coaler

For examples see the paper

Core Aligner

Building locally

To build the project locally, you need to have a valid GCC installation as well as python (>3.10 with venv support) installed. You can build the project with the following commands:

./confgiure
make
sudo make install

The configure script will create a virtual environment in the venv directory and install the conan package manager. The make targets will use conan to build the project. The binary will be installed to /usr/local/bin/coaler. You might have to add /usr/local/bin to your PATH variable.

Building Containerized

If you want to use Podman to run the application, you can use the following command:

make container

This will build an container image with the name coaler:latest. You can run the container with the following command:

./run.sh

The script will mount the current directory to your PWD in the container and run the application passing all arguments to it.

Setup Clion

In the output of conan build you should get an output containing lines like this:

======== Calling build() ========
conanfile.py (aligner/0.0.1): Calling build()
conanfile.py (aligner/0.0.1): Running CMake.configure()
conanfile.py (aligner/0.0.1): RUN: cmake -G "Unix Makefiles" -DCMAKE_TOOLCHAIN_FILE="/home/niklas/projects/uni/coaler/build/Debug/generators/conan_toolchain.cmake" -DCMAKE_INSTALL_PREFIX="/home/niklas/projects/uni/coaler" -DCMAKE_POLICY_DEFAULT_CMP0091="NEW" -DCMAKE_BUILD_TYPE="Debug" "/home/niklas/projects/uni/coaler"

Copy this part (it will be different for on your PC):

-DCMAKE_TOOLCHAIN_FILE="/home/niklas/projects/uni/coaler/build/Debug/generators/conan_toolchain.cmake" -DCMAKE_INSTALL_PREFIX="/home/niklas/projects/uni/coaler" `

1. Open your Project in Clion and tell it that it is a CMake project
2. In Clion Goto Settings->Build,Execution...->CMAKE and add the thing you just copied to CMake Options.
3. Change "Build directory" from cmake-build-debug to build (Conan uses this one)
4. You'll get a CMake plugin tab in your plugins -> Run "Reload CMake"
5. If your build worked, this should work without error.

Now you should be able to see the RDKit headers you linked under External Libraries -> Header Search Paths -> include