To do list

1. Mark the low-RMSD points
(a) Get the correct Complex object
(b) Push the target pair into a container
(c) Use DockChecker to get RMSD
(d) If it falls within threshold, then mark it with a special colour
2. Research into the BSP tree and other collision facet-detection algorithms
3. Designing the interface to fire up more runs

Revision 1000

I set up the BioSimz project on SourceForge in March 2007.
Till just now the repository has accumulated 1000 revisions.

Cont'd 2

The real problem turned to be a bug in the MemPool of which the initialisation with 0 size shall not be allowed. The bug has been rectified and thus the previous statements are no longer valid.

However, there are serious stability issues (seg faults/mem violations) whenever something is pushed into the m_objVis container in the WnMolView class, regardless of the container's type.

Cont'd

Maybe it's not the general container's problem. It looks as if the GLTextList class cannot survive a copy construction -- most probably because of the copy construction of LinkedList<>.

Default copy constructors

Do not rely on compiler-generated copy constructors for objects which have container members such as Container<>, LinkedList<>. The copy constructors of those containers have unsafe copy routines, at the benefit of type-tolerance, that could result in memory violations.

Further improvements can be made to introduce an internal push_back() operation that is strictly typed (non-templated) to eliminate this imcompatibility.

Versions

Last stable version without molecular paths: rev 985.
New code for molecular paths (unfinished): rev 986/987.

The (finally coming) MolView in BioSimzLab

Feature/task list

• Have the MolInfo window fully linked to MolView, including triggering launch of the MolView window, as well as identifying existing ones.
• The MolView should have central QGLViewer widget like the SimReplay one without the tool bar for play control. Instead it should have 3 small QGLViewer widgets aligned to the top right of the window providing views for x-y, y-z, and x-z planes
• A list with selection boxes/or "*" marks should be placed beneath the 3 small GL widgets. It is a list of all the data layers plotted in the view, including the molecular surface, any traces/paths, etc. Double-clicking each items should toggle the display of that layer on/off.