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protocols::branch_angle Namespace Reference

Classes

class  BranchAngleOptimizer
 
class  BranchCoef1
 a class to store coefficients for branching angle optimization around a single atom atom with three bonded neighbors More...
 
class  BranchCoef2
 a class to store coefficients for branching angle optimization around a single atom atom with three bonded neighbors More...
 
class  BranchParam1
 a class to store bond angle energy parameters around a single atom atom with three bonded neighbors More...
 
class  BranchParam2
 a class to store bond angle energy parameters around a single atom atom with four bonded neighbors More...
 

Functions

void branching_atomid1 (core::pose::Pose const &pose, core::id::AtomID main_atomid1, core::id::AtomID center_atomid, core::id::AtomID main_atomid2, core::id::AtomID &branch_atomid1)
 get all atoms bonded to another More...
 
void branching_atomids2 (core::pose::Pose const &pose, core::id::AtomID main_atomid1, core::id::AtomID center_atomid, core::id::AtomID main_atomid2, core::id::AtomID &branch_atomid1, core::id::AtomID &branch_atomid2)
 get 2 branching atoms ordered according their torsion offsets More...
 
void get_branching_atoms2 (core::kinematics::tree::AtomCOP const main_atom2, core::kinematics::tree::AtomCOP &branch_atom1, core::kinematics::tree::AtomCOP &branch_atom2)
 get 2 siblings of an atom ordered according their torsion offsets More...
 

Function Documentation

void protocols::branch_angle::branching_atomid1 ( pose::Pose const &  pose,
id::AtomID  main_atomid1,
id::AtomID  center_atomid,
id::AtomID  main_atomid2,
id::AtomID branch_atomid1 
)

get all atoms bonded to another

get ordered branching atom around an atom with 3 neighbors

get 1 branching atom

References core::conformation::Conformation::bonded_neighbor_all_res(), and core::pose::Pose::conformation().

Referenced by protocols::branch_angle::BranchAngleOptimizer::optimize_angles(), and protocols::branch_angle::BranchAngleOptimizer::overall_params().

void protocols::branch_angle::branching_atomids2 ( pose::Pose const &  pose,
id::AtomID  main_atomid1,
id::AtomID  center_atomid,
id::AtomID  main_atomid2,
id::AtomID branch_atomid1,
id::AtomID branch_atomid2 
)

get 2 branching atoms ordered according their torsion offsets

get ordered branching atoms such that the torsion offset from main_atomid2 to branch_atomid1 is less than that to branch_atomid2, given that both are in the range [0, 2*pi). In other words the atoms will be returned clockwise from main_atomid2, when looking from main_atomid1 to center_atomid.

References core::conformation::Conformation::bonded_neighbor_all_res(), core::pose::Pose::conformation(), and core::pose::Pose::xyz().

Referenced by protocols::branch_angle::BranchAngleOptimizer::optimize_angles(), and protocols::branch_angle::BranchAngleOptimizer::overall_params().

void protocols::branch_angle::get_branching_atoms2 ( kinematics::tree::AtomCOP const  main_atom2,
kinematics::tree::AtomCOP branch_atom1,
kinematics::tree::AtomCOP branch_atom2 
)

get 2 siblings of an atom ordered according their torsion offsets

get ordered branching atoms such that the torsion offset from main_atom2 to branch_atom1 is less than that to branch_atom2, given that both are in the range [0, 2*pi). In other words the atoms will be returned clockwise from main_atom2, when looking from main_atom1 to the central atom.

References protocols::TR().