qp.structure.convert_nhie_oxo

Convert NHIE active sites to reactive OXO/succinate state.

This module provides specialized functions for converting non-heme iron enzyme (NHIE) active sites from the resting state (with alpha-ketoglutarate and water/NO ligands) to the reactive ferryl-oxo state (with succinate and OXO ligands). This is useful for modeling the reactive intermediate in NHIE catalysis.

Note: This is a specialized module for NHIE enzyme studies and is not part of the standard QuantumPDB workflow.

Functions

add_oxo_sin	Convert an NHIE structure from resting to reactive state.
calculate_dihedral	Calculate the dihedral angle defined by four points.
convert_akg_to_sin	Convert alpha-ketoglutarate (AKG) to succinate (SIN).
find_and_convert_ligands_to_oxo	Convert water or NO ligands near iron to OXO residues.
find_histidines	Find histidine NE2 atoms coordinating an iron center.
place_oxo_manually	Place an OXO ligand opposite the coordinating histidines.
read_pdb	Parse a PDB file and extract all ATOM/HETATM records.
remove_oxo_hydrogens	Remove hydrogen atoms from OXO residues.
update_oxo_sdf	Append OXO entries to the ligand SDF file.
update_sin_sdf	Replace AKG entries with SIN entries in the ligand SDF file.
write_pdb	Write a list of atom dictionaries to a PDB file.