schrodinger.protein.captermini.CapTermini

Class CapTermini

Instance Methods

__init__(self, st, verbose=False, frag_min_atoms=150)
Add caps to uncapped terminal residues in the input structure 'st'.

capSequences(self, st, what_to_cap)
Cap either the N or C ends of all sequences of the given structure.

bool

capSequence(self, st, seqi, seq, what_to_cap)
Cap the given Sequence.

outputStructure(self)

cappedResidues(self)
Returns residue strings for residues that were capped.

capResidues(self)
Returns residue strings for the added cap residues.

findOxygenToReplace(self, st, c_atom)
Check whether c_atom is bound to 2 terminal oxygens.

findHydrogenToReplace(self, st, atom)
Return atom number of a hydrogen bound to atom.

_getLowerName(self, residue)
Return resnum & inscode corresponding with the residue that would be lower in sequence than the specified residue.

_getHigherName(self, residue)
Return resnum & inscode corresponding to a residue which would be one higher in sequence than the input residue.

_addCCap(self, residue)
Add a NMA residue to the ' C ' atom of the specified residue

attachCap(self, residue, fromatom, replace_atom, fragname)
Attaches the specified fragment and returns the new Residue object

_addNCap(self, residue)
Add an ACE residue to " N " atom of the specified residue

init(self, st, verbose=False, frag_min_atoms=150)
(Constructor)

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.

capSequence(self, st, seqi, seq, what_to_cap)

Cap the given Sequence.

Parameters:

seqi (int) - The CT for the sequence.
seqi (int) - The index of the sequence
seq (sequence.Sequence object) - Sequence to cap
what_to_cap (int) - Either CAPC or CAPN
st (structure.Structure object)

Returns: bool

True if the sequence was capped, False otherwise.

findOxygenToReplace(self, 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.

findHydrogenToReplace(self, 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.

Class CapTermini

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

capSequence(self, st, seqi, seq, what_to_cap)

findOxygenToReplace(self, st, c_atom)

findHydrogenToReplace(self, st, atom)

init(self, st, verbose=False, frag_min_atoms=150)
(Constructor)