diff --git a/singularity/README.rst b/singularity/README.rst
index 7dbc72271e821a69dcafaa066a5e8940c4ae45b3..69daf50bce89ee1c4530eea41b33cb74ff853810 100644
--- a/singularity/README.rst
+++ b/singularity/README.rst
@@ -9,7 +9,7 @@ In order to build OST Singularity image:
.. code-block:: bash
cd <OST ROOT>/singularity
- sudo singularity build ost.img Singularity.1.9.0
+ sudo singularity build ost.img Singularity
.. note::
diff --git a/singularity/Singularity.1.10.0 b/singularity/Singularity
similarity index 100%
rename from singularity/Singularity.1.10.0
rename to singularity/Singularity
diff --git a/singularity/Singularity.1.9.0 b/singularity/Singularity.1.9.0
deleted file mode 100644
index c890b6e93a71b4350d48304b6fd4b175fd98b61a..0000000000000000000000000000000000000000
--- a/singularity/Singularity.1.9.0
+++ /dev/null
@@ -1,435 +0,0 @@
-BootStrap: docker
-From: ubuntu:16.04
-
-%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:${PYTHONPATH}"
-# When changing OPENSTRUCTURE_VERSION make sure to change it also in the
-# environment section of singularity recipe (this file).
-export OPENSTRUCTURE_VERSION="1.9.0"
-export OPENSTRUCTURE_SHARE="/usr/local/share/ost"
-export MSMS_VERSION="2.6.1"
-export OPENMM_VERSION="7.1.1"
-export DSSP_VERSION="2.2.1"
-export OPENMM_INCLUDE_PATH=/usr/local/openmm/include/
-export OPENMM_LIB_PATH=/usr/local/openmm/lib/
-export JUPYTER_CONFIG_DIR="/usr/local/etc/jupyter"
-export JUPYTER_PATH="/usr/local/share/jupyter"
-export JUPYTER_RUNTIME_DIR="$JUPYTER_PATH/runtime"
-export VIRTUALENV_DIR="/usr/local/share/ost_venv"
-
-
-# INSTALL SYSTEM DEPS
-#####################
-apt-get update -y && apt-get install -y cmake \
- 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 \
- python-pip \
- tar \
- libbz2-dev \
- doxygen \
- swig \
- clustalw \
- python-virtualenv \
- libsqlite3-dev \
- 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
-
-# COMPILE AND INSTALL DSSP
-##############
-cd ${SRC_FOLDER}
-if [ ! -f dssp-${DSSP_VERSION}.tgz ]; then
- 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
-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>
-
-