molsysmt.build.get_missing_residues#

molsysmt.build.get_missing_residues(molecular_system, sequence=None, selection='all', syntax='MolSysMT', engine='MolSysMT')[source]#

Identify residues that are missing from a molecular system relative to a reference sequence.

This function compares the residues present in the molecular system against a reference sequence and returns a mapping of insertion positions to the names of the residues that are absent.

Parameters:

  • molecular_system (molecular system) – Molecular system in any supported MolSysMT format.

  • sequence (object, default=None) – Argument sequence.

  • selection (str, list, tuple, or numpy.ndarray, default='all') – Selection string or boolean/integer array specifying elements.

  • syntax (str, default='MolSysMT') – Selection syntax used to evaluate selection (e.g., ‘MolSysMT’, ‘MDTraj’).

  • engine (object, default='MolSysMT') – Argument engine.

Returns:

Dictionary mapping (chain_index, insertion_position) tuples to lists of residue names (str). chain_index is the 0-based index of the chain in the (sub)system; insertion_position is the 0-based index within that chain’s structural sequence before which the missing residues should be inserted. For insertions after the last residue of a chain the insertion_position equals the number of residues in that chain.

Return type:

dict

Raises:

NotImplementedMethodError – Raised if the requested engine is not supported.

Notes

engine=’MolSysMT’ limitations: Only amino-acid and nucleotide chains with a detectable reference sequence are analysed. Non-standard residues in the reference that are absent from the structure will be reported as missing; non-standard residues present in the structure but absent from the reference will be silently ignored.

Post-1.0 roadmap: When sequence=None and the molecular system has no embedded sequence information, a future version will optionally query UniProt or the PDB REST API using the entity name or PDB ID.

Added in version 1.0.0.

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