROM ubuntu:18.04
# ARGUMENTS
###########
-# OBLIGATORY
-ARG OPENSTRUCTURE_VERSION
-RUN if [ -z "${OPENSTRUCTURE_VERSION}" ]; then \
- echo "OPENSTRUCTURE_VERSION argument is obligatory. Run with --build-arg OPENSTRUCTURE_VERSION=<VERSION>"; \
- exit 1; \
- else : ; fi
-
-# OPTIONAL
+ARG OPENSTRUCTURE_VERSION="1.10.0"
ARG SRC_FOLDER="/usr/local/src"
ARG CPUS_FOR_MAKE=8
ARG PYTHONPATH="/usr/local/lib64/python2.7/site-packages:${PYTHONPATH}"
@@ -24,6 +17,7 @@ ARG OPENMM_LIB_PATH="/usr/local/openmm/lib/"
# INSTALL SYSTEM DEPS
#####################
RUN apt-get update -y && apt-get install -y cmake \
+ g++ \
sip-dev \
libtiff-dev \
libfftw3-dev \
@@ -32,11 +26,9 @@ RUN apt-get update -y && apt-get install -y cmake \
libpng-dev \
python-all \
python2.7 \
- python-qt4 \
- qt4-qtconfig \
- qt4-qmake \
- libqt4-dev \
- libpng-dev \
+ python-pyqt5 \
+ qt5-qmake \
+ qtbase5-dev \
wget \
git \
gfortran \
@@ -48,9 +40,12 @@ RUN apt-get update -y && apt-get install -y cmake \
clustalw \
python-virtualenv \
libsqlite3-dev \
+ dssp \
+ python-enum34 \
locales && \
- # CLEANUP
- rm -rf /var/lib/apt/lists/*
+ # CLEANUP
+ rm -rf /var/lib/apt/lists/*
+
# INSTALL SOME PYTHON PACKAGES GLOBALY
######################################
RUN pip install -U pip==9.0.3 && \
@@ -92,18 +87,6 @@ RUN cd ${SRC_FOLDER} && \
rm -rf ${SRC_FOLDER}/openmm-${OPENMM_VERSION}.tar.gz && \
rm -rf ${SRC_FOLDER}/openmm-${OPENMM_VERSION}
-
-# COMPILE AND INSTALL DSSP
-##########################
-RUN cd ${SRC_FOLDER} && \
- wget ftp://ftp.cmbi.umcn.nl/pub/molbio/software/dssp-2/dssp-${DSSP_VERSION}.tgz && \
- tar -xvzf dssp-${DSSP_VERSION}.tgz && \
- cd dssp-${DSSP_VERSION} && \
- make -j ${CPUS_FOR_MAKE} && \
- make install && \
- rm -rf ${SRC_FOLDER}/dssp-${DSSP_VERSION}.tgz && \
- rm -rf ${SRC_FOLDER}/dssp-${DSSP_VERSION}
-
# INSTALL OST
#############
RUN cd ${SRC_FOLDER} && \
@@ -112,6 +95,7 @@ RUN cd ${SRC_FOLDER} && \
mkdir openstructure-${OPENSTRUCTURE_VERSION} && \
tar xf openstructure-${OPENSTRUCTURE_VERSION}.tar.gz -C ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION} --strip-components=1 && \
mkdir -p ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION}/build
+
WORKDIR ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION}/build
# cmake ost
diff --git a/singularity/Singularity.1.10.0 b/singularity/Singularity.1.10.0
new file mode 100644
index 0000000000000000000000000000000000000000..308254163e2baf8ca6ec36391f0d42e85df09d3b
--- /dev/null
+++ b/singularity/Singularity.1.10.0
@@ -0,0 +1,425 @@
+BootStrap: docker
+From: ubuntu:18.04
+
+%post
+##############################################################################
+# POST
+##############################################################################
+
+# CHANGE DASH TO BASH
+rm /bin/sh
+ln -sf /bin/bash /bin/sh
+
+# DEFINE SOME ENV VARS USED DURING THE IMAGE BUILD
+##########################
+export SRC_FOLDER="/usr/local/src"
+export CPUS_FOR_MAKE=8
+export PYTHONPATH="/usr/local/lib64/python2.7/site-packages:${PYTHONPATH}"
+# When changing OPENSTRUCTURE_VERSION make sure to change it also in the
+# environment section of singularity recipe (this file).
+export OPENSTRUCTURE_VERSION="1.10.0"
+export OPENSTRUCTURE_SHARE="/usr/local/share/ost"
+export MSMS_VERSION="2.6.1"
+export OPENMM_VERSION="7.1.1"
+export OPENMM_INCLUDE_PATH=/usr/local/openmm/include/
+export OPENMM_LIB_PATH=/usr/local/openmm/lib/
+export JUPYTER_CONFIG_DIR="/usr/local/etc/jupyter"
+export JUPYTER_PATH="/usr/local/share/jupyter"
+export JUPYTER_RUNTIME_DIR="$JUPYTER_PATH/runtime"
+export VIRTUALENV_DIR="/usr/local/share/ost_venv"
+
+
+# INSTALL SYSTEM DEPS
+#####################
+apt-get update -y && apt-get install -y cmake \
+ g++ \
+ sip-dev \
+ libtiff-dev \
+ libfftw3-dev \
+ libeigen3-dev \
+ libboost-all-dev \
+ libpng-dev \
+ python-all \
+ python2.7 \
+ python-pyqt5 \
+ qt5-qmake \
+ qtbase5-dev \
+ wget \
+ git \
+ gfortran \
+ python-pip \
+ tar \
+ libbz2-dev \
+ doxygen \
+ swig \
+ clustalw \
+ python-virtualenv \
+ libsqlite3-dev \
+ dssp \
+ python-enum34 \
+ python-ipaddress \
+ locales
+
+# SET LOCALE
+############
+echo "LC_ALL=en_US.UTF-8" >> /etc/environment
+echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen
+echo "LANG=en_US.UTF-8" > /etc/locale.conf
+locale-gen en_US.UTF-8
+
+# INSTALL SOME PYTHON PACKAGES GLOBALY
+######################################
+pip install --no-cache-dir numpy==1.10.4 \
+ scipy==1.0.0 \
+ pandas==0.22.0
+
+
+# SET UP VIRTUALENV
+###################
+virtualenv --system-site-packages $VIRTUALENV_DIR
+. $VIRTUALENV_DIR/bin/activate
+
+
+# INSTALL REQUIRED PYTHON PACKAGES
+##################################
+pip install jupyter==1.0.0 \
+ nglview==1.1.6
+
+# DOWNLOAD AND INSTALL MSMS
+##############
+cd ${SRC_FOLDER}
+if [ ! -f msms_i86_64Linux2_${MSMS_VERSION}.tar.gz ]; then
+ mkdir -p msms
+ cd msms
+ wget http://mgltools.scripps.edu/downloads/tars/releases/MSMSRELEASE/REL${MSMS_VERSION}/msms_i86_64Linux2_${MSMS_VERSION}.tar.gz
+ tar -xvzf msms_i86_64Linux2_${MSMS_VERSION}.tar.gz
+ cp -v ${SRC_FOLDER}/msms/msms.x86_64Linux2.${MSMS_VERSION} /usr/local/bin/msms
+ cp -v ${SRC_FOLDER}/msms/pdb_to_xyzr /usr/local/bin/pdb_to_xyzr
+ cp -v ${SRC_FOLDER}/msms/pdb_to_xyzrn /usr/local/bin/pdb_to_xyzrn
+fi
+
+# COMPILE OPENMM FROM SOURCES. INSTALL TO /usr/local
+############################
+cd ${SRC_FOLDER}
+if [ ! -f openmm-${OPENMM_VERSION}.tar.gz ]; then
+ wget -O openmm-${OPENMM_VERSION}.tar.gz -nc https://github.com/pandegroup/openmm/archive/${OPENMM_VERSION}.tar.gz
+ mkdir ${SRC_FOLDER}/openmm-${OPENMM_VERSION}
+ tar xf openmm-${OPENMM_VERSION}.tar.gz -C ${SRC_FOLDER}/openmm-${OPENMM_VERSION} --strip-components=1
+ mkdir -p ${SRC_FOLDER}/openmm-${OPENMM_VERSION}/build && cd ${SRC_FOLDER}/openmm-${OPENMM_VERSION}/build
+ cmake .. && make -j $CPUS_FOR_MAKE && make install
+ cd ${SRC_FOLDER}/openmm-${OPENMM_VERSION}/build/python && python setup.py build && python setup.py install
+fi
+
+# INSTALL OST
+#############
+
+cd ${SRC_FOLDER}
+if [ ! -f openstructure-${OPENSTRUCTURE_VERSION}.tar.gz ]; then
+ # copy ost release
+ wget -O openstructure-${OPENSTRUCTURE_VERSION}.tar.gz -nc https://git.scicore.unibas.ch/schwede/openstructure/repository/${OPENSTRUCTURE_VERSION}/archive.tar.gz
+ mkdir openstructure-${OPENSTRUCTURE_VERSION}
+ tar xf openstructure-${OPENSTRUCTURE_VERSION}.tar.gz -C ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION} --strip-components=1
+ mkdir -p ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION}/build && cd ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION}/build
+
+ # cmake ost
+ cmake .. -DPYTHON_LIBRARIES=/usr/lib/x86_64-linux-gnu/libpython2.7.so \
+ -DOPTIMIZE=ON \
+ -DENABLE_MM=ON \
+ -DCOMPILE_TMTOOLS=1 \
+ -DUSE_NUMPY=1 \
+ -DOPEN_MM_LIBRARY=$OPENMM_LIB_PATH/libOpenMM.so \
+ -DOPEN_MM_INCLUDE_DIR=$OPENMM_INCLUDE_PATH \
+ -DOPEN_MM_PLUGIN_DIR=$OPENMM_LIB_PATH/plugins \
+ -DENABLE_GFX=ON \
+ -DENABLE_GUI=ON
+
+ # Build chemdict_tool
+ make -j ${CPUS_FOR_MAKE} chemdict_tool
+
+ # get the compound library
+ wget ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz
+ stage/bin/chemdict_tool create components.cif.gz compounds.chemlib pdb
+ stage/bin/chemdict_tool update ../modules/conop/data/charmm.cif compounds.chemlib charmm
+ mkdir -p $OPENSTRUCTURE_SHARE
+ chmod a+rw -R $OPENSTRUCTURE_SHARE
+ mv compounds.chemlib $OPENSTRUCTURE_SHARE
+
+ # Build and install OST
+ cmake .. -DPYTHON_LIBRARIES=/usr/lib/x86_64-linux-gnu/libpython2.7.so \
+ -DOPTIMIZE=ON \
+ -DENABLE_MM=ON \
+ -DCOMPILE_TMTOOLS=1 \
+ -DUSE_NUMPY=1 \
+ -DOPEN_MM_LIBRARY=$OPENMM_LIB_PATH/libOpenMM.so \
+ -DOPEN_MM_INCLUDE_DIR=$OPENMM_INCLUDE_PATH \
+ -DOPEN_MM_PLUGIN_DIR=$OPENMM_LIB_PATH/plugins \
+ -DENABLE_GFX=ON \
+ -DENABLE_GUI=ON \
+ -DCOMPOUND_LIB=$OPENSTRUCTURE_SHARE/compounds.chemlib
+
+ # Build chemdict_tool
+ make -j ${CPUS_FOR_MAKE}
+ make check
+ make install
+fi
+
+# SETUP JUPYTER
+###############
+mkdir -p /usr/local/share/ipython
+mkdir -p $JUPYTER_PATH
+mkdir -p $JUPYTER_RUNTIME_DIR
+mkdir -p $JUPYTER_CONFIG_DIR
+mkdir -p $JUPYTER_PATH/kernels/ost-kernel
+chmod a+rw -R /usr/local/share/ipython
+chmod a+rw -R $JUPYTER_PATH
+chmod a+rw -R $JUPYTER_CONFIG_DIR
+chmod a+rw -R $JUPYTER_RUNTIME_DIR
+cat > $JUPYTER_PATH/kernels/ost-kernel/kernel.json <<EOF
+{
+ "display_name": "OST",
+ "language": "python",
+ "argv": [
+ "python",
+ "-m", "ipykernel",
+ "-f", "{connection_file}",
+ "--InteractiveShellApp.exec_PYTHONSTARTUP=False",
+ "--InteractiveShellApp.exec_files=['/usr/local/lib64/python2.7/site-packages/ost/ost_startup.py']"
+ ],
+ "env": {
+ }
+}
+EOF
+
+jupyter nbextension enable nglview --py --sys-prefix
+
+# GO HOME AND CLEANUP
+#####################
+apt-get purge -y cmake \
+ wget \
+ git \
+ gfortran \
+ python-pip \
+ libbz2-dev \
+ doxygen \
+ swig
+apt-get clean
+apt-get autoremove -y
+
+cd $SRC_FOLDER && rm -rf $SRC_FOLDER/*
+
+cd /home
+
+%environment
+##############################################################################
+# ENVIRONMENT
+##############################################################################
+export OST_ROOT="/usr/local"
+export OPENSTRUCTURE_VERSION="1.9.0"
+export OPENMM_LIB_PATH=/usr/local/openmm/lib/
+export PYTHONPATH="/usr/local/lib64/python2.7/site-packages:${PYTHONPATH}"
+export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib64:${OPENMM_LIB_PATH}"
+export QT_X11_NO_MITSHM=1
+export IPYTHONDIR="/usr/local/share/ipython"
+export JUPYTER_CONFIG_DIR="/usr/local/etc/jupyter"
+export JUPYTER_PATH="/usr/local/share/jupyter"
+export JUPYTER_RUNTIME_DIR="$JUPYTER_PATH/runtime"
+export VIRTUALENV_DIR="/usr/local/share/ost_venv"
+
+%apprun ChemdictTool
+##############################################################################
+# CHEMDICT TOOL APP
+##############################################################################
+$OST_ROOT/bin/chemdict_tool "$@"
+
+%apprun lDDT
+##############################################################################
+# lDDT APP
+##############################################################################
+$OST_ROOT/bin/lddt "$@"
+
+%apphelp lDDT
+The Local Distance Difference Test.
+
+Usage:
+
+ singularity run --app lDDT <IMAGE> [options] <mod1> [mod1 [mod2]] <re1>[,ref2,ref3]
+
+Options:
+ -s selection performed on ref
+ -c use Calphas only
+ -f perform structural checks and filter input data
+ -t fault tolerant parsing
+ -p <file> use specified parmeter file. Mandatory
+ -v <level> verbosity level (0=results only,1=problems reported, 2=full report)
+ -b <value> tolerance in stddevs for bonds
+ -a <value> tolerance in stddevs for angles
+ -r <value> distance inclusion radius
+ -i <value> sequence separation
+ -e print version
+ -x ignore residue name consistency checks
+
+%apprun Molck
+##############################################################################
+# MOLCK APP
+##############################################################################
+$OST_ROOT/bin/molck "$@"
+
+%apphelp Molck
+This is molck - the molecule checker
+
+Usage:
+ singularity run --app Molck <IMAGE> [options] file1.pdb [file2.pdb [...]]
+
+Options:
+ --complib=path location of the compound library file. If not provided, the
+ following locations are searched in this order:
+ 1. Working directory, 2. OpenStructure standard library location (if the
+ executable is part of a standard OpenStructure installation)
+ --rm=<a>,<b> remove atoms and residues matching some criteria
+ zeroocc - Remove atoms with zero occupancy
+ hyd - Remove hydrogen atoms
+ oxt - Remove terminal oxygens
+ nonstd - Remove all residues not one of the 20 standard amino acids
+ unk - Remove unknown and atoms not following the nomenclature
+ --fix-ele clean up element column
+ --stdout write cleaned file(s) to stdout
+ --out=filename write cleaned file(s) to disk. % characters in the filename are
+ replaced with the basename of the input file without extension.
+ Default: %-molcked.pdb
+ --color=auto|on|off
+ whether output should be colored
+ --map-nonstd maps modified residues back to the parent amino acid, for example
+ MSE -> MET, SEP -> SER.
+
+%apprun OST
+##############################################################################
+# OST APP
+##############################################################################
+$OST_ROOT/bin/ost "$@"
+
+%apphelp OST
+The OST app exposes OpenStructure binary and can be used to run interactive shell
+and scripts.
+
+Usage:
+ singularity run --app OST <IMAGE> [ost options] [script to execute] [script parameters]
+
+Options:
+ -i, --interactive start interpreter interactively (must be first
+ parameter, ignored otherwise)
+ -h, --help show this help message and exit
+ -v VLEVEL, --verbosity_level=VLEVEL
+ sets the verbosity level [default: 2]
+
+If script requires some external files eg. PDBs, they have to be located in the
+path accessible via mounted volumes. By default Singularity mounts $HOME and
+goes to CWD. Thus this sould work as expected out of the box.
+
+
+%appenv IPython
+##############################################################################
+# NOTEBOOK ENV
+##############################################################################
+export DNG_ROOT=$OST_ROOT
+export DNG_INITDIR=${DNG_ROOT}/lib64/python2.7/site-packages/ost
+
+%apprun IPython
+##############################################################################
+# OST IPYTON APP
+##############################################################################
+. $VIRTUALENV_DIR/bin/activate && ipython -i $DNG_INITDIR/ost_startup.py "$@"
+
+%apphelp IPython
+OST-powered iPython shell.
+
+Usage:
+
+ singularity run --app IPython <IMAGE> [options]
+
+Detailed help:
+
+ singularity run --app IPython <IMAGE> --help
+
+%appenv Notebook
+##############################################################################
+# NOTEBOOK ENV
+##############################################################################
+export BIN_DIR=$OST_ROOT/bin
+export XDG_RUNTIME_DIR=""
+. $OST_ROOT/libexec/openstructure/ost_config
+
+%apprun Notebook
+##############################################################################
+# NOTEBOOK APP
+##############################################################################
+. $VIRTUALENV_DIR/bin/activate && jupyter notebook --NotebookApp.iopub_data_rate_limit=10000000 --no-browser "$@"
+
+%apphelp Notebook
+A Jupyter notebook palyground with OST and nglview.
+
+Usage:
+
+ singularity run --app Notebook <IMAGE> [options]
+
+The Jupyter notebook is run by default with `--NotebookApp.iopub_data_rate_limit=10000000`
+and `--no-browser` options.
+
+Useful options when running on remote server:
+ --ip=<Unicode> (NotebookApp.ip)
+ Default: 'localhost'
+ The IP address the notebook server will listen on.
+ --port=<Integer> (NotebookApp.port)
+ Default: 8888
+ The port the notebook server will listen on.
+
+Copy the URL to the browser and launch the notebook with OST kernel. This will
+load all necessary OST components just like in the OST shell. We also enabled
+the nglview widget to interactively view molecular structures and trajectories.
+For more details on how to use nglview see http://nglviewer.org/nglview/latest/.
+
+As the Singularity mounts $HOME by default Jupyter and Ipython config files
+are moved to separate directories. Proper environmental variables are also set.
+In addition, Jupyter is run in a separate virtualenv to not interact with possibly
+installed host version.
+
+To list of all available options:
+
+ singularity run --app Notebook <IMAGE> --help
+
+
+%runscript
+##############################################################################
+# RUNSCRIPT
+##############################################################################
+cat << EOF
+Singularity container for OST $OPENSTRUCTURE_VERSION.
+
+This container includes the following apps:
+ * OST - OpenStructure binary
+ * IPython - OST-powered iPython shell
+ * Notebook - A Jupyter notebook palyground with OST and nglview
+ * lDDT - The Local Distance Difference Test
+ * Molck - Molecular checker
+ * ChemdictTool - Creating or update a compound library
+
+To see the help for each individual app run:
+
+ singularity help --app <APP NAME> <IMAGE NAME>
+EOF
+
+%help
+Singularity container for OST.
+
+This container includes the following apps:
+ * OST - OpenStructure binary
+ * IPython - OST-powered iPython shell
+ * Notebook - A Jupyter notebook palyground with OST and nglview
+ * lDDT - The Local Distance Difference Test
+ * Molck - Molecular checker
+ * ChemdictTool - Creating or update a compound library
+
+To see the help for each individual app run:
+
+ singularity help --app <APP NAME> <IMAGE NAME>
+
+