docs: SCHWED-3096 Update docker README

docker/README.rst

 OST Docker
 ==========
 
+.. note::
+
+  In order to run docker commands there might be a need to run them as root (sudo).
+
 Build Docker image
 ------------------
 
@@ -9,7 +13,7 @@ In order to build OST image:
 .. code-block:: bash
 
   cd <OST ROOT>/docker
-  (sudo) docker build --tag <TAG> .
+  docker build --tag <TAG> .
 
 One can chose any tag eg. ost.
 
@@ -20,7 +24,58 @@ In order to run OST script do:
 
 .. code-block:: bash
 
-  (sudo) docker run --rm -v <PATH TO SCRIPT DIR>:/home <IMAGE NAME> /home/<SCRIPT NAME> [OPTIONS]
+  docker run [DOCKER OPTIONS] --rm -v <PATH TO SCRIPT DIR>:/home <IMAGE NAME> /home/<SCRIPT NAME> [SCRIPT OPTIONS]
+
+.. warning::
+
+  If script requires some external files eg. PDBs, they have to be located in the
+  path accessible via mounted volume and should be accessed via docker (NOT LOCAL)
+  path. Eg. assuming that we have a struc.pdb file in /home/user/pdbs directory and
+  a script.py in /home/user we could mount the /home/user to /home in docker as
+  above by specifying -v /home/user:/home. To run the script we thus need to
+  provide the (relative) path to the script and (relative) path to the file eg:
+
+  .. code-block:: bash
+
+    docker run --rm -v /home/user:/home <IMAGE NAME> script.py pdbs/struct.pdb
+
+  or with absolute paths:
+
+  .. code-block:: bash
+
+    docker run --rm -v /home/user:/home <IMAGE NAME> home/script.py /home/pdbs/struct.pdb
+
+One can find a exemplary script (`test_docker.py`) in the <OST ROOT>/docker
+directory. To run it do:
+
+.. code-block::
+
+  cd <OST ROOT>/docker
+  docker run --rm -v <OST ROOT>/docker:/home <IMAGE NAME> test_docker.py
+
+Run script with utility command
+###############################
+
+One can also use provided utility bash script `run_docker_ost` to run basic
+scripts:
+
+.. code-block:: bash
+
+  <OST ROOT>/docker/run_docker_ost <IMAGE_NAME> [<SCRIPT_PATH>] [SCRIPT OPTIONS]
+
+One just needs to provide image name and optionally a script and its options. It
+is useful to link the command to the binary directory eg. in linux:
+
+.. code-block:: bash
+
+  ln -s <OST ROOT>/docker/run_docker_ost /usr/bin/run_docker_ost
+
+In order to run an exemplary script (`test_docker.py`) do:
+
+.. code-block::
+
+  cd <OST ROOT>/docker
+  ./run_docker_ost <IMAGE NAME> test_docker.py
 
 Run GUI
 -------
@@ -30,4 +85,25 @@ In order to run GUI do (tested on linux machine):
 .. code-block:: bash
 
   xhost +local:docker
-  (sudo) docker run -ti --rm -e DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix --entrypoint dng <IMAGE NAME>
+  docker run -ti --rm -e DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix --entrypoint dng <IMAGE NAME>
+
+Running other commands
+----------------------
+
+The default entrypoint of the Docker image is "ost" thus in order to run other
+available commands (or other commands in general) one need to override
+the entrypoint:
+
+.. code-block::
+
+  sudo docker run --rm -ti --entrypoint <COMMAND> <IMAGE NAME> [COMMAND OPTIONS]
+
+Eg. to run molck type:
+
+.. code-block::
+
+  sudo docker run --rm -ti --entrypoint molck <IMAGE NAME> --help
+
+.. note::
+
+  Note how the options to the command are specified after the image name.