Package rosetta :: Package protocols :: Package membrane :: Module _protocols_membrane_
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Module _protocols_membrane_

Classes [hide private]
  AddMPLigandMover
Add Membrane protein ligand mover Accommodate membrane protein ligand in the membrane foldtree
  AddMPLigandMoverAP
  AddMPLigandMoverCAP
  AddMPLigandMoverCreator
Mover Creator
  AddMPLigandMoverCreatorAP
  AddMPLigandMoverCreatorCAP
  AddMembraneMover
Add Membrane components to the pose, sets up MembraneInfo object includes: spanning topology, lips info, embeddings, and a membrane virtual residue describing the membrane position
  AddMembraneMoverAP
  AddMembraneMoverCAP
  AddMembraneMoverCreator
Mover Creator
  AddMembraneMoverCreatorAP
  AddMembraneMoverCreatorCAP
  FlipMover
Takes a pose and flips the downstream partner around the axis between the COMs of the partners, projected into the membrane plane.
  FlipMoverAP
  FlipMoverCAP
  FlipMoverCreator
Mover Creator
  FlipMoverCreatorAP
  FlipMoverCreatorCAP
  MembranePositionFromTopologyMover
Compute the initial position of the membrane based upon sequence or structure
  MembranePositionFromTopologyMoverAP
  MembranePositionFromTopologyMoverCAP
  MembranePositionFromTopologyMoverCreator
Mover Creator
  MembranePositionFromTopologyMoverCreatorAP
  MembranePositionFromTopologyMoverCreatorCAP
  RandomPositionRotationMover
Random Position Rotation Move Rotate the orientation of the membrane position to a new normal position.
  RandomPositionRotationMoverAP
  RandomPositionRotationMoverCAP
  RandomPositionTranslationMover
Random Position Translation Move
  RandomPositionTranslationMoverAP
  RandomPositionTranslationMoverCAP
  RotationMover
Rotates the pose such that a vector in the old orientation will be overlayed in the new orientation.
  RotationMoverAP
  RotationMoverCAP
  RotationMoverCreator
Mover Creator
  RotationMoverCreatorAP
  RotationMoverCreatorCAP
  SetMembraneCenterMover
Membrane Position Translation Move Translate the center of the membrane stub ot the specified position
  SetMembraneCenterMoverAP
  SetMembraneCenterMoverCAP
  SetMembraneCenterMoverCreator
Mover Creator for membrane translation mover
  SetMembraneCenterMoverCreatorAP
  SetMembraneCenterMoverCreatorCAP
  SetMembraneNormalMover
Membrane Position Rotation Move Rotate the orientation of the membrane position to a new normal position.
  SetMembraneNormalMoverAP
  SetMembraneNormalMoverCAP
  SetMembraneNormalMoverCreator
Mover creator for membrane rotation mover
  SetMembraneNormalMoverCreatorAP
  SetMembraneNormalMoverCreatorCAP
  SetMembranePositionMover
Membrane Position Translation-Rotation Mover
  SetMembranePositionMoverAP
  SetMembranePositionMoverCAP
  SetMembranePositionMoverCreator
Mover Creator for composed RT mover
  SetMembranePositionMoverCreatorAP
  SetMembranePositionMoverCreatorCAP
  SingletonBase_T_core_chemical_ChemicalManager_T
SingletonBase is meant to serve as a base class for singleton classes in Rosetta handling the initialization of the singleton in a thread-safe way.
  SingletonBase_T_core_chemical_ChemicalManager_TAP
  SingletonBase_T_core_chemical_ChemicalManager_TCAP
  TransformIntoMembraneMover
Takes a pose, calculates the best possible center and normal from the topology object (through spanfile from OCTOPUS) and the coordinates of the pose CAUTION: THIS MOVER ONLY WORKS FOR A FIXED MEMBRANE WHERE THE MEMBRANE VIRTUAL RESIDUE IS AT THE ROOT OF THE FOLDTREE!!!
  TransformIntoMembraneMoverAP
  TransformIntoMembraneMoverCAP
  TransformIntoMembraneMoverCreator
Mover Creator
  TransformIntoMembraneMoverCreatorAP
  TransformIntoMembraneMoverCreatorCAP
  TranslationMover
Translation vector can be defined in -mp:setup center flag to translate the new pose to.
  TranslationMoverAP
  TranslationMoverCAP
  TranslationMoverCreator
Mover Creator
  TranslationMoverCreatorAP
  TranslationMoverCreatorCAP
  TranslationRotationMover
Translation and Rotation of a pose.
  TranslationRotationMoverAP
  TranslationRotationMoverCAP
  TranslationRotationMoverCreator
Mover Creator
  TranslationRotationMoverCreatorAP
  TranslationRotationMoverCreatorCAP
  __CPP_AddMPLigandMoverCreator__
  __CPP_AddMPLigandMover__
  __CPP_AddMembraneMoverCreator__
  __CPP_AddMembraneMover__
  __CPP_FlipMoverCreator__
  __CPP_FlipMover__
  __CPP_MembranePositionFromTopologyMoverCreator__
  __CPP_MembranePositionFromTopologyMover__
  __CPP_RandomPositionRotationMover__
  __CPP_RandomPositionTranslationMover__
  __CPP_RotationMoverCreator__
  __CPP_RotationMover__
  __CPP_SetMembraneCenterMoverCreator__
  __CPP_SetMembraneCenterMover__
  __CPP_SetMembraneNormalMoverCreator__
  __CPP_SetMembraneNormalMover__
  __CPP_SetMembranePositionMoverCreator__
  __CPP_SetMembranePositionMover__
  __CPP_TransformIntoMembraneMoverCreator__
  __CPP_TransformIntoMembraneMover__
  __CPP_TranslationMoverCreator__
  __CPP_TranslationMover__
  __CPP_TranslationRotationMoverCreator__
  __CPP_TranslationRotationMover__
Functions [hide private]
 
mem_all_atom_rmsd_no_super(...)
mem_all_atom_rmsd_no_super( (Pose)native_pose, (Pose)pose) -> float : Compute No Super Membrane RMSD - all atom without super Compute the root mean squared deviation of the backbone atoms between in the transmembrane spanning regions of a membrane protein @throws If not a membrane protein
 
mem_all_atom_rmsd_with_super(...)
mem_all_atom_rmsd_with_super( (Pose)native_pose, (Pose)pose) -> float : Compute Membrane RMSD - all atom with superposiiton Compute the root mean squared deviation of the backbone atoms between in the transmembrane spanning regions of a membrane protein
 
mem_bb_rmsd_no_super(...)
mem_bb_rmsd_no_super( (Pose)native_pose, (Pose)pose) -> float : Compute No Super Membrane RMSD Compute the root mean squared deviation of the backbone atoms between in the transmembrane spanning regions of a membrane protein @throws If not a membrane protein
 
mem_bb_rmsd_with_super(...)
mem_bb_rmsd_with_super( (Pose)native_pose, (Pose)pose) -> float : Compute Membrane RMSD Compute the root mean squared deviation of the backbone atoms between in the transmembrane spanning regions of a membrane protein
Variables [hide private]
  __package__ = None
Function Details [hide private]

mem_all_atom_rmsd_no_super(...)

 

mem_all_atom_rmsd_no_super( (Pose)native_pose, (Pose)pose) -> float :
    Compute No Super Membrane RMSD - all atom without super
    Compute the root mean squared deviation of the backbone atoms between
    in the transmembrane spanning regions of a membrane protein
    @throws If not a membrane protein
    

    C++ signature :
        double mem_all_atom_rmsd_no_super(core::pose::Pose {lvalue},core::pose::Pose {lvalue})

mem_all_atom_rmsd_with_super(...)

 

mem_all_atom_rmsd_with_super( (Pose)native_pose, (Pose)pose) -> float :
    Compute Membrane RMSD - all atom with superposiiton
    Compute the root mean squared deviation of the backbone atoms between
    in the transmembrane spanning regions of a membrane protein
    

    C++ signature :
        double mem_all_atom_rmsd_with_super(core::pose::Pose {lvalue},core::pose::Pose {lvalue})

mem_bb_rmsd_no_super(...)

 

mem_bb_rmsd_no_super( (Pose)native_pose, (Pose)pose) -> float :
    Compute No Super Membrane RMSD
    Compute the root mean squared deviation of the backbone atoms between
    in the transmembrane spanning regions of a membrane protein
    @throws If not a membrane protein
    

    C++ signature :
        double mem_bb_rmsd_no_super(core::pose::Pose {lvalue},core::pose::Pose {lvalue})

mem_bb_rmsd_with_super(...)

 

mem_bb_rmsd_with_super( (Pose)native_pose, (Pose)pose) -> float :
    Compute Membrane RMSD
    Compute the root mean squared deviation of the backbone atoms between
    in the transmembrane spanning regions of a membrane protein
    

    C++ signature :
        double mem_bb_rmsd_with_super(core::pose::Pose {lvalue},core::pose::Pose {lvalue})