Comments (7)
Unfortunately this is breaking cross compatibility with mmtf-python
, which by default dumps everything as 64bit floats (doubles).
The msgpack-python
implementation doesn't support packing a particular field (the transforms) as 64bit floats, and everything else as 32bit floats - see here.
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I have a partial workaround, by making mmtf-python
follow the same decisions as here (all 32bit except the transforms list) - rcsb/mmtf-python#50.
from mmtf-java.
Good catch @zacharyrs ! Thanks for the detailed report.
Changing the RCSB mmtf files is doable but as you say may cause quite some trouble. I like your python workaround as a solution. However, to be consistent the spec would have to officially acknowledge that ncsOperList uses doubles, right?
One important note. MMTF is now is in minimal maintenance mode. The preferred compressed format for PDB data is BinaryCIF.
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Thanks @josemduarte!
Yes, the python solution basically just means both implementations violate the specification in the same way. It avoids the hassle of breaking things.
I didn't realise mmtf
had been dropped to maintenance... I assume BinaryCIF
follows the CIF
spec, it's just encoded?
I recall CIF
not caring about bond information, which was what I liked about mmtf
- I guess I'll have to read into it more.
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I assume BinaryCIF follows the CIF spec, it's just encoded?
Yes, that's correct
I recall CIF not caring about bond information, which was what I liked about mmtf - I guess I'll have to read into it more.
Bond information is available but indirectly via the chemical component dictionary
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Bond information is available but indirectly via the chemical component dictionary
Is that guaranteed for all molecules or is it optional?
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The chemical component dictionary contains all intra-residue bond information. But it is not embedded within the structure BCIF files. We will consider offering the whole chemical component dictionary as one BCIF bundle that should make it more convenient to use.
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Related Issues (18)
- needs a readme.md HOT 1
- API function mapping Chain Index to Entitity info HOT 1
- Reuse ObjectMapper objectMapper = new ObjectMapper(new MessagePackFactory()); HOT 1
- Encoder utils setUpBiojava should return the atom cache HOT 1
- simple alternative needed HOT 22
- GenericEncoder: remove invalid constructor
- Support https HOT 2
- Support loading of reduced structures HOT 1
- How can the version number of the mmtf-java library be accessed programmatically? HOT 4
- Need method to set mmtfProducer HOT 1
- Dead code in DecoderUtils.addEntityInfo
- AdapterToStructureData must be serializable for Spark HOT 1
- Unit test for: testReadFromReducedUrl() fails HOT 1
- ReducedEncoder: DOD not handled as solvent
- Release version 1.0.8 HOT 1
- use https instead of http HOT 1
- Extra residue bonds present in MMTF data from v1.0.9. HOT 2
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