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.


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, verbose=False, frag_min_atoms=150)

Bases: object

__init__(st, verbose=False, frag_min_atoms=150)

Add caps to uncapped terminal residues in the input structure ‘st’. Returns a list of residues capped frag_min_atoms - peptide fragments with less than this number of atoms will not be capped (default 150). Set to 0 to cap all fragments.


Cap both ends of each sequence in the given structure.


Returns residue strings for residues that were capped.


Returns residue strings for the added cap residues.

findOxygenToReplace(st, c_atom)

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


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.

  • st (Structure) – Structure to add oxygens to

  • frag_min_atoms (int) – Minimal atoms required for fragment to be considered a poly-peptide chain


List of capped residues

Return type