taskAdun - Tasks: task #5501, DCD and PSF Reading

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task #5501: DCD and PSF Reading

Submitted by:  Michael Johnston <mjohnston>
Submitted on:  Tue Oct 2 11:22:48 2007  
Should Start On: Tue Oct 2 00:00:00 2007Should be Finished on: Fri Feb 1 00:00:00 2008
Category: AdunPriority: 5 - Normal
Status: NonePrivacy: Public
Percent Complete: 0%Assigned to: Michael Johnston <mjohnston>
Open/Closed: OpenPlanned Release: Adun 1.0
Effort: 0.00

Tue Oct 2 11:22:48 2007, original submission:

Adun simulations contain both dcd and psf data so to import a dcd you also must provide a psf.

MDTools, which is what chimera uses, parse dcd and psf files and is in python. However it hasnt seen an official release in 10 years. Then again its included in chimeras distribution and I believe they are maintaining it. Doesn't seem to have any license problems (at least chimera already use and distribute it).

Bio3Di in R parses dcd files and is much more recent (this year) - however no psf support.

There doesnt seem to be any dedicated psf parser library. VMD contains psf and dcd parsing code in C++. But its got a restrictive liscense which probably means we can't take it and it in C++....

Parsing a dcd will basically consist of reading it and writing pdbs for each frame. Then having a separate program to read the back into an Adun simulation.
Psf is more troublesome since we can't easily use python from obj-c. This means the python script will have to write out the psf data in a way that is easily parsable by the obj-c program.
Could embed the python in C but thats probably more trouble then its worth.

In the end the tool can run as a filter service. When every Adun is requested to read a dcd and/or a psf it runs the filter service on the data which returns an AdSimulationData/AdDataSource instance.

Michael Johnston <mjohnston>
Project AdministratorIn charge of this item.


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