Hello everyone,

I am working with Cytoscape to study the 3D conformations of oligomers. Basically, we perform molecular dynamics simulations and save one snapshot (one conformation, one "3D structure") of the molecule each nanosecond. Then, we can isolate one snapshot of our molecule and create a network where all heavy atoms are nodes. An edge is considered when the distance between two nodes is below a threshold. We can then create a .graph file which contains the list of connected nodes, by pairs. This .graph file is then analyzed with Cytoscape as a network, to see how are connected the different atoms of the molecule.

The thing is, in our molecular dynamics simulations, we have thousands of nanoseconds and thus thousands of snapshots. I would like to know if it would be possible to import all the .graph files at once with the same "import parameters" instead of doing it for each individual file (import, selecting "source nodes", "target nodes"). All the .graph files contain 3 columns: the first one contains the "source nodes" and the second one contains the "target nodes" (the third one can be ignored). Also, the Advanced Options would be the same for all files: space as a delimiter, dot as decimal separator, "Use first line as column names" unchecked. I guess that a simple script could do the job but I have very few knowledge in scripting/programming. If you have any idea of how to automatize it, please let me know, as it would be very tedious to do it manually for thousands of files.

The idea then would be to import all those networks and perform a merging of them all (with the Merge built-in tool). Concerning merging, would you have any additional information about how it is done in more details? The manual does not contain much information about how it works exactly. Is merging indeed a good way to get an "average network"?

Thank you very much in advance for your time and do not hesitate to tell me if there is anything unclear in my question, Best regards,

David.