Neighbour's list

Time to add a neighbour's list to the Measure concept.
A trait class (proposed name: Neighbours) should be written for this purpose.

The collision solver should examine the neighbours list for the persistence of collision pairs.

The current collision solver is too glue-some that once a participant is added, it cannot go unless the whole thing dissociates.

To do on Monday (again)

1) Complete Trajectory::WriteInfo() routine with config information.
2) Complete Trajectory::Read() member for reading traj dirs.
3) Modify biosimzstats, biosimzapp and biosimzlab to adapt changes.
4) Test FileAttached class for path manipulations in BioSimzTest.
5) Test Trajectory in BioSimzTest.
6) Test all file-related functions are working normally.
7) Test CollisionSheet in simulations.

To do (Tuesday on):

8) Modify submission scripts adapting the changes made to trajectory management.
9) Set up simulations for barnase/barstar and ras/effectors.
10) Write code for parsing CollisionSheet into tables/svg graphs.
11) GUI improvement and manuscript preparation.

Also pending:

12) Prepare a figure for Paul's annual report on BioSimz.

!!!!!!!!!!!!!!

To do on Monday

Add event counter system to the collision solver to be able to serialise the binding event history of a trajectory. This is for future expansion on biosimzstats regarding reaction rate calculation.

Further investigation on how to calculate the rate constants (wrt BioSimz) needs to be carried out.

It has been suggested that for known interactions in MolView data plots, the centre-of-mass of the interface residues should be plotted instead of that of the whole protein.

Literature search for the "sticky" nature of protein-protein interactions should be performed.

To do in the evening

To do:

a) modify the variable name m_effDist to m_maxPtl in vdw and hbond forcefields
b) increase the vdw attraction to stabilise dynamic interactions.

Parameters for the OLD vdw settings

min distance: 2.99
attractive scale: 2.3

To do: the desolvation forcefield

Claimed in Camacho's paper it is the major factor, besides electrostatic forces, that governs or helps protein binding, elevating the k-on constant by several orders of magnitude.

Inspired on their implementation I should realise the desolvation forcefield in this way

a) find the surface patches that are less than 4.2A in distance;
b) add the area of the surface to a total value;
c) proportionate this value to energy;
d) find the unit vector of this virtual desolvation force;
e) calculate the force.

Before doing this, a robust reading-from/writing-to-file routine should be written to automate the surface meshing to save computing time/power.

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