SSAxgeo

This software performs protein Secondary Structure Assignment using differential geometry and knot theory descriptors.

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How to install?

1. Clone the repository:

git clone --recurse-submodules https://github.com/labstructbioinf/SSAxgeo.git
cd SSAxgeo

2. Create and activate conda environment:

conda create -n ssaxgeo python=3.10 "pyarrow>=16,<21" ldc dub -c conda-forge -y
conda activate ssaxgeo

3. Install SSAxgeo:

# Be sure to use pip from the activated conda environment!
pip install -e .

4. Compile diffgeo:

cd diffgeo
dub build --build=release --compiler=ldc2
cd ..

Test the installation

cd test
ssaxgeo -can_dir ../canonical 3tsi_70_91_A.pdb -gen_plots
# For more options see
ssaxgeo -h

Build a Singularity container

sudo singularity build ssaxgeo.sif SingularityFile
singularity exec ssaxgeo.sif ssaxgeo -h