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.

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, 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.

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, 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(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.

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

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.protein.captermini', '__init__': <function CapTermini.__init__>, 'capSequences': <function CapTermini.capSequences>, 'outputStructure': <function CapTermini.outputStructure>, 'cappedResidues': <function CapTermini.cappedResidues>, 'capResidues': <function CapTermini.capResidues>, 'findOxygenToReplace': <function CapTermini.findOxygenToReplace>, 'findHydrogenToReplace': <function CapTermini.findHydrogenToReplace>, '_getLowerName': <function CapTermini._getLowerName>, '_getHigherName': <function CapTermini._getHigherName>, '_addCCap': <function CapTermini._addCCap>, 'adjustDihedral': <function CapTermini.adjustDihedral>, 'resCapped': <function CapTermini.resCapped>, 'attachCap': <function CapTermini.attachCap>, '_addNCap': <function CapTermini._addNCap>, '__dict__': <attribute '__dict__' of 'CapTermini' objects>, '__weakref__': <attribute '__weakref__' of 'CapTermini' objects>, '__doc__': None})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.protein.captermini'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

schrodinger.protein.captermini.cap_termini(st)

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