This program aims to provide an interactive tool to analyze hydrogen bonds and hydrophobic interactions in crystal structures and Molecular Dynamics (MD) simulations. It is compatible with topology and coordinate file types that are supported by MDAnalysis. The corresponding publication with an examplatory application can be found here.
For Linux and Windows, there are pre-packed binary versions of the program here. If you encounter problems with the binaries, you can also download the source code, install the dependencies and use the bridge2 script to start the program:
IMPORTANT: Deactivate any other virtual environment or conda environment before the installation and before running bridge.
sudo apt-get install libxcb-xinerama0 build-essential python3-dev python3-venv (Ubuntu/Debian)
bash rhel8_dependencies (RHEL8)
sudo dnf install python3-devel (Fedora)
In order to install the required software for Bridge2 to work, we recommend using the Homebrew package manager. The later commands assume it is installed on your system. You can install Homebrew by running the following command in a terminal:
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"
Then install the prerequisites:
xcode-select --install
brew install qt5 python
Install Python3.10 from the Windows App Store.
./bridge2 (Linux, macOS)
bridge2.bat (Windows)
This will create a python virtual environment containing all the necessary packages and start Bridge2 then. If you have any problems with python packages bridge is depending on, please remove the python3env folder to reinstall the virtual environment the next time the bridge script is run.
The usual analysis is split into 4 steps:
After clicking the "New Analysis" icon in the top left menu, the "New Analysis" dialog opens and all parameters for the new analysis, such as the input files and the algorithm of interest, can be set. Bridge2 then computes a portable set of information from the input files that can be saved and opened without the necessity of having the trajectory or structure files. This step is computationally costly and can take a long time for long trajectories. The progress is indicated in the lower left corner. When done, an analysis summary can be saved under the "File" menu. After the graph of interactions (H-bonds, water wires or hydrophobic interactions) becomes visible in the main window, the three tool tabs on the right can be used. They are titled "Layout", "Filters" and "Computations and Plots".
The initial computations can be performed in batches. To run the computations with identical parameters for multiple structures and trajectories, create two text files, one listing the paths to the structure files (one per line), and one listing the corresponding trajectories (all trajectory file paths per structure in one line, separated by a comma). In the file dialogs, those text files can be selected and for every structure, a corresponding bridge analysis file is created.
The "Layout" tab allows for graphical settings such as colors or descriptions for nodes and edges. Here, it is possible to visualize the degree centrality or the betweenness centrality by coloring the nodes respectively. It is generally possible to move nodes by dragging them across the canvas to allow for custom positioning.
In the "Filters" tab several restrictions can be defined to filter for interactions of interest. If a field requests a node name it is always possible to click into that field and then on the node of interest. Here, shortest paths or connected components can be computed or the graph can be reduced to hand-picked nodes of interest.
This tab contains additional computational plugins that aim to produce plots on statistical properties of interactions in MD simulations or to further visualize centrality measures.
Bridge2 can save and reopen an analysis in a .baf file. Those files contain all initial computations results and are independent of the analyzed data files.
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.
Author: Malte Siemers, Freie Universität Berlin
If you use this software or anything it produces for work to be published, please cite:
Malte Siemers, Michalis Lazaratos, Konstantina Karathanou, Federico Guerra, Leonid Brown, and Ana-Nicoleta Bondar. Bridge: A graph-based algorithm to analyze dynamic H-bond networks in membrane proteins, Journal of Chemical Theory and Computation 2019 15 (12) 6781-6798
and
Malte Siemers and Ana-Nicoleta Bondar. Interactive Interface for Graph-Based Analyses of Dynamic H-Bond Networks: Application to Spike Protein S, Journal of Chemical Information and Modeling 2021 61 (6), 2998-3014