calculate-slice-areas.py creates n slices in z, then calculates a convex hull on each of them, returning the area per slice, per frame.
calculate-slice-distances.py creates n slices in z, then calculates the average distance of each atom/bead/particle of the protein in that slice from the protein center of mass (in that same slice).
calculate_voxel_area.py splits the box into voxels of area -v (in angstrom), and returns the total area of voxels which contain any protein atom/bead. This method can originally be found in the ACS Central Science Paper "Lipid–Protein Interactions Are Unique Fingerprints for Membrane Proteins" by Corradi et al., 2018 doi: 10.1021/acscentsci.8b00143. Please cite the original work as well!
git clone [email protected]:MoMS-MMSB/protein-cross-sections.git
cd protein-geometry
uv venv
source .venv/bin/activate
uv pip install -e .
python calculate-slice-{areas/distances}.py -s ${structure.gro/.tpr} -t ${trajectory.xtc/.trr} -n 100
where -n is the number of slices (default 50), -o specifies the names of the resulting .png and .csv files.
python calculate-voxel-{areas/distances}.py -s ${structure.gro/.tpr} -t ${trajectory.xtc/.trr} -v 3
where -v is the voxel length in angstrom (default 3), -o specifies the names of the resulting .png and .csv files.