core::kinematics::jacobian Namespace Reference

Classes
class	JacobianStructure
	The JacobianStructure class is the upper-level wrapper of the Jacobian analysis of a protein's kinematics relations. More...
class	ModuleType1
	The ModuleType1 class covers the Jacobian analysis at the lower-level for type-1 systems, which have internal DoFs that can be organized as three sets of two torsion angles with intersecting axes. More...
class	SeriesJacobians
	The SeriesJacobians class is the mid-level of the Jacobian analysis of a protein's kinematics relations. More...

Typedefs
using	JacobianStructureOP = utility::pointer::shared_ptr< JacobianStructure >
using	JacobianStructureCOP = utility::pointer::shared_ptr< JacobianStructure const >
using	ModuleType1OP = utility::pointer::shared_ptr< ModuleType1 >
using	ModuleType1COP = utility::pointer::shared_ptr< ModuleType1 const >
using	SeriesJacobiansOP = utility::pointer::shared_ptr< SeriesJacobians >
using	SeriesJacobiansCOP = utility::pointer::shared_ptr< SeriesJacobians const >

Enumerations
enum class	SeriesJacobianTypeEnum { ALPHA_AA = 1 , OTHER = 2 , num_types = OTHER }
	List of supported residue types in the loop that is to be represented by a series Jacobian. More...

Functions
static basic::Tracer	TR ("core.kinematics.jacobian.util")
void	weigh_columns_inversely_squared (utility::vector1< numeric::MathVector< core::Real > > &input_cols)
	method that gives weights to different columns (that all represent the same error twist in their respective torsion space), inversely proportional to the norm of the required torsion changes More...
void	weigh_columns_by_energy_grad (utility::vector1< numeric::MathVector< core::Real > > &input_cols, utility::vector1< numeric::MathVector< core::Real > > const &gradient_cols, core::Real const scaling=0.1)
	method that gives weights to different columns (that all represent the same error twist in their respective torsion space), according to a sigmoid function that gives greatest weight to input_cols alligned with negative gradient_cols. The shape of the sigmoid can be controlled using the variable 'scaling' More...
numeric::xyzVector< core::Real >	project_ZYX_euler_on_cart (numeric::xyzVector< core::Real > const euler_angles, numeric::xyzVector< core::Real > const euler_error)
	projects intrinsic Euler angles onto extrinsic Euler angles in order XYZ (i.e. projected onto Cartesian unit vectors) More...
ModuleType1::Screw	calculate_error_twist (core::kinematics::RT const RT_current, core::kinematics::RT const RT_target)
	Extract the error twist (linearized rotations) from the current and target position and orientation (in Euler angles) More...

Variables
constexpr core::Real	margin_from_zero_in_jacobian_util = 1e-6

Typedef Documentation

JacobianStructureCOP

using core::kinematics::jacobian::JacobianStructureCOP = typedef utility::pointer::shared_ptr< JacobianStructure const >

JacobianStructureOP

using core::kinematics::jacobian::JacobianStructureOP = typedef utility::pointer::shared_ptr< JacobianStructure >

ModuleType1COP

using core::kinematics::jacobian::ModuleType1COP = typedef utility::pointer::shared_ptr< ModuleType1 const >

ModuleType1OP

using core::kinematics::jacobian::ModuleType1OP = typedef utility::pointer::shared_ptr< ModuleType1 >

SeriesJacobiansCOP

using core::kinematics::jacobian::SeriesJacobiansCOP = typedef utility::pointer::shared_ptr< SeriesJacobians const >

SeriesJacobiansOP

using core::kinematics::jacobian::SeriesJacobiansOP = typedef utility::pointer::shared_ptr< SeriesJacobians >

Enumeration Type Documentation

SeriesJacobianTypeEnum

enum core::kinematics::jacobian::SeriesJacobianTypeEnum

strong

List of supported residue types in the loop that is to be represented by a series Jacobian.

Enumerator
ALPHA_AA
OTHER
num_types

Function Documentation

calculate_error_twist()

ModuleType1::Screw core::kinematics::jacobian::calculate_error_twist	(	core::kinematics::RT const	RT_current,
		core::kinematics::RT const	RT_target
	)

Extract the error twist (linearized rotations) from the current and target position and orientation (in Euler angles)

calculates the error twist between two RT objects, i.e. the linearised dual vector between them

References core::kinematics::RT::get_rotation(), core::kinematics::RT::get_translation(), and project_ZYX_euler_on_cart().

Referenced by protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::apply().

project_ZYX_euler_on_cart()

numeric::xyzVector<core::Real> core::kinematics::jacobian::project_ZYX_euler_on_cart	(	numeric::xyzVector< core::Real > const	euler_angles,
		numeric::xyzVector< core::Real > const	euler_error
	)

projects intrinsic Euler angles onto extrinsic Euler angles in order XYZ (i.e. projected onto Cartesian unit vectors)

Referenced by calculate_error_twist().

TR()

static basic::Tracer core::kinematics::jacobian::TR ( "core.kinematics.jacobian.util"  )

static

Referenced by core::kinematics::jacobian::ModuleType1::get_jacobian_matrices(), and core::kinematics::jacobian::ModuleType1::get_orthogonal_wrenches_from_twists().

weigh_columns_by_energy_grad()

void core::kinematics::jacobian::weigh_columns_by_energy_grad	(	utility::vector1< numeric::MathVector< core::Real > > &	input_cols,
		utility::vector1< numeric::MathVector< core::Real > > const &	gradient_cols,
		core::Real const	scaling
	)

method that gives weights to different columns (that all represent the same error twist in their respective torsion space), according to a sigmoid function that gives greatest weight to input_cols alligned with negative gradient_cols. The shape of the sigmoid can be controlled using the variable 'scaling'

References margin_from_zero_in_jacobian_util.

weigh_columns_inversely_squared()

void core::kinematics::jacobian::weigh_columns_inversely_squared

(

utility::vector1< numeric::MathVector< core::Real > > &

input_cols

)

method that gives weights to different columns (that all represent the same error twist in their respective torsion space), inversely proportional to the norm of the required torsion changes

References margin_from_zero_in_jacobian_util.

Referenced by protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::apply().

Variable Documentation

margin_from_zero_in_jacobian_util

constexpr core::Real core::kinematics::jacobian::margin_from_zero_in_jacobian_util = 1e-6

constexpr

Referenced by weigh_columns_by_energy_grad(), and weigh_columns_inversely_squared().