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The type spec:
ProteinStructureUtils/KBaseStructure.spec
Lines 49 to 56 in 0582b51
| typedef structure { | |
| mol_id id; | |
| string sequence; | |
| string md5; | |
| uniref_id uniref_id; | |
| genome_ref genome_ref; | |
| cds_id cds_id; | |
| } ProteinData; |
The usage:
ProteinStructureUtils/lib/ProteinStructureUtils/Utils/PDBUtils.py
Lines 66 to 82 in 0582b51
| for pp in ppb.build_peptides(structure): | |
| pp_no += 1 | |
| my_seq= pp.get_sequence() | |
| pp_list += str(my_seq) | |
| seq = ''.join(pp_list) | |
| data = { | |
| 'name': os.path.basename(file_path), | |
| 'num_chains': chain_no, | |
| 'num_residues': res_no, | |
| 'num_atoms': atom_no, | |
| 'protein': { | |
| 'id': os.path.basename(file_path), | |
| 'sequence': seq, | |
| 'md5': hashlib.md5(seq.encode()).hexdigest() | |
| }, | |
| } |
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