Getting Organism information from PDB data
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10 days ago

For example, the Organism feature of the 6HX5 protein is known as Homo sapiens.

I printed the features that I can extract from the pdb data below, but I couldn't find anything related to the Organism feature. How can I do it.

parser = MMCIFParser()
structure = parser.get_structure('6hx5', 'hx/6hx5.cif')

def cleandir(obj):
    print(", ".join([a for a in dir(obj) if not a.startswith("_")]))

cleandir(structure)

Output:

add, atom_to_internal_coordinates, center_of_mass, child_dict, child_list, copy, detach_child, detach_parent, full_id, get_atoms, get_chains, get_full_id, get_id, get_iterator, get_level, get_list, get_models, get_parent, get_residues, has_id, header, id, insert, internal_to_atom_coordinates, level, parent, set_parent, transform, xtra

Briefly, can you share some code that can show that 6HX5 is homo_sapiens?

python biopython pdb protein • 239 views
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Briefly, can you share some code that can show that 6HX5 is homo_sapiens?

Using EntrezDirect:

$ esearch -db protein -query 6HX5 | elink -target taxonomy | esummary | xtract -pattern DocumentSummary -element ScientificName,CommonName
Homo sapiens    human
$ esearch -db protein -query 5Z78 | elink -target taxonomy | esummary | xtract -pattern DocumentSummary -element ScientificName,CommonName
Mus musculus    house mouse
Homo sapiens    human
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My whole project works with Python unfortunately I can't use this solution but it will be useful for other people, thank you.

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