Add chain annotation from COMPND and SOURCE records

Overview of New Code/Feature

I have recently been working using this tool, it has been very helpful!

At one point I needed to know, for each of the chains involved in a PDB structure, the source organism it came from. Right now, the ORGANISM_SCIENTIFIC subfield under the SOURCE field is parsed but kept only as an annotation for the whole PDB file; moreover in case of multiple chains existing in a PDB file, one is arbitrarily picked.

I've made changes that allows one to get general meta-information about a chain through the Chain object, such as the name of the molecule, the organism it comes from, etc (basically, information that can be deduced from COMPND and SOURCE records).

Example Code

>>> import atomium
>>> pdb = atomium.fetch("7BWJ.pdb")
>>> pdb.model.chains()
{<Chain E (194 residues)>, <Chain L (213 residues)>, <Chain H (229 residues)>}
>>> pdb.model.chain("E").information
{'mol_id': '1', 'molecule': 'SPIKE PROTEIN S1', 'chain': 'E', 'synonym': 'S GLYCOPROTEIN,E2,PEPLOMER PROTEIN,SARS-COV-2 RECEPTOR BINDING DOMAIN', 'engineered': 'YES', 'organism_scientific': 'SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS 2', 'organism_common': '2019-NCOV', 'organism_taxid': '2697049', 'gene': 'S, 2', 'expression_system': 'SPODOPTERA FRUGIPERDA', 'expression_system_taxid': '7108'}
>>> pdb.model.chain("E").information["organism_scientific"]
'SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS 2'
>>> pdb.model.chain("L").information["organism_scientific"]
'HOMO SAPIENS'
>>> pdb.model.chain("H").information["organism_scientific"]
'HOMO SAPIENS'
>>> pdb.model.chain("H").information
{'mol_id': '3', 'molecule': 'ANTIBODY HEAVY CHAIN', 'chain': 'H', 'engineered': 'YES', 'organism_scientific': 'HOMO SAPIENS', 'organism_taxid': '9606', 'expression_system': 'HOMO SAPIENS', 'expression_system_taxid': '9606', 'expression_system_cell_line': 'HEK 293F'}
>>> pdb.model.chain("H").information["molecule"]
'ANTIBODY HEAVY CHAIN'
>>> pdb.model.chain("E").information["molecule"]
'SPIKE PROTEIN S1'
>>> pdb.model.chain("L").information["molecule"]
'ANTIBODY LIGHT CHAIN'

Checklist

[x] I have read CONTRIBUTING.rst.
[x] I have documented any new functions.
[ ] I have added unit tests for the new code.
[x] I have added an integration test (if appropriate).
[x] I have run all tests.
[ ] I am requesting to merge into the appropriate branch.

samirelanduk / atomium