schrodinger.protein.captermini module

Module for capping uncapped terminal residues in a protein structure by adding NME or ACE caps as appropriate.

Usage: capped_st = cap_termini(input_st)

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.protein.captermini.CapTermini(st, verbose=False, frag_min_atoms=150)

adjustDihedral(st, atom1, atom2, atom3, atom4)

Adjust dihedral between the original residue and the cap to 0 degrees.

attachCap(residue, fromatom, replace_atom, fragname)

Attaches the specified fragment and returns the new Residue object

capResidues()

Returns residue strings for the added cap residues.

capSequences(st)

Cap both ends of each sequence in the given structure.

cappedResidues()

Returns residue strings for residues that were capped.

findHydrogenToReplace(st, atom)

Return atom number of a hydrogen bound to atom. In no hydrogens are present, perform htreat, and return one of the new hydrogens while deleting all other added hydrogens (if more than 1 was added). Return None if can’t find any after adding hydrogens either.

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.

outputStructure()

resCapped(residue, capres)

Record this capping in the internal lists.

schrodinger.protein.captermini.cap_termini(st)

Cap the termini on the specified st Function interface for CapTermini class

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.