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Author Topic: JSON or similar machine-readable output for 3DNA  (Read 744 times)

Offline jms89

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JSON or similar machine-readable output for 3DNA
« on: September 24, 2016, 05:30:01 pm »
Hello, it would be great to have a machine-readable output for 3DNA and indeed all the software tools in the 3DNA suite. If such an option were present, it would also be great to be able to suppress other output files.

Currently, it's very annoying to parse the 3DNA ouput files, and slight changes in the ouput format from version 2.1 to 2.3 may break scripts to do so. A machine readable format would solve this and give 3DNA a big advantage over competitors in my mind.

Offline xiangjun

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Re: JSON or similar machine-readable output for 3DNA
« Reply #1 on: September 24, 2016, 06:20:51 pm »
Hi,

Thanks for your request for a machine-readable output for 3DNA v2.x. I fully understand your point. Indeed, a JSON output also allows me freedom to change the human-readable file as necessary, as illustrated in DSSR.

Now for the 3DNA 2.x series, the current (stable) version is v2.3. Except for a new section on "simple" parameters, v2.3 has the same output format as v2.1. So it should not take much effort to revise your parser script for v2.3. Moreover, the v2.3-2016sept06 release also includes the C source code so users can make direct changes as they see fit. See my blogpost "3DNA C source code is available". At this stage, I'd decided to support 3DNA 2.3 in "maintenance" mode. No more new features, but I'd still fix any identified bugs.

As I mentioned in several other occasions, DSSR is a representative of what'd constitute 3DNA v3, which has a completely new code base. DSSR has already incorporated find_pair, some features of analyze, frame_mol, rotate_mol, and blocview etc. In due time, I will incorporate all key features of analyze into DSSR. I welcome users' comments in this endeavor. Do you have anything specific in 3DNA 2.3 you'd like a JSON output?

Best regards,

Xiang-Jun
« Last Edit: September 24, 2016, 07:28:59 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.