ost.mol.alg.views Namespace Reference

Functions
	_GetChain (view)
	_GetChains (view_a, view_b)
	_EmptyView (view)
	PairResiduesByNum (view_a, view_b, view_add_flags=mol.ViewAddFlag.INCLUDE_ATOMS)
	RepresentativeAtoms (ent, chain=None, alpha_and_beta=False)

Detailed Description

A bunch of algorithms operating on two views. 

Authors: Marco Biasini, Pascal Benkert

Function Documentation

_EmptyView()

_EmptyView (   view )

protected

Definition at line 18 of file views.py.

_GetChain()

_GetChain (   view )

protected

Definition at line 9 of file views.py.

_GetChains()

_GetChains (   view_a,   view_b  )

protected

Definition at line 14 of file views.py.

PairResiduesByNum()

PairResiduesByNum	(		view_a,
			view_b,
			view_add_flags = mol.ViewAddFlag.INCLUDE_ATOMS
	)

Pair residues by residue number.

Definition at line 24 of file views.py.

RepresentativeAtoms()

RepresentativeAtoms	(		ent,
			chain = None,
			alpha_and_beta = False
	)

Returns a view with one or two representative atom per amino acid residue. 

There are two basic modes, controlled by the alpha_and_beta parameter:

When the parameter is false, for residues with a sidechain, the C-beta atom is 
used, for residues without  sidechain, the C-alpha atom is used. Note that this 
is different from using the selection

  (aname=CA and rname=GLY) or (aname=CB and rname!=GLY)

When the alpha_and_beta parameter is true, both C-alpha and C-beta (if
available) are added to the view.

If chain is not equal to None, only atoms of the chain with that chain name
will be added to the view.

Definition at line 54 of file views.py.