Rosetta 3.4
Public Types | Public Member Functions
protocols::scoring::Interface Class Reference

#include <Interface.hh>

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List of all members.

Public Types

typedef
core::pack::task::PackerTaskOP 
PackerTaskOP
typedef core::Real Real

Public Member Functions

 Interface ()
 Interface (Size const jump_number_in)
 Interface (ObjexxFCL::FArray1D_bool partner)
void jump (Size const jump_number)
void calculate (core::pose::Pose const &pose)
 base for calculating the interface
void print (core::pose::Pose const &pose)
 print out the interface information
void show (core::pose::Pose const &pose)
void set_pack (core::pose::Pose const &pose, PackerTaskOP task)
 sets up which residues are to be packed
core::Size closest_interface_residue (core::pose::Pose const &pose, core::Size src_rsd, core::Real &distance)
 find the nearest residue at the interface to a given residue
void distance (Real const distance_in)
core::Vector center (core::pose::Pose const &pose)
 calculates the center of mass of interface residues
bool is_interface (core::conformation::Residue const &rsd) const
bool is_interface (Size const position) const
Size interface_nres ()
 returns the total number of residues on both sides of the interface for a given jump
bool is_pair (core::conformation::Residue const &rsd1, core::conformation::Residue const &rsd2)
 returns whether the rsd1 and rsd2 are considered a contact pair based on contact_list_ array
void set_symmetric_pack (core::pose::Pose const &pose, PackerTaskOP task)
utility::vector1
< utility::vector1_int > 
pair_list ()
 Get two lists containing the residues on each side of the interface.
utility::vector1
< utility::vector1_size > 
contact_list ()
 The contact_list is pose.total_residue() long, each element (contact_list_[i]) contains a list of residues from the other partner that interacts with residue i. This is calculated in protein_calculate, and used by Interface.is_pair() function as well as the interchain_vdw, interchain_env, and interchain_pair scoring components.

Member Typedef Documentation


Constructor & Destructor Documentation

protocols::scoring::Interface::Interface ( ) [inline]
protocols::scoring::Interface::Interface ( Size const  jump_number_in) [inline]
protocols::scoring::Interface::Interface ( ObjexxFCL::FArray1D_bool  partner) [inline]

Member Function Documentation

void protocols::scoring::Interface::calculate ( core::pose::Pose const &  pose)
core::Vector protocols::scoring::Interface::center ( core::pose::Pose const &  pose)

calculates the center of mass of interface residues

interface_center

Detailed:
calculate the center of mass of the interface loops over all residues at the interface and gets the xyz coordinates for the c-alpha atom of that residue
References: pose_docking_calc_interface from pose_docking.cc
Authors:
Monica Berrondo June 14 2007
Last Modified: June 29 2007

References core::conformation::Residue::nbr_atom_xyz(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

core::Size protocols::scoring::Interface::closest_interface_residue ( core::pose::Pose const &  pose,
core::Size  src_rsd,
core::Real distance 
)

find the nearest residue at the interface to a given residue

Interface:closest_interface_residue

Authors:
Monica Berrondo November 18, 2010

References core::conformation::Residue::nbr_atom_xyz(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

utility::vector1< utility::vector1_size > protocols::scoring::Interface::contact_list ( ) [inline]

The contact_list is pose.total_residue() long, each element (contact_list_[i]) contains a list of residues from the other partner that interacts with residue i. This is calculated in protein_calculate, and used by Interface.is_pair() function as well as the interchain_vdw, interchain_env, and interchain_pair scoring components.

void protocols::scoring::Interface::distance ( Real const  distance_in)
core::Size protocols::scoring::Interface::interface_nres ( )

returns the total number of residues on both sides of the interface for a given jump

bool protocols::scoring::Interface::is_interface ( core::conformation::Residue const &  rsd) const
bool protocols::scoring::Interface::is_interface ( Size const  position) const
bool protocols::scoring::Interface::is_pair ( core::conformation::Residue const &  rsd1,
core::conformation::Residue const &  rsd2 
)

returns whether the rsd1 and rsd2 are considered a contact pair based on contact_list_ array

Function to determine whether two residues are a "pair" for docking-type scoring calculations, such as vdw and pair across an interface

References core::conformation::Residue::seqpos().

Referenced by protocols::protein_interface_design::movers::DisulfideMover::disulfide_list().

void protocols::scoring::Interface::jump ( Size const  jump_number)
utility::vector1< utility::vector1_int > protocols::scoring::Interface::pair_list ( ) [inline]

Get two lists containing the residues on each side of the interface.

You might expect something called pair_list() to output pairs or somehow relate to the is_pair function, but it does not. It returns a two element list.

  • The first element is a list of all residues on the lower partner of the interface.
  • The second element is a list of all the residues in the interface on the upper partner. Both lists are sorted by residue number, so the indices of one list have no relationship to the other list.
    Todo:

    rename this to something more logical & give it a better return type

    make a function that returns a vector1<pair<Size,Size> > containing all interacting pairs. This would be easy to implement.

Referenced by protocols::protein_interface_design::movers::DisulfideMover::disulfide_list().

void protocols::scoring::Interface::print ( core::pose::Pose const &  pose)

print out the interface information

Interface::print

Authors:
Monica Berrondo November 07 2007
Last Modified: November 07 2007

Referenced by protocols::ddG_main().

void protocols::scoring::Interface::set_pack ( core::pose::Pose const &  pose,
PackerTaskOP  task 
)

sets up which residues are to be packed

set_pack

Detailed:
References: pose_docking_repack from pose_docking.cc
Authors:
Monica Berrondo June 14 2007
Last Modified: June 29 2007

References core::kinematics::FoldTree::cutpoint_by_jump(), core::pose::Pose::fold_tree(), core::conformation::Residue::is_ligand(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

void protocols::scoring::Interface::set_symmetric_pack ( core::pose::Pose const &  pose,
PackerTaskOP  task 
)
void protocols::scoring::Interface::show ( core::pose::Pose const &  pose)

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