A small package for making point cloud objects whole in the presence of PBC
Project description
mdvwhole
Density based object completion over PBC. This repository will eventually be merged with MDVoxelSegmentation.
No copies of the box are made to complete the PBC, instead we use a graph based approach. Therefore object completion is very light on memory and can cover an arbitrary amount of consecutive PBC crossings.
How to cite
For now it is best to cite the original MDVoxelSegmentation article with the note that you used the new beta 'Whole' feature.
@article{Bruininks2021,
doi = {10.1021/acs.jctc.1c00446},
url = {https://doi.org/10.1021/acs.jctc.1c00446},
year = {2021},
month = oct,
publisher = {American Chemical Society ({ACS})},
volume = {17},
number = {12},
pages = {7873--7885},
author = {Bart M. H. Bruininks and Albert S. Thie and Paulo C. T. Souza and Tsjerk A. Wassenaar and Shirin Faraji and Siewert J. Marrink},
title = {Sequential Voxel-Based Leaflet Segmentation of Complex Lipid Morphologies},
journal = {Journal of Chemical Theory and Computation}
}
Install
pip install mdvwhole
Usage
Making a single gro whole:
mdvwhole -f your_gro.gro -x your_gro -o whole.gro
Making a trajectory whole:
mdvwhole -f your_gro.gro -x your_xtc -o whole.xtc
Using a non-default selection:
mdvwhole -f your_gro.gro -x your_xtc -o whole.xtc -sel 'not resname W WF ION and not name PO4'
Project details
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.