Rosetta 3.4
Public Types | Public Member Functions | Protected Member Functions
protocols::enzdes::ModifyStoredRBConfs Class Reference

virtual base class that has some common functionality More...

#include <ModifyStoredLigandRBConfsMovers.hh>

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List of all members.

Public Types

typedef core::Size Size
typedef core::Real Real
typedef protocols::moves::Mover parent
typedef utility::vector1
< utility::vector1
< core::conformation::ResidueCOP > > 
RBConfLists

Public Member Functions

 ModifyStoredRBConfs (std::string const name)
 ~ModifyStoredRBConfs ()
virtual void apply (core::pose::Pose &pose)=0
virtual std::string get_name () const
 Each derived class must specify its name. The class name.
void swap_coordinates_in_pose (core::pose::Pose &pose, core::conformation::Residue &rescoords) const
 helper function to exchange coordinates in a pose this function doesn't actually exchange the residues, but sets all the coords of pose.residue( rescoords.seqpos() ) to what is in rescoords and vice versa
utility::vector1< Realclosest_orient_atoms_msd (core::pose::Pose const &pose, utility::vector1< core::conformation::ResidueCOP > const &confs) const
 calculates the closest orient atom (i.e. atoms used in rotamer placement msd between every conf and the confs coming before it in the pose or in the vector

Protected Member Functions

RBConfLists get_rigid_body_confs (core::pose::Pose const &pose) const
 this function is the function that all derived classes should call to get access to pose stored additional rb confs. right now it only returns the confs in the proper format, but in the future some logic might be added as to for which seqpos to return the stored confs
void set_rigid_body_confs (RBConfLists rbs, core::pose::Pose &pose) const
 same as for above function. all derived classes should use this function to communicate new/changed rigid body confs back to the pose/enzdes cacheable observer
void set_rigid_body_confs_for_seqpos (core::Size seqpos, utility::vector1< core::conformation::ResidueCOP > &confs, core::pose::Pose &pose) const
 see comments for set_rigid_body_confs

Detailed Description

virtual base class that has some common functionality


Member Typedef Documentation


Constructor & Destructor Documentation

protocols::enzdes::ModifyStoredRBConfs::ModifyStoredRBConfs ( std::string const  name)
protocols::enzdes::ModifyStoredRBConfs::~ModifyStoredRBConfs ( )

Member Function Documentation

virtual void protocols::enzdes::ModifyStoredRBConfs::apply ( core::pose::Pose pose) [pure virtual]
utility::vector1< ModifyStoredRBConfs::Real > protocols::enzdes::ModifyStoredRBConfs::closest_orient_atoms_msd ( core::pose::Pose const &  pose,
utility::vector1< core::conformation::ResidueCOP > const &  confs 
) const

calculates the closest orient atom (i.e. atoms used in rotamer placement msd between every conf and the confs coming before it in the pose or in the vector

References core::conformation::Residue::atom_name(), core::kinematics::tree::distance_squared(), core::conformation::Residue::name3(), core::pose::Pose::residue(), protocols::kinmatch::xyz(), and core::conformation::Residue::xyz().

Referenced by protocols::enzdes::DiversifyStoredRBConfs::diversify_all_confs().

std::string protocols::enzdes::ModifyStoredRBConfs::get_name ( ) const [virtual]
ModifyStoredRBConfs::RBConfLists protocols::enzdes::ModifyStoredRBConfs::get_rigid_body_confs ( core::pose::Pose const &  pose) const [protected]

this function is the function that all derived classes should call to get access to pose stored additional rb confs. right now it only returns the confs in the proper format, but in the future some logic might be added as to for which seqpos to return the stored confs

References protocols::toolbox::match_enzdes_util::get_enzdes_observer(), core::chemical::ResidueType::is_ligand(), core::pose::Pose::residue(), and core::conformation::Residue::type().

Referenced by protocols::enzdes::DiversifyStoredRBConfs::apply(), protocols::enzdes::MinimizeStoredRBConfs::apply(), protocols::enzdes::ApplyRandomStoredRBConf::apply(), and protocols::enzdes::GenerateStoredRBConfs::apply().

void protocols::enzdes::ModifyStoredRBConfs::set_rigid_body_confs ( RBConfLists  rbs,
core::pose::Pose pose 
) const [protected]

same as for above function. all derived classes should use this function to communicate new/changed rigid body confs back to the pose/enzdes cacheable observer

References set_rigid_body_confs_for_seqpos().

Referenced by protocols::enzdes::ApplyRandomStoredRBConf::apply().

void protocols::enzdes::ModifyStoredRBConfs::set_rigid_body_confs_for_seqpos ( core::Size  seqpos,
utility::vector1< core::conformation::ResidueCOP > &  confs,
core::pose::Pose pose 
) const [protected]
void protocols::enzdes::ModifyStoredRBConfs::swap_coordinates_in_pose ( core::pose::Pose pose,
core::conformation::Residue rescoords 
) const

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