Free modeling tool software for linux

Visual Paradigm SDE for JDeveloper is a UML CASE tool/plug-in tightly integrated with JDeveloper. This UML modeling software supports full software lifecycle - analysis, design, implementation, testing and deployment. This UML CASE tool helps you build quality applications faster, better and cheaper. You can draw all types of UML diagrams in JDeveloper, reverse engineer Java code to class diagrams, generate Java code and generate documentation.
SDE-JD Features:
+Support UML version 2.1
+Business Workflow diagram
+Modeling collaboratively with CVS and Subversion (New Feature)
+Support UML2 model through XMI (New Feature)
+Shape editor
+Data flow diagram
+Fast project loading and saving speed
+Use Case Details Editor - An all-in-one environment for specifying a use cases details including general model specification and use case descriptions
+EJB Diagram - Visualize EJB systems.
+EJB Code Generation and Deployment - Generate beans for your application development and deployment.
+ORM support - generate Java objects from database
+Database generation - ERD to database tables
+Database reverse - existing DBMS to ERD
+Reverse engineering - code to model, code to diagram
+Instant Reverse for Java, C++, .NET exe/dll, XML, XML Schema,IDL
+Code Generation - model to code, diagram to code
+Round-trip engineering
+Automatic synchronization between source code and diagrams
+Automatic diagram layout - rearrange shapes and connectors on diagrams in elegant styles
+Import Rational Rose project
+Import XMI/export XMI
+Export diagrams to JPG, PNG, SVG
+Visio Integration - draw UML diagrams with MS Visio stencils
+PDF/HTML Report generator
+Version control
+More...
Other UML Modeling Tools / UML Plugins:
Java Platform (Windows/Linux/Mac OS X):
+SDE for Eclipse
+SDE for Borland JBuilder
+SDE for IntelliJ IDEA
+SDE for NetBeans
+SDE for Sun ONE
+SDE for WebLogic Workshop
Windows Platform:
+SDE for Microsoft Visual Studio
+More SDE...

Major Features:

1. Structure factor calculation and R factor validation
2. Fast fourier transformation for electron density synthesis
3. Reflection data analysis
4. Auto-fit residues side-chain against density data
5. Customize molecular electronic density map contouring
6. Easy to add/delete HOH, hetero atom Group, residue
7. Real 3D Stereo Visualizing Support (need a Quad Buffer Graphic Adapter and a Stereo Glasses)
8. Easy to make a animate stream of molecular model
9. Solid surface creating and electrostatic potential calculation
10. WYSIWYG Labeling method
11. Easy to compare similar structures
12. Auto structure checking and hydrogen atoms adding
13. Predict possible motifs (sites) in the molecule
14. Auto-determinate secondary structures
15. Build related molecules and contacts according to molecular crystallographic symmetries
16. Calculate molecular accessible surface, embedded surface, residue ccessibility
17. Details of Hetero atom interactions in the molecule
18. Details of Hydrogen bonds in the molecule
19. Structure validation and quantify structure on the fly
20. More precise ribbon model representation
21. Novel Cartoon model representation
22. Report many useful information both in text and plots for structure analysis
23. High quality rendering and many types of output (such as TIFF, PNG, BMP, PS)