IMP
2.2.1
The Integrative Modeling Platform
|
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... | |
The solutions offered by this class are just an initial position of the components to be fed to HEX
Definition at line 228 of file buildxlinks.py.
def IMP.em2d.buildxlinks.InitialDockingFromXlinks.get_residue_coordinates | ( | self, | |
h, | |||
ch, | |||
res | |||
) |
h | atom.Hierarchy object |
ch | The chain id |
res | Residue index |
Definition at line 302 of file buildxlinks.py.
def IMP.em2d.buildxlinks.InitialDockingFromXlinks.get_residue_particle | ( | self, | |
h, | |||
ch, | |||
res | |||
) |
h | atom.Hierarchy containing the residue |
ch | The chain id |
res | index of the residue |
Definition at line 292 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 343 of file buildxlinks.py.
def IMP.em2d.buildxlinks.InitialDockingFromXlinks.set_hierarchies | ( | self, | |
h_receptor, | |||
h_ligand | |||
) |
h_receptor | |
h_ligand |
Definition at line 260 of file buildxlinks.py.
def IMP.em2d.buildxlinks.InitialDockingFromXlinks.set_pdbs | ( | self, | |
fn_receptor, | |||
fn_ligand | |||
) |
fn_receptor | |
fn_ligand |
Definition at line 248 of file buildxlinks.py.
def IMP.em2d.buildxlinks.InitialDockingFromXlinks.set_rigid_bodies | ( | self, | |
rb_receptor, | |||
rb_ligand | |||
) |
rb_receptor | |
rb_ligand |
Definition at line 270 of file buildxlinks.py.
def IMP.em2d.buildxlinks.InitialDockingFromXlinks.set_xlinks | ( | self, | |
xlinks_list | |||
) |
xlinks_list | A list of Xlink classes residue1 belongs to the receptor and residue2 belongs to the ligand |
Definition at line 239 of file buildxlinks.py.
def IMP.em2d.buildxlinks.InitialDockingFromXlinks.write_ligand | ( | self, | |
fn | |||
) |
fn |
Definition at line 312 of file buildxlinks.py.