schrodinger.protein.captermini module¶
Module for capping uncapped terminal residues in a protein structure by adding NME or ACE caps as appropriate. Also has functionality for adding a C-terminal oxygen in places where this is missing.
Usage for capping: capped_st = cap_termini(input_st)
Usage for adding C-terminal oxygens: capped_st = add_terminal_oxygens(input_st)
Copyright Schrodinger, LLC. All rights reserved.
- schrodinger.protein.captermini.count_atom_hbonds(st, atom)¶
Return the number of hydrogens bonds that the given atom is involved in.
- schrodinger.protein.captermini.res_can_be_capped(res)¶
Determines whether a fragment is able to be capped. Returns CAPN if specified residue can be N-capped, CAPC if C-capped; DONTCAP if it can’t be capped.
- class schrodinger.protein.captermini.CapTermini(st: schrodinger.structure._structure.Structure, verbose: bool = False, frag_min_atoms: int = 150, sample_carboxylate_oxygens: bool = True, logger: logging.Logger = None)¶
Bases:
object- __init__(st: schrodinger.structure._structure.Structure, verbose: bool = False, frag_min_atoms: int = 150, sample_carboxylate_oxygens: bool = True, logger: logging.Logger = None)¶
Add caps to uncapped terminal residues in the input structure ‘st’.
- Parameters
st – Input structure to cap N- and C-termini of
verbose – Generate more stdout. Does not apply if custom logger is specified.
frag_min_atoms – Peptide fragments with less than this number of atoms will not be capped. Set to 0 to cap all fragments.
sample_carboxylate_oxygens – Score carboxylate oxygens based on the number of hydrogen bonds formed to determine NMA attachment point.
logger – A logging.Logger instance used for logging messages within the class. If not provided, a default logger will be used.
- capSequences(st)¶
Cap both ends of each sequence in the given structure.
- outputStructure()¶
- cappedResidues()¶
Returns residue strings for residues that were capped.
- capResidues()¶
Returns residue strings for the added cap residues.
- findOxygenToReplace(st: schrodinger.structure._structure.Structure, c_atom: schrodinger.structure._structure.StructureAtom) Optional[schrodinger.structure._structure.StructureAtom]¶
Check whether c_atom is bound to 2 terminal oxygens. If so, determine which one to replace with a cap, and return its atom index.
Return None if can’t find 2 terminal oxygens.
- adjustDihedral(st, atom1, atom2, atom3, atom4)¶
Adjust dihedral between the original residue and the cap to 0 degrees.
- resCapped(residue, capres)¶
Record this capping in the internal lists.
- attachCap(residue, fromatom, replace_atom, fragname)¶
Attaches the specified fragment and returns the new Residue object
- schrodinger.protein.captermini.cap_termini(st)¶
Cap the termini on the specified st Function interface for CapTermini class
- schrodinger.protein.captermini.add_terminal_oxygens(st, frag_min_atoms=150)¶
Add OXT oxygen to the C-terminal of each poly-peptide chain. A hydrogen will first be added to the residue and converted to an oxygen. The bond length is not adjusted, and a minimization would be in order to fix this.