mdscan 0.0.3

RMSD-Based HDBSCAN Clustering of Long Molecular Dynamics

MDSCAN

RMSD-Based HDBSCAN Clustering of Long Molecular Dynamics

MDSCAN is a Python command-line interface (CLI) conceived to speed up and significantly lower the RAM memory needs of the HDBSCAN clustering of long Molecular Dynamics.

Installation

There are some easy-to-install dependencies you should have before running MDSCAN. MDTraj (mandatory) will perform the heavy RMSD calculations, while VMD (optional) will help with visualization tasks. The rest of the dependencies (see the requirements.txt file) will be automatically managed while installing MDSCAN.

1. MDTraj

It is recommended that you install MDTraj using conda.

conda install -c conda-forge mdtraj

2. MDSCAN

• Via pip

After successfully installing MDTraj, you can easily install MDSCAN and the rest of its dependencies using pip.

pip install mdscan

• Via GitHub

git clone https://github.com/LQCT/MDScan.git
cd mdscan/
python setup.py install

Then, you should be able to see MDSCAN help by typing in a console:

mdscan -h

3. VMD and VMD clustering plugin (optional)

MDSCAN clusters can be visualized by loading a .log file in VMD via a clustering plugin. Please see this VMD visualization tutorial.

The official site for VMD download and installation can be found here.

Instructions on how to install the clustering plugin of VMD are available here.

Basic Usage

You can display the primary usage of RCDPeaks by typing mdscan -h in the command line.

$ mdscan -h

usage: mdscan -traj trajectory [options]

MDScan: RMSD-Based HDBSCAN Clustering of Long Molecular Dynamics

optional arguments:
  -h, --help            show this help message and exit

Trajectory options:
  -traj trajectory      Path to trajectory file (pdb/dcd) [default: None]
  -top topology         Path to the topology file (psf/pdb)
  -first first_frame    First frame to analyze (start counting from 0) [default: 0]
  -last last_frame      Last frame to analyze (start counting from 0) [default: last frame]
  -stride stride        Stride of frames to analyze [default: 1]
  -sel selection        Atom selection (MDTraj syntax) [default: all]

Clustering options:
  -min_samples k        Number of k nearest neighbors to consider [default: 5]
  -min_clust_size m     Minimum number of points in agrupations to be considered as clusters [default: 5]
  -clust_sel_met {eom,leaf}
                        Method used to select clusters from the condensed tree [default: eom]
  -nsplits NSPLITS      Number of binary splits to perform on the Vantage Point Tree [default: 3]

Output options:
  -odir .               Output directory to store analysis [default: ./]

In the examples folder, you can find a coordinate (pdb) and a trajectory (dcd) files to run an MDSCAN test. Type the next command in the console and check if you can reproduce the content of the examples directory:

mdscan -traj aligned_original_tau_6K.dcd -top aligned_tau.pdb -odir output_dir

Citation (work in-press)

If you make use of MDSCAN in your scientific work, cite it ;)

Licence

MDSCAN is licensed under GNU General Public License v3.0.