Species in snapshots in kappa format should be sorted

[pirbo]

The order in which species are listed in snapshots is arbitrary. Sorting them may be useful. Question then is "For what sort?" abundance of the species? Size of it? ...? Discussion is opened!

[hmedina]

I can think of two sorts:

• list of complexes in the snapshot
• list of agents within a complex

From what I gather of KaCommandLineSim, it already sorts the complexes by decreasing size, with the largest (measured in number of agents), are first. I consider this fine behavior for the other KaSims.

To sort agents in a complex, I would suggest alphabetical order for the agent name, then for their sites, then for their states (if any). I would consider bonds to be the last element of the alphabetical sort (i.e. first unbound sites, then bound sites).

[feret]

Within complexes, I would prefer a normal form: Depth-first exploration of the spanning tree, starting from the agent that minimize the obtained word (for lexical order).

Le 14 févr. 2017 à 20:38, Hector Medina [email protected] a écrit :

I can think of two sorts:

list of complexes in the snapshot list of agents within a complex From what I gather of KaCommandLineSim, it already sorts the complexes by decreasing size, with the largest (measured in number of agents), are first. I consider this fine behavior for the other KaSims.

To sort agents in a complex, I would suggest alphabetical order for the agent name, then for their sites, then for their states (if any). I would consider bonds to be the last element of the alphabetical sort (i.e. first unbound sites, then bound sites).

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