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chainNameList, chainIdList are limited to 4 characters #37
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One idea there: for decoders it should be fairly simple to accept Now for your proposed change this would mean that the encoders would have to become "smarter" and choose an appropriate encoding for the chain names. If there is a reasonable max. chain name length (e.g. <= 4), the binary encoding can be used, and otherwise an The alternative of course is to change the spec to be fixed to All of this is assuming that noone is currently strictly assuming that chain names are fixed at length 4. In terms of implementing it, I can only speak for the rcsb/mmtf-cpp library where I don't see any problem with using chain names/ids of variable length. |
I support having long chain names... but just for the record,
which is sad. |
mmtf-c and simplemmtf-python already supports this. Example: d = simplemmtf.fetch('1rx1')
d._data['chainNameList'] = ['ABCD', 'EFGHIJKL', 'MNOPQRSTUVWXY', 'Z']
open('foo.mmtf', 'wb').write(d.encode()) The file can be loaded into PyMOL, which uses mmtf-c. For the record, no length limitations mentioned here: http://mmcif.wwpdb.org/dictionaries/mmcif_mdb.dic/Items/_atom_site.auth_asym_id.html |
For some use cases longer chain names/Ids are required, e.g., to encode the symmetry operator when creating biological assemblies.
It would be best if the chain names/Ids can have a flexible length.
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