mdvwhole 0.0.7.1

A small package for making point cloud objects whole in the presence of PBC

mdvwhole

Density based object completion over all 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. The contact distance is based on the voxel resolution (26 neighbors).

Version

0.0.7.1 This version is safe to use for production.

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

Make sure you are installing for python 3.8 or newer.

pip install mdvwhole

Or clone this repository for the latest beta features and install using pip from inside the cloned folder.

pip install -e .

Usage

Print help:

mdvwhole -h

Making a single gro whole:

mdvwhole -f your_gro.gro

Making a single gro whole and also complete single molecules:

mdvwhole -f your_tpr.tpr -x your_gro.gro -mol True -o whole.gro

Making a trajectory whole:

mdvwhole -f your_gro.gro -x your_xtc.xtc -o whole.xtc

Making a trajectory whole and also complete single molecules:

mdvwhole -f your_tpr.tpr -x your_xtc.xtc -mol True -o whole.xtc

Using a non-default selection:

mdvwhole -f your_gro.gro -x your_xtc.xtc -o whole.xtc -sel 'not resname W WF ION and not name PO4'

Using multiple selections to make whole:

mdvwhole -f your_gro.gro -x your_xtc.xtc -o whole.xtc -sel 'resname POPC; not resname W WF ION POPC'

Writing all atoms even if they were not included in a selection:

mdvwhole -f your_gro.gro -x your_xtc.xtc -o whole.xtc -sel 'not resname W WF ION' -wa True

Using an mdvoxelsegmentation 'clusters.npy' to make whole (can also be used without whole molecules and on a single gro).

mdvwhole -f your_tpr.tpr -x your_xtc.xtc -o whole.xtc -wa True -mol True -clus your_clusters.npy

https://user-images.githubusercontent.com/1488903/177659765-98287099-5619-4e45-b890-1de573437347.mp4

Using associative mdvwhole, a subselection of a molecules can be used for the selection. The displacement of the subselection is projected on the whole molecules:

mdvwhole -f your_tpr.tpr -x your_xtc.xtc -o whole.xtc -sel 'name C3A C3B D3A D3B C4A C4B D4A D4B' -res 0.7 -wa True -mol True -asso True

https://user-images.githubusercontent.com/1488903/177778628-ca61c694-fdd6-45f0-af78-644d63db9fe8.mp4

Sneak peak at new feature, the aggregate shaped tile

https://user-images.githubusercontent.com/1488903/184648757-35735f05-bc7f-483e-b789-a74b834a1b6b.mp4

https://user-images.githubusercontent.com/1488903/185187491-0ba19d6e-cac3-460d-a97e-b1752060c050.mp4

https://user-images.githubusercontent.com/1488903/187438795-b5148b0d-f3de-4a4a-8f82-c45fbfb1b827.mp4