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What is also interesting is that the parser that produces this (found at the above website) appears
to optionally use the pdbx/mmCIF dictionary (in json form) and apply all the type information found
there to produce the correctly-typed arrays that appear in the above example. As far as I know
the wwPDB enforces a strict use of quotes to surround any non-numerical value so such
double-checking is not strictly required.
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Re: mmJSON (CIF-JSON-like format from PDBj)
- Subject: Re: mmJSON (CIF-JSON-like format from PDBj)
- From: James Hester <jamesrhester@xxxxxxxxx>
- Date: Thu, 29 Jun 2017 13:05:01 +1000
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It is interesting to see the different choices made here. As far as I can tell (I couldn't find any formal spec) the values for each data name are put into an array, which are then attached to a data names in an associative array (much like CIF-JSON). The key difference is that these per-loop associative arrays are then attached to category names in a higher-level associative array.
The github site for this project (https://github.com/gjbekker/cif-parsers) has an example: { "data_PDBID": { "pdbx_category1": { "field1": [1, 2, 3, 4], "field2": ["one", "two", "three", "four"], "field3": [1.0, 2.0, 3.0, 4.0] }, "pdbx_category2": { "field1": [1, 2], "field2": ["one", "two"], "field3": [1.0, 2.0] }, "pdbx_category3": { "field1": [1], "field2": ["one"], "field3": [1.0] } } }
What is also interesting is that the parser that produces this (found at the above website) appears
to optionally use the pdbx/mmCIF dictionary (in json form) and apply all the type information found
there to produce the correctly-typed arrays that appear in the above example. As far as I know
the wwPDB enforces a strict use of quotes to surround any non-numerical value so such
double-checking is not strictly required.
On 28 June 2017 at 20:46, Marcin Wojdyr <wojdyr@gmail.com> wrote:
Hi All,
I just came across mmJSON format:
https://pdbj.org/help/mmjson
and just wanted to share it. It's similar to CIF-JSON but tailored for
mmCIF files.
The paper about it says[1]:
An analysis showed that the compressed mmJSON is on average
approximately 33 or 56 % smaller than a compressed mmCIF or PDBML
formatted file, respectively, making it more suitable for web
deployment.
[1] https://jcheminf.springeropen.com/articles/10.1186/s13321- 016-0155-1
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