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IMP Reference Guide  2.11.1
The Integrative Modeling Platform
IMP.EMageFit.buildxlinks.InitialDockingFromXlinks Class Reference

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

Detailed Description

Puts two subunits together using the Xlinkins restraints.

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

Note
This class is only available in Python.

Definition at line 227 of file buildxlinks.py.

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() More...
 
def move_one_xlink
 Put the residues in a random distance between 0 and the maximum cross-linkin distance. More...
 
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 initial rough docking solution. More...
 
def write_ligand
 Write a pdb file the coordinates of the ligand. More...
 

Member Function Documentation

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

Get the coordinates for a residue in a molecular hierarchy.

Parameters
hatom.Hierarchy object
chThe chain id
resResidue index

Definition at line 301 of file buildxlinks.py.

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

Get the particle representing a residue in a hierarchy.

Parameters
hatom.Hierarchy containing the residue
chThe chain id
resindex of the residue

Definition at line 291 of file buildxlinks.py.

def IMP.EMageFit.buildxlinks.InitialDockingFromXlinks.move_ligand (   self)

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

Definition at line 279 of file buildxlinks.py.

def IMP.EMageFit.buildxlinks.InitialDockingFromXlinks.move_one_xlink (   self)

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

Definition at line 318 of file buildxlinks.py.

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

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

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

Definition at line 342 of file buildxlinks.py.

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

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

Parameters
h_receptor
h_ligand

Definition at line 259 of file buildxlinks.py.

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

Set the name of the PDB files of the receptor and the ligand.

Parameters
fn_receptor
fn_ligand

Definition at line 247 of file buildxlinks.py.

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

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

Parameters
rb_receptor
rb_ligand

Definition at line 269 of file buildxlinks.py.

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

Sets the xlinks used for the computation fo the initial rough docking solution.

Parameters
xlinks_listA list of Xlink classes residue1 belongs to the receptor and residue2 belongs to the ligand

Definition at line 238 of file buildxlinks.py.

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

Write a pdb file the coordinates of the ligand.

Parameters
fn

Definition at line 311 of file buildxlinks.py.


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