download zipped program

MolView

Exploratory 3D Molecule Viewer

Douglas Cameron
www.AlphaSquared.com


Arginine potential energy surface MolView is a free 3D molecule viewer that demonstrates the numerical and graphical capabilities of the AlphaSquared libraries. Similar capabilities can be readily built into specialized applications for molecular modeling and dynamics or the interactive viewing of any three dimensional object.

The library is concise and self contained. Its only dependencies are on the C++ Standard Library and the operating system platform for bitmap addressing and rectangular clipping.


This program is freely available as a simple demonstration
of the development capabilities of
AlphaSquared.com 

Specializing in writing high quality software for mathematical and scientific applications. Including software for any field that pushes the technological boundaries of speed and complexity.

Douglas B. Cameron


The complete program is available here as a zipped file. It is a small program that runs on any Windows (95/98/NT/XP) platform. Download it from the link above and unzip it into any directory. Included with it are a few sample input files for visualization.

The program makes no modifications to your files nor does it use the system registry. Simply deleting its files will remove all traces of it from your system. (more info on downloading)

The main C++ file is available here MolView.cpp for those who are interested.

ProgImage.jpg (38516 bytes)


Thyroliberin potential energy surface
Force field around a small molecule
drawn with a fine grid.

 

The MolView demonstration program:

  • handles 2-1,000,000 atoms
  • draws ball-and-stick models
  • interactively rotates and zooms
  • draws grids or shaded energy surfaces
  • presents stereographic projections for red-green glasses

 

Telomere DNA fragment
Ball-and-stick model of a small section of human (telomere) DNA.

c70movie.gif (89054 bytes)
A highly symmetric molecule of
70 carbon atoms - C70
(click stop in browser to halt)


 

Surface of a molecule - drawn for red-green glasses
Surface of a molecule - drawn for red-green glasses

Running the program

Upon starting MolView it will request a sample geometry (*.geo) file to open. Select one of the smaller example files for the first run. Two windows will then open up: a primary graphical interface and a simple console window with a few bits of additional information.

 

standard view Standard View: The initial graphic window shows a ball-and-stick model of the molecule. This view is fast and handles large molecules easily.
volume.gif (5043 bytes) Surface View: Activating the volume view from the Views selector opens a second panel that can draw the molecular surface with a space filling view. This view is closer to reality but a bit slower to manipulate.

All panels can be easily zoomed (small blue icon), moved (with the right mouse button) and stretched (control- right mouse button). More information on the graphical user interface is here.


File formats

Geo file format: This is a simple text format that can easily be extracted from other common molecular geometry file formats. Examples are included in the zipped file above. The format is simply this:

Hemoglobin by x-ray diffraction First line is a comment line.
1.65 Second line is the maximum bond length. Atoms closer than this are considered bonded.
H  1.0654  1.0654  1.0654 <atom name or atomic #> x y z coordinates
C  2.0123  2.0123  2.0123 continue for every atom in molecule
O  0.9876  0.9876  0.9876  
...  
   

Filters for a few common file formats (e.g. PBD from Protein Data Bank) are available on request.


Security Concerns

Due to the poor security in Microsoft's operating systems it is generally not a good idea to execute an untrusted application. We look forward to the day when safe 'sandboxes' are available on Windows and hope that Microsoft's new .Net begins to achieve this. That being said, we can only offer our assurance that this program is in no way malicious. It reads only the requested file and is not capable of writing any files. It also has no interaction with any network ports. If it is of any consolation here is the main C++ file: MolView.cpp. We would be glad to answer any further questions and, if asked, would show you the rest of the source code as well.


 

 

 

Related links:

Geometric Tools for Computer Graphics, Philip J. Schneider, David H. Eberly (book)

The Visualization ToolKit (VTK) is a C++ open source 3D graphics and visualization library.