Rosetta 3.4
Typedefs | Functions
core::pack::task::operation::util Namespace Reference

Typedefs

typedef std::pair< std::set
< core::Size >, std::set
< core::Size > > 
InterfacePair
typedef
numeric::HomogeneousTransform
< core::Real
HTReal

Functions

void find_interface_pointing_residues_from_neighbs (core::pose::Pose const &pose, InterfacePair const &interface_pair, core::Real const nearby_atom_cutoff, core::Real const vector_angle_cutoff, core::Real const vector_dist_cutoff, utility::vector1_bool &interface_residues)
 looks at the big set and figures out what is actually pointing towards the interface
bool any_atoms_within_cutoff (core::conformation::Residue &res1, core::conformation::Residue &res2, core::Real cutoff)
 find nearby atoms to other in interface
InterfacePair find_neighbors_within_CB_cutoff (core::pose::Pose const &pose, core::Real big_cutoff, core::Size chain1, core::Size chain2)
 neighbors to look for vectors within (big set here)
InterfacePair find_jump_partners_within_CB_cutoff (core::pose::Pose const &pose, core::Real big_cutoff, int jump_num)
 find neighbors to look for vectors within using a big cutoff for CBs
numeric::xyzVector< core::Realcbeta_vector (core::conformation::Residue &res)
 the Cbeta vector(s) from on rsd to another
numeric::xyzVector< core::Realselect_coord_for_residue (core::conformation::Residue &res)
 the action coordinate for each residue
bool res1_pointed_at_res2 (core::conformation::Residue &res1, core::conformation::Residue &res2, core::Real angle_cutoff, core::Real dist_cutoff)
 out if res1 and res2 are pointing at eachother
void fill_in_chain_terminii (core::pose::Pose const &pose, core::Size chain1, core::Size chain2)
utility::vector1_bool calc_interface_vector (core::pose::Pose const &pose, core::Size const chain1_number, core::Size const chain2_number)
utility::vector1_bool calc_interface_vector (core::pose::Pose const &pose, core::Size const chain1_number, core::Size const chain2_number, core::Real const CB_dist_cutoff, core::Real const nearby_atom_cutoff, core::Real const vector_angle_cutoff, core::Real const vector_dist_cutoff)
utility::vector1_bool calc_interface_vector (core::pose::Pose const &pose, int const interface_jump, core::Real const CB_dist_cutoff, core::Real const nearby_atom_cutoff, core::Real const vector_angle_cutoff, core::Real const vector_dist_cutoff)
utility::vector1_bool calc_interface_vector (core::pose::Pose const &pose, int const interface_jump)

Typedef Documentation

typedef numeric::HomogeneousTransform< core::Real > core::pack::task::operation::util::HTReal

Function Documentation

bool core::pack::task::operation::util::any_atoms_within_cutoff ( core::conformation::Residue res1,
core::conformation::Residue res2,
core::Real  cutoff 
)

find nearby atoms to other in interface

looks are residue 1 and sees if any of the side chain atoms are within the cutoff distance to residue 2

References core::conformation::Residue::atom_begin(), core::chemical::ResidueType::has(), core::conformation::Residue::heavyAtoms_end(), select_coord_for_residue(), core::conformation::Residue::sidechainAtoms_begin(), and core::conformation::Residue::type().

Referenced by find_interface_pointing_residues_from_neighbs().

utility::vector1_bool core::pack::task::operation::util::calc_interface_vector ( core::pose::Pose const &  pose,
core::Size const  chain1_number,
core::Size const  chain2_number 
)

minimal chain number definition

Calculates the residues at an interface between two protein chains or jump. The calculation is done in the following manner. First the point graph is used to find all residues within some big cutoff of residues on the other chain. For these residues near the interface, two metrics are used to decide if they are actually possible interface residues. The first metric is to itterate through all the side chain atoms in the residue of interest and check to see if their distance is less than the nearby atom cutoff, if so then they are an interface residue. If a residue does not pass that check, then two vectors are drawn, a CA-CB vector and a vector from CB to a CB atom on the neighboring chain. The dot product between these two vectors is then found and if the angle between them is less than some cutoff then they are classified as interface.

minimal chain number definition

Referenced by protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation::apply(), and calc_interface_vector().

utility::vector1_bool core::pack::task::operation::util::calc_interface_vector ( core::pose::Pose const &  pose,
core::Size const  chain1_number,
core::Size const  chain2_number,
core::Real const  CB_dist_cutoff,
core::Real const  nearby_atom_cutoff,
core::Real const  vector_angle_cutoff,
core::Real const  vector_dist_cutoff 
)
utility::vector1_bool core::pack::task::operation::util::calc_interface_vector ( core::pose::Pose const &  pose,
int const  interface_jump,
core::Real const  CB_dist_cutoff,
core::Real const  nearby_atom_cutoff,
core::Real const  vector_angle_cutoff,
core::Real const  vector_dist_cutoff 
)
utility::vector1_bool core::pack::task::operation::util::calc_interface_vector ( core::pose::Pose const &  pose,
int const  interface_jump 
)

minimal jump runner

References calc_interface_vector().

numeric::xyzVector< core::Real > core::pack::task::operation::util::cbeta_vector ( core::conformation::Residue res)

the Cbeta vector(s) from on rsd to another

find the Cbeta vector(s) from one residue to another, returns the normalized vector needed

References core::conformation::Residue::atom(), select_coord_for_residue(), and core::conformation::Atom::xyz().

Referenced by res1_pointed_at_res2().

void core::pack::task::operation::util::fill_in_chain_terminii ( core::pose::Pose const &  pose,
core::Size  chain1,
core::Size  chain2 
)
void core::pack::task::operation::util::find_interface_pointing_residues_from_neighbs ( core::pose::Pose const &  pose,
InterfacePair const &  interface_pairs,
core::Real const  nearby_atom_cutoff,
core::Real const  vector_angle_cutoff,
core::Real const  vector_dist_cutoff,
utility::vector1_bool &  interface_residues 
)

looks at the big set and figures out what is actually pointing towards the interface

does the real work, looks at the big set and figures out what is actually pointing towards the interface sets a vector bool value to true if a residue is at the interface

References any_atoms_within_cutoff(), res1_pointed_at_res2(), and core::pose::Pose::residue().

Referenced by calc_interface_vector().

InterfacePair core::pack::task::operation::util::find_jump_partners_within_CB_cutoff ( core::pose::Pose const &  pose,
core::Real  big_cutoff,
int  jump_num 
)
InterfacePair core::pack::task::operation::util::find_neighbors_within_CB_cutoff ( core::pose::Pose const &  pose,
core::Real  big_cutoff,
core::Size  chain1,
core::Size  chain2 
)

neighbors to look for vectors within (big set here)

find based on chains neighbors to look for vectors within using a big cutoff for CBs

References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), and core::conformation::residue_point_graph_from_conformation().

Referenced by calc_interface_vector().

bool core::pack::task::operation::util::res1_pointed_at_res2 ( core::conformation::Residue res1,
core::conformation::Residue res2,
core::Real  angle_cutoff,
core::Real  dist_cutoff 
)

out if res1 and res2 are pointing at eachother

figures out if res1 and res2 are pointing at eachother

the angle is the max angle between the two residues, dist_cutoff is how far the coords are from eachother

References cbeta_vector(), and select_coord_for_residue().

Referenced by find_interface_pointing_residues_from_neighbs().

numeric::xyzVector< core::Real > core::pack::task::operation::util::select_coord_for_residue ( core::conformation::Residue res)
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