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IMP
2.1.1
The Integrative Modeling Platform
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IMP
2.1.1
The Integrative Modeling Platform
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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 229 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 301 of file buildxlinks.py.
Here is the call graph for this function:| 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 291 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 342 of file buildxlinks.py.
Here is the call graph for this function:| def IMP.em2d.buildxlinks.InitialDockingFromXlinks.set_hierarchies | ( | self, | |
| h_receptor, | |||
| h_ligand | |||
| ) |
| h_receptor | |
| h_ligand |
Definition at line 259 of file buildxlinks.py.
| def IMP.em2d.buildxlinks.InitialDockingFromXlinks.set_pdbs | ( | self, | |
| fn_receptor, | |||
| fn_ligand | |||
| ) |
| fn_receptor | |
| fn_ligand |
Definition at line 247 of file buildxlinks.py.
| def IMP.em2d.buildxlinks.InitialDockingFromXlinks.set_rigid_bodies | ( | self, | |
| rb_receptor, | |||
| rb_ligand | |||
| ) |
| rb_receptor | |
| rb_ligand |
Definition at line 269 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 238 of file buildxlinks.py.
| def IMP.em2d.buildxlinks.InitialDockingFromXlinks.write_ligand | ( | self, | |
| fn | |||
| ) |
| fn |
Definition at line 311 of file buildxlinks.py.