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

Detailed:

get ordered branching atom around an atom with 3 neighbors

get 1 branching atom

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

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

Detailed:

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(), numeric::dihedral_radians(), pi_2, runtime_assert, 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

Detailed:

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 pi_2, runtime_assert, and protocols::TR().