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

How to download the project

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

How to build the project

JDK8: Make sure your JDK includes JavaFX (e.g. Liberica 8 Full-JDK). Then run the following in a terminal on Linux, Macintosh, or Windows with bash shell support:

./buildAll

JDK11+: Adapt JDKBIN and FXPATH in buildAndRunJDK18 and run

./buildAndRunJDK18

How to run the project

After building the project double click fxmolviewer.jar or type in a shell:

java -jar fxmolviewer.jar

For starting in test-mode, which gives immediate access to test cases as a protein-ligand complex, small molecules, colored surfaces, metal-organics, etc. run

java -Dtest=true -jar fxmolviewer.jar

How to build and run the project with Maven

cd fxmolviewer
mvn clean package
java -jar ./target/fxmolviewer-0.0.1-SNAPSHOT-shaded.jar

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/.