Merge branch 'master' into develop

CMakeLists.txt

@@ -34,8 +34,8 @@ endif()
 project(OpenStructure CXX C)
 set (CMAKE_EXPORT_COMPILE_COMMANDS 1)
 set (OST_VERSION_MAJOR 2)
-set (OST_VERSION_MINOR 9)
-set (OST_VERSION_PATCH 3)
+set (OST_VERSION_MINOR 10)
+set (OST_VERSION_PATCH 0)
 set (OST_VERSION_STRING ${OST_VERSION_MAJOR}.${OST_VERSION_MINOR}.${OST_VERSION_PATCH} )
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR}/cmake_support)
 include(OST)

README.md

@@ -21,20 +21,59 @@ making deployment easier. Deploying a docker image just needs a
 docker pull which typically finishes in about a minute depending
 on your local hardware and internet connection. Singularity
 containers bootstrap from the docker container but must be built
-by the user. Detailed instructions can be found here:
+by the user. 
 
-* Docker: [OpenStructure Docker Instructions](https://git.scicore.unibas.ch/schwede/openstructure/tree/master/docker)
-* Singularity: [OpenStructure Singularity Instructions](https://git.scicore.unibas.ch/schwede/openstructure/tree/master/singularity)
+### Docker
+
+For complete documentation on using Docker with OpenStructure, 
+[click here](https://git.scicore.unibas.ch/schwede/openstructure/tree/master/docker).
+This section provides a quick-start guide to help you get OpenStructure up and running using Docker.
+Most docker installations require you to add `sudo` in front of the docker commands.
+
+Get the latest Docker image from the OpenStructure registry:
+
+```
+docker pull registry.scicore.unibas.ch/schwede/openstructure:latest
+```
+
+And run a test script:
+
+```
+echo print\(\"Hello OST\"\) > test.py
+docker run --rm -v $(pwd):/home registry.scicore.unibas.ch/schwede/openstructure:latest test.py
+```
+### Singularity
+
+For complete documentation on using Singularity with OpenStructure, 
+[click here](https://git.scicore.unibas.ch/schwede/openstructure/tree/master/singularity).
+This section provides a quick-start guide to help you get OpenStructure up and running using Singularity.
+
+Building the singularity container requires root permissions:
+
+```
+wget https://git.scicore.unibas.ch/schwede/openstructure/-/raw/master/singularity/Singularity
+sudo singularity build ost.img Singularity
+```
+
+And run a test script:
+
+```
+echo print\(\"Hello OST\"\) > test.py
+singularity run --app OST ost.img test.py
+```
+
+### Build from source
 
 OpenStructure is developed and tested across various Linux distributions.
-You can find detailed build instructions and a list of required dependencies here:
-https://openstructure.org/docs/install/
+You can find [detailed build instructions and a list of required dependencies
+in the online documentation](https://openstructure.org/docs/install/).
 
 ## Getting started
 
-The installation and container instructions will help you set up
-OpenStructure for scripting. Additionally, here are some advanced
-use cases worth highlighting.
+Once you have OpenStructure installed, check out the [online
+documentation](https://openstructure.org/docs/).
+
+Additionally, here are some advanced use cases worth highlighting.
 
 ### Benchmarking and Scoring
 

docker/Dockerfile

@@ -2,7 +2,7 @@ FROM ubuntu:22.04
 
 # ARGUMENTS
 ###########
-ARG OPENSTRUCTURE_VERSION="2.9.2"
+ARG OPENSTRUCTURE_VERSION="2.10.0"
 ARG SRC_FOLDER="/usr/local/src"
 ARG CPUS_FOR_MAKE=2
 

examples/scoring/README.md

@@ -8,21 +8,32 @@ OpenStructure provides "actions" for general benchmarking use cases.
 * **compare-ligand-structures**: Focuses on comparisons of interactions between
   polymer entities and non-polymer entities, i.e. small molecule ligands
   
+# Before doing any scoring
+Pull example data from the repository:
+
+```
+wget https://git.scicore.unibas.ch/schwede/openstructure/-/archive/master/openstructure-master.zip?path=examples/scoring -O example.zip
+unzip -j example.zip
+```
+
+# Run the examples
+
 The example commands here assume an OpenStructure installation
-(compile instructions: https://openstructure.org/docs/install/). 
+([compile instructions](https://openstructure.org/docs/install/)).
 Running the computations in containers provide a considerably easier setup than
 compiling OpenStructure from source. Instructions for setup and running
-equivalent computations are available for
+equivalent computations are available below for
 
 * [Docker](#docker)
 * [Singularity](#singularity)
 
 A detailed list of options can be found in the
 [action documentation](https://openstructure.org/docs/actions/).
-Alternatively, the command
+Alternatively, the commands
 
 ```
-ost <ACTION> -h
+ost compare-structures -h
+ost compare-ligand-structures -h
 ```
 
 will list all available options of the respective action. Both actions compute
@@ -34,9 +45,11 @@ default output (out.json):
 ost compare-structures -m model.pdb -r reference.cif.gz --lddt --local-lddt --qs-score
 ```
 
-Results should be computed within seconds and example output can be found
-[here](compare-structures_example_out.json). We refer to the action
-documentation for in-depth description of the provided data items.
+Results should be computed within seconds and saved in the `out.json` file
+([see example output](compare-structures_example_out.json)). We refer to the
+[action documentation](https://openstructure.org/docs/actions/) for in-depth
+description of the provided data items and description of optional flags that
+compute additional scores.
 
 By default, model-reference chains are aligned using Needleman-Wunsch.
 Many benchmarking efforts such as CASP and CAMEO assume residue numbers
@@ -55,9 +68,10 @@ We can compute LDDT-PLI and BiSyRMSD with:
 ost compare-ligand-structures -m model.pdb -r reference.cif.gz -ml *.sdf --rmsd --lddt-pli
 ```
 
-Results should be computed within seconds and example output can be found
-[here](compare-ligand-structures_example_out.json). We refer to the action
-documentation for in-depth description of the provided data items.
+Results should be computed within seconds and saved in the `out.json` file
+([See example output ](compare-ligand-structures_example_out.json)). We refer
+to the action documentation for in-depth description of the provided data
+items.
 
 Again, it is advised to use the `-rna` flag if applicable. In this example,
 reference ligands are directly extracted from the provided mmCIF file based on
@@ -66,8 +80,9 @@ This only works in case of mmCIF input AND if the respective ligand is in the
 PDB component dictionary which defines connectivity (matching based on compound
 name).
 Container solutions come with such a dictionary which has been created at build
-time. Check the Docker/Singularity instructions linked above on how to set the
-latest dictionary, i.e. "Compound Library".
+time. Check the detailed
+[Docker](https://git.scicore.unibas.ch/schwede/openstructure/tree/master/docker)/[Singularity](https://git.scicore.unibas.ch/schwede/openstructure/tree/master/singularity)
+instructions on how to set the latest dictionary, i.e. "Compound Library".
 You can override automatic extraction by providing SDF files with ligand
 coordinates and connectivity information. If the receptor is provided in
 PDB format, ligands must be provided in SDF format.
@@ -77,18 +92,17 @@ PDB format, ligands must be provided in SDF format.
 For complete documentation on using Docker with OpenStructure, 
 [click here](https://git.scicore.unibas.ch/schwede/openstructure/tree/master/docker).
 This section provides a quick-start guide to help you get up and running with scoring using Docker.
-Most docker installations require you to add `sudo` in front of the following commands.
 
 Get the latest Docker image from the OpenStructure registry:
 
 ```
-docker pull registry.scicore.unibas.ch/schwede/openstructure:latest
+sudo docker pull registry.scicore.unibas.ch/schwede/openstructure:latest
 ```
 
 run one of the scoring examples, other examples need to be adapted accordingly:
 
 ```
-docker run --rm -v $(pwd):/home registry.scicore.unibas.ch/schwede/openstructure:latest compare-structures -m model.pdb -r reference.cif.gz --lddt --local-lddt --qs-score
+sudo docker run --rm -v $(pwd):/home registry.scicore.unibas.ch/schwede/openstructure:latest compare-structures -m model.pdb -r reference.cif.gz --lddt --local-lddt --qs-score
 ```
 
 # Singularity
@@ -100,7 +114,7 @@ This section provides a quick-start guide to help you get up and running with sc
 Building the singularity container requires root permissions:
 
 ```
-cd <OST_ROOT>/singularity
+wget https://git.scicore.unibas.ch/schwede/openstructure/-/raw/master/singularity/Singularity
 sudo singularity build ost.img Singularity
 ```
 
@@ -109,5 +123,3 @@ run one of the scoring examples, other examples need to be adapted accordingly:
 ```
 singularity run --app OST ost.img compare-structures  -m model.pdb -r reference.cif.gz --lddt --local-lddt --qs-score
 ```
-
-

singularity/Singularity

 BootStrap: docker
-From: registry.scicore.unibas.ch/schwede/openstructure:2.9.2
+From: registry.scicore.unibas.ch/schwede/openstructure:2.10.0
 %post
 ##############################################################################
 # POST