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IMP Reference Guide
develop.63b38c487d,2024/12/21
The Integrative Modeling Platform
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Puts two subunits together using the Xlinkins restraints. More...
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
Definition at line 221 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 for the initial rough docking solution. More... | |
| def | write_ligand |
| Write a pdb file the coordinates of the ligand. More... | |
| def IMP.EMageFit.buildxlinks.InitialDockingFromXlinks.get_residue_coordinates | ( | self, | |
| h, | |||
| ch, | |||
| res | |||
| ) |
Get the coordinates for a residue in a molecular hierarchy.
| h | atom.Hierarchy object |
| ch | The chain id |
| res | Residue index |
Definition at line 295 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.
| h | atom.Hierarchy containing the residue |
| ch | The chain id |
| res | index of the residue |
Definition at line 285 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 273 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 312 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 336 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.
| h_receptor | |
| h_ligand |
Definition at line 253 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.
| fn_receptor | |
| fn_ligand |
Definition at line 241 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.
| rb_receptor | |
| rb_ligand |
Definition at line 263 of file buildxlinks.py.
| def IMP.EMageFit.buildxlinks.InitialDockingFromXlinks.set_xlinks | ( | self, | |
| xlinks_list | |||
| ) |
Sets the xlinks used for the computation for the initial rough docking solution.
| xlinks_list | A list of Xlink classes residue1 belongs to the receptor and residue2 belongs to the ligand |
Definition at line 232 of file buildxlinks.py.
| def IMP.EMageFit.buildxlinks.InitialDockingFromXlinks.write_ligand | ( | self, | |
| fn | |||
| ) |
Write a pdb file the coordinates of the ligand.
| fn |
Definition at line 305 of file buildxlinks.py.