forgi.threedee.utilities.modified_res module¶

A module for dealing with modified residues.

For now the only functionality is to find out the corresponding unmodified residue.

class forgi.threedee.utilities.modified_res.ModifiedResidueLookup(query_db=False)[source]¶

Bases: future.types.newobject.newobject

Convenience wrapper to access modified_res_lookup.RESIDUE_DICT. If a key does not exist, query the database to add it.

Parameters:	query_db – If true, query PDBeChem whenever a 3-letter code is not understood.

clean_failed()[source]¶

forgi.threedee.utilities.modified_res.change_residue_id(residue, new_id)[source]¶

forgi.threedee.utilities.modified_res.dict_from_pdbs(filenames)[source]¶

forgi.threedee.utilities.modified_res.query_PDBeChem(three_letter_code)[source]¶

Query the PDBeChem and return a dictionary with key-value pairs.

Unfortunately, this information does not seem to be provided in any machine-readable format. We have to parse the html.

forgi.threedee.utilities.modified_res.to_4_letter_alphabeth(chain, query_db=False)[source]¶

Rename the modified residues so that they have the same names as unmodified residues.

If a residue’s name is unknown, query PDBeChem.

If the residue is not a ribonucleotide, remove it from the chain.

If it is a modified ribonucleotde, replace it by the unmodified “standard parent”

Parameters:	chain – A Bio.PDB.Chain structure query_db – If true, query PDBeChem whenever a 3-letter code is unknown.
Returns:	The same chain, but with only AUGC residues.