Source code for prody.atomic.selection

# -*- coding: utf-8 -*-
"""This module defines :class:`Selection` class for handling arbitrary subsets
of atom."""

from .subset import AtomSubset

__all__ = ['Selection']


ellipsis = lambda s: s[:15] + '...' + s[-15:] if len(s) > 33 else s

[docs]class Selection(AtomSubset): """A class for accessing and manipulating attributes of selection of atoms in an :class:`.AtomGroup` instance. Instances can be generated using :meth:`` method. Following built-in functions are customized for this class: * :func:`len` returns the number of selected atoms * :func:`iter` yields :class:`.Atom` instances""" __slots__ = ['_ag', '_indices', '_acsi', '_selstr'] def __init__(self, ag, indices, selstr, acsi=None, **kwargs): kwargs['selstr'] = selstr AtomSubset.__init__(self, ag, indices, acsi, **kwargs) def __repr__(self): n_csets = self._ag.numCoordsets() selstr = ellipsis(self._selstr) if n_csets: if n_csets == 1: return ('<Selection: {0} from {1} ({2} atoms)>' ).format(repr(selstr), self._ag.getTitle(), len(self)) else: return ('<Selection: {0} from {1} ({2} atoms; ' 'active #{3} of {4} coordsets)>' ).format(repr(selstr), self._ag.getTitle(), len(self), self.getACSIndex(), n_csets) else: return ('<Selection: {0} from {1} ({2} atoms; no ' 'coordinates)>').format(repr(selstr), self._ag.getTitle(), len(self)) def __getitem__(self, index): if isinstance(index, (str, tuple)): return self.getHierView()[index] else: try: index = self._indices[index] return self._ag[index] except: raise TypeError('invalid index') def __str__(self): return 'Selection {0}'.format(repr(ellipsis(self._selstr)))
[docs] def getSelstr(self): """Returns selection string that selects this atom subset.""" return self._selstr
[docs] def getHierView(self, **kwargs): """Returns a hierarchical view of the atom selection.""" return HierView(self, **kwargs)
[docs] def update(self): """Update selection.""" self._indices = SELECT.getIndices(self._ag, self._selstr)