moleculekit.tools.backbone module#

exception moleculekit.tools.backbone.MissingBackboneError#

Bases: Exception

moleculekit.tools.backbone.check_backbone(mol, remove_broken_terminals=True, terminal_min_heavy_atoms=4)#

Checks the backbone of all canonical aminoacids in a Molecule object and adds missing atoms if needed.

If single atoms are missing in the backbone of a residue, they will be reconstructed. If multiple atoms are missing in the backbone of a residue and the residue is at a terminal, the residue will be removed.

Parameters:

  • mol (Molecule) – The molecule to check the backbone of

  • remove_broken_terminals (bool) – Whether to remove residues that are at a terminal and have less than terminal_min_heavy_atoms heavy atoms. Default is True.

  • terminal_min_heavy_atoms (int) – The minimum number of heavy atoms required at a terminal to not be removed.

Returns:

mol – The molecule with the missing backbone atoms added

Return type:

moleculekit.molecule.Molecule

:raises MissingBackboneError : If the molecule has missing backbone atoms that cannot be reconstructed: