bwang-ecnu/fxmolviewer

JavaFX based viewer and editor for molecules and proteins with surfaces

FXMolViewer

FXMolViewer is a small project with the original purpose to check, whether JavaFX and its 3D-API may serve as a robust technology to display and manipulate molecules and protein structures interactively in 3D. A particular focus is put on triangle meshes to display opaque and translucent molecular surfaces, which are colored to indicate surface region specific molecular properties or atom types.

Features

• Interactive small molecule/protein viewer supporting wire, ball, stick, ball&stick modes
• PDB-entries can be downloaded, protein surfaces generated and binding site cropped in one step
• An Improved Marching Cubes algorithm creates fast and smooth molecular surfaces
• Visible molecules can be energy-minimized using a MMFF94s+ forcefield
• Entire scene or individual molecules (Ctrl) can be rotated/translated with right/middle mouse button
• Atoms can be selected with lasso selection (left mouse button)
• Front and rear clipping planes are accessible on popup with right mouse click
• Surfaces can be colored by atomic no, polarity, donor/acceptor potential
• Surfaces can be cut smoothly by clipping planes or lasso selection
• A side panel allows to show and hide individual molecules
• The open source ray-tracer SunFlow was built in to render scenes and molecules in high quality

Dependencies

All dependencies are part of this project and can be found in the ./lib folder:

• OpenChemLib: Cheminformatics base functionality to handle molecules and generate conformers
• SunFlow source code and janino.jar: Ray-Tracer to build photo-realistic images of 3-dimensional scenes
• mmtf-all: Java library to download and parse binary structure files from the PDB-database
• controlsfx-8.40.15.jar: Controls extending JavaFX functionality, used for the molecule side panel

How to download the project

git clone https://github.com/thsa/fxmolviewer.git

How to build the project

On Linux or Macintosh just run the 'buildAll' shell script.

How to run the project

After building it double click fxmolviewer.jar or type in a shell: 'java -jar fxmolviewer.jar'. Note that this project requires Java 8. For Java 9 and above you need to replace controlsfx-8.40.15.jar by controlsfx-11.0.0.jar or a newer version.

How to contribute

Contact the author under the e-mail shown on www.openmolecules.org

License

FXMolViewer, showing and manipulating molecules and protein structures in 3D. Copyright (C) 2019 Thomas Sander

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/.