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'.

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, atomobj)
Return atom number of a hydrogen bound to atomobj.

_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

reorderByConnectivity(self, orig_st)
Reorders the atoms by residue numbers.

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.

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, atomobj)

Return atom number of a hydrogen bound to atomobj. 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.

reorderByConnectivity(self, orig_st)

Reorders the atoms by residue numbers. This step is *crucial* as without it this capped protein can not be converted to PDB format.

Apparently pdbconvert can already convert such structures if it is run with -reorder_by_resnum flag (Ev:58331)

Ideally, we should sort by connectivity, and NOT just by residue numbers as we are currently doing.

The current protocol is to separate the added caps from the protein, then sort the resulting structures by residue numbers, merge them into one Structure, and re-create the bonds between fragments and protein.

Class CapTermini

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

findOxygenToReplace(self, st, c_atom)

findHydrogenToReplace(self, st, atomobj)

reorderByConnectivity(self, orig_st)

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