protocols::backrub Namespace Reference

Classes
class	BackrubMover
	class for applying backrub moves to arbitrary protein segments More...
class	BackrubMoverCreator
class	BackrubSegment
	a class for holind information about individual backrub segments More...
class	BackrubSidechainMover
class	BackrubSidechainMoverCreator

Typedefs
typedef utility::pointer::shared_ptr < BackrubMover >	BackrubMoverOP
typedef utility::pointer::shared_ptr < BackrubMover const >	BackrubMoverCOP
typedef utility::pointer::shared_ptr < BackrubSidechainMover >	BackrubSidechainMoverOP
typedef utility::pointer::shared_ptr < BackrubSidechainMover const >	BackrubSidechainMoverCOP

Functions
void	init_backrub_mover_with_options (BackrubMover &mover)
int	tree_distance (kinematics::tree::AtomCOP ancestor, kinematics::tree::AtomCOP descendent)
	calculate the number of atom tree bonds between the two atoms possibly move this into the Atom class More...
core::Size	connected_mainchain_atomids (Pose const &pose, core::id::AtomID atomid, utility::vector1< core::id::AtomID > &atomids)
void	backrub_rotation_constants (core::kinematics::tree::AtomCOP PM2_atom, core::kinematics::tree::AtomCOP PM1_atom, core::kinematics::tree::AtomCOP P_atom, core::kinematics::tree::AtomCOP PP1_atom, core::kinematics::tree::AtomCOP PP2_atom, core::kinematics::tree::AtomCOP REF_atom, utility::vector0< double > &constants, core::Real const alpha_min=0, core::Real const alpha_max=numeric::NumericTraits< core::Real >::pi(), numeric::IntervalSet< core::Real > *tau_intervals=NULL)
	calculate constants necessary for calculating internal angles/derivatives More...
void	backrub_rotation_angles (utility::vector0< core::Real > const &constants, core::Real const tau, core::Real &bondange, core::Real &torsion1, core::Real &torsion2)
	calculate internal coordinate values for any tau value More...

Typedef Documentation

typedef utility::pointer::shared_ptr< BackrubMover const > protocols::backrub::BackrubMoverCOP

typedef utility::pointer::shared_ptr< BackrubMover > protocols::backrub::BackrubMoverOP

typedef utility::pointer::shared_ptr< BackrubSidechainMover const > protocols::backrub::BackrubSidechainMoverCOP

typedef utility::pointer::shared_ptr< BackrubSidechainMover > protocols::backrub::BackrubSidechainMoverOP

Function Documentation

void protocols::backrub::backrub_rotation_angles	(	utility::vector0< Real > const &	constants,
		Real const	tau,
		Real &	bondange,
		Real &	torsion1,
		Real &	torsion2
	)

calculate internal coordinate values for any tau value

Detailed:

tau is the angular displacement

References numeric::sin_cos_range(), and sin_cos_range().

Referenced by protocols::backrub::BackrubMover::rotate_segment().

void protocols::backrub::backrub_rotation_constants	(	core::kinematics::tree::AtomCOP	PM2_atom,
		core::kinematics::tree::AtomCOP	PM1_atom,
		core::kinematics::tree::AtomCOP	P_atom,
		core::kinematics::tree::AtomCOP	PP1_atom,
		core::kinematics::tree::AtomCOP	PP2_atom,
		core::kinematics::tree::AtomCOP	REF_atom,
		utility::vector0< Real > &	constants,
		core::Real const	alpha_min,
		core::Real const	alpha_max,
		numeric::IntervalSet< core::Real > *	tau_intervals
	)

calculate constants necessary for calculating internal angles/derivatives

Detailed:

PM1 & PM2 are the parent and grandparent atoms (respectively) of the pivot atom, P. PP1 and PP2 are the child and grandchiled atoms (respectively) of the pivot atom. PM2 and PP2 are optional and may be NULL. REF is the other (reference) pivot atom that defines the rotation axis.

The first 9 constants returned represent A1-A3, B1-B3, & C1-C3 as described in Betancourt 2005. The last 6 constants allow calculation of the signs of phi and psi. They could be called B4-B6 & C4-C6. For a given tau angle, phi is negative if the following is true:

B4 < B5 * cos(B6 + tau)

Similarly, psi is negative if the following is true:

C4 < C5 * cos(C6 + tau)

References C, protocols::frag_picker::CA, cross(), dot(), in_sin_cos_range(), numeric::in_sin_cos_range(), N, numeric::nearest_angle_radians(), normalize(), pi, numeric::conversions::radians(), numeric::IntervalSet< class >::set(), numeric::sin_cos_range(), sin_cos_range(), U, V, and W.

Referenced by protocols::backrub::BackrubMover::random_angle(), and protocols::backrub::BackrubMover::rotate_segment().

core::Size protocols::backrub::connected_mainchain_atomids	(	Pose const &	pose,
		core::id::AtomID	atomid,
		utility::vector1< core::id::AtomID > &	atomids
	)

References core::id::AtomID::atomno(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::id::AtomID::rsd().

Referenced by protocols::backrub::BackrubMover::add_mainchain_segments().

void protocols::backrub::init_backrub_mover_with_options

(

BackrubMover &

mover

)

References option, protocols::backrub::BackrubMover::set_max_atoms(), protocols::backrub::BackrubMover::set_min_atoms(), protocols::backrub::BackrubMover::set_pivot_atoms(), and protocols::backrub::BackrubMover::set_pivot_residues().

Referenced by protocols::backrub::BackrubMover::init_with_options().

int protocols::backrub::tree_distance	(	kinematics::tree::AtomCOP	ancestor,
		kinematics::tree::AtomCOP	descendent
	)

calculate the number of atom tree bonds between the two atoms possibly move this into the Atom class

References core::kinematics::tree::Atom::parent().

Referenced by protocols::backrub::BackrubMover::add_segment().