protein-cross-sections
various tools for calculating protein geometries across trajectories
Science Score: 49.0%
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Repository
various tools for calculating protein geometries across trajectories
Basic Info
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 1
Metadata Files
README.md
small tools for calculating protein geometries
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!
Install:
git clone git@github.com:MoMS-MMSB/protein-cross-sections.git
cd protein-geometry
uv venv
source .venv/bin/activate
uv pip install -e .
Usage:
Calculation by slices
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.
Calculation by voxels
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.
Owner
- Name: MoMS-MMSB
- Login: MoMS-MMSB
- Kind: organization
- Repositories: 1
- Profile: https://github.com/MoMS-MMSB
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Last Year
- Push event: 3
Dependencies
- matplotlib >=3.9.2
- mdanalysis >=2.7.0
- numpy >=1.26.4
- matplotlib >=3.9.2
- mdanalysis >=2.7.0
- numpy >=1.26.4