TransportTools library builds on and extends results of CAVER and AQUA-DUCT analyses to provide comprehensive insights into molecular details of transport processes related to biomolecules.
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Overview

Using the TransportTools engine, end-users can get access to

efficient analyses of molecular tunnels in extensive MD simulations, including those originating from massively parallel calculations or very long simulations,
information on molecular voids in the biomolecules with their actual utilization by small molecules,
rigorous comparison of transport processes in different simulation sets, e.g., contrasting transport in the original system and system perturbed by mutations, different solvents, presence of ligands, etc.

From a programmatic point of view, the library will also help to

simplify custom-made analyses of transport processes, application of various filters on explored molecular voids,
facilitate further development of tools focusing on the study of transport processes by providing a rich environment and interface to the popular packages in the field.

Currently, TransportTools engine can perform its action in 10 consecutive stages:

Preparatory stage including defining transformations needed for unified analyses
Processing of input datasets of tunnel networks
Layering tunnel clusters to get their simplified representation
Computing distances among the layered clusters
Clustering the layered clusters into superclusters and creating initial outputs
Filtering superclusters and creating filtered outputs
Processing datasets of transport events of ligands
Layering transport events to get their simplified representation
Assigning transport events to tunnel networks in superclusters and creating initial outputs
Filtering supercluster with events and creating filtered outputs with events

Note that stages 7-10 depend on the availability of data on transport events from AQUA-DUCT and hence are optional.

Availability

TransportTools is licensed under: GNU GPL v3 license, and the source code is available at github.com.

Installation

TransportTools can be installed either: via CONDA:

if you do not have already, get conda management system
create new environment for transport tools: conda create --name transporttools python=3.8
activate the environment: conda activate transporttools
install TransportTools and all required dependencies: conda install transporttools -c labbit -c conda-forge

or PyPi:

pip install transporttools

Additionally, you might want to install following packages to enhance your experience using TransportTools:

AmberTools to speed-up trajectory processing with pytraj engine; by following these instructions
PyMCubes to enable supercluster visualization with surface: pip install --upgrade PyMCubes
MSMS to speed-up supercluster visualization with the surface

To start using TransportTools type:
tt_engine.py --help

Troubleshooting

If you encounter any problems with installation or the use of TransportTools please contact us at github.com.

Documentation

Documentation can be found at github.com.

References

Funding

The initial development of this library was funded by the National Science Centre, Poland - grant no. 2017/25/B/NZ1/01307 and 2017/26/E/NZ1/00548.