Puts two subunits together using the Xlinkins restraints. More...

Public Member Functions
def	get_residue_coordinates
	Get the coordinates for a residue in a molecular hierarchy. More...

def	get_residue_particle
	Get the particle representing a residue in a hierarchy. More...

def	move_ligand
	Movest the ligand close to the receptor based on the xlinks provided by set_xlinks()

def	move_one_xlink
	Put the residues in a random distance between 0 and the maximum cross-linkin distance.

def	move_xlinks
	Function equivalent to move_one_xlink() for the case where there are more than one cross-link restraints available. More...

def	set_hierarchies
	Set the hierarchies (atom.Hierarchy objects) for the receptor and the ligand. More...

def	set_pdbs
	Set the name of the PDB files of the receptor and the ligand. More...

def	set_rigid_bodies
	Sets the rigid bodies (core.RigidBody objects) for the receptor and the ligand. More...

def	set_xlinks
	Sets the xlinks used for the computation fo the intial rough docking solution. More...

def	write_ligand
	Write a pdb file the coordinates of the ligand. More...

Detailed Description

The solutions offered by this class are just an initial position of the components to be fed to HEX

Definition at line 86 of file buildxlinks.py.

Member Function Documentation

def IMP.em2d.buildxlinks.InitialDockingFromXlinks.get_residue_coordinates	(	self,
		h,
		ch,
		res
	)

Parameters

Definition at line 130 of file buildxlinks.py.

def IMP.em2d.buildxlinks.InitialDockingFromXlinks.get_residue_particle	(	self,
		h,
		ch,
		res
	)

Parameters

h	atom.Hierarchy containing the residue
ch	The chain id
res	index of the residue

Definition at line 123 of file buildxlinks.py.

def IMP.em2d.buildxlinks.InitialDockingFromXlinks.move_xlinks ( self )

Puts the ligand residues as close as possible to the receptor residues

Definition at line 147 of file buildxlinks.py.

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def IMP.em2d.buildxlinks.InitialDockingFromXlinks.set_hierarchies	(	self,
		h_receptor,
		h_ligand
	)

Parameters

h_receptor
h_ligand

Definition at line 104 of file buildxlinks.py.

def IMP.em2d.buildxlinks.InitialDockingFromXlinks.set_pdbs	(	self,
		fn_receptor,
		fn_ligand
	)

Parameters

fn_receptor
fn_ligand

Definition at line 97 of file buildxlinks.py.

def IMP.em2d.buildxlinks.InitialDockingFromXlinks.set_rigid_bodies	(	self,
		rb_receptor,
		rb_ligand
	)

Parameters

rb_receptor
rb_ligand

Definition at line 111 of file buildxlinks.py.

def IMP.em2d.buildxlinks.InitialDockingFromXlinks.set_xlinks	(	self,
		xlinks_list
	)

Parameters

xlinks_list A list of Xlink classes residue1 belongs to the receptor and residue2 belongs to the ligand

Definition at line 91 of file buildxlinks.py.

def IMP.em2d.buildxlinks.InitialDockingFromXlinks.write_ligand	(	self,
		fn
	)

Parameters

fn

Definition at line 135 of file buildxlinks.py.

The documentation for this class was generated from the following file: