MesoRD Code

Molecule tracking successfully runs with two compartments.

When a mature molecule moves to another compartment and the diffusion constant is different in the new compartment, then this event is added to reactions.txt

Updated some of the test files.

Ran the tests, everything ran successfully.

Fixed a bug where dead molecules were still printed in the first line of trajectories.txt

The id of the first molecule created is now 1 instead of 0 in order to facilitate the processing of output files by Matlab.

The name of the fluorescent maturation reaction is now "maturation" instead of "fluorescence".

The path to config.h file was modified from:

../config.h

to

../../config.h

Now the trackingTimeStep and trackingTimeInit for molecule tracking are options that can be set in the command line with:

-w : set the tracking time step, i.e how often you want the trajectories to be updated (seconds)

-x: set the tracking initial time, i.e when should the outputs (reactions.txt and trajectories.txt) start being updated. (seconds)

The letters are maybe ill-chosen but there are not so many available anymore, so I picked consecutive letters.

The reactions.txt and trajectories.txt are now only updated after the time defined by tracking_time_init (in seconds) to only print out the reactions and the trajectories once the system is stable.

trajectories.txt does not print out a molecule once it disappeared (previously it printed the last position of the known molecule, ie where it died).

Fixed a bug reagrding the number of reactants when one species turns into another (A->B).

Fixed compilation issues on Linux. Inlcude paths and configure script changes

bootstrap and Makefile (root folder) have Unix style end of line.

Fixed a bug regarding the number of reactants in a subvolume (incremented for the molecule tracker after a destruction event).

First working version of the molecule tracking addition to MesoRD. To activate it, set HAVE_MOLECULE_TRACKING to 1.

Reactions where 2 or more reactants have a fluorophore are not supported.

When a reaction with more than one product happens, then the product which should inherit the fluorophore has to be the first in the list of products in the xml file.

The binary folder should not be in here. My mistake.