Rosetta 3.4
Classes | Typedefs | Functions
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::owning_ptr
< BackrubMover
BackrubMoverOP
typedef
utility::pointer::owning_ptr
< BackrubMover const > 
BackrubMoverCOP
typedef
utility::pointer::owning_ptr
< BackrubSidechainMover
BackrubSidechainMoverOP
typedef
utility::pointer::owning_ptr
< BackrubSidechainMover const > 
BackrubSidechainMoverCOP

Functions

void init_backrub_mover_with_options (BackrubMover &mover)
int tree_distance (kinematics::tree::Atom const *ancestor, kinematics::tree::Atom const *descendent)
 calculate the number of atom tree bonds between the two atoms possibly move this into the Atom class
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::Atom const *PM2_atom, core::kinematics::tree::Atom const *PM1_atom, core::kinematics::tree::Atom const *P_atom, core::kinematics::tree::Atom const *PP1_atom, core::kinematics::tree::Atom const *PP2_atom, core::kinematics::tree::Atom const *REF_atom, utility::vector0< Real > &constants, core::Real const alpha_min, core::Real const alpha_max, numeric::IntervalSet< core::Real > *tau_intervals)
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
void backrub_rotation_constants (core::kinematics::tree::Atom const *PM2_atom, core::kinematics::tree::Atom const *PM1_atom, core::kinematics::tree::Atom const *P_atom, core::kinematics::tree::Atom const *PP1_atom, core::kinematics::tree::Atom const *PP2_atom, core::kinematics::tree::Atom const *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

Typedef Documentation


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

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

void protocols::backrub::backrub_rotation_constants ( core::kinematics::tree::Atom const *  PM2_atom,
core::kinematics::tree::Atom const *  PM1_atom,
core::kinematics::tree::Atom const *  P_atom,
core::kinematics::tree::Atom const *  PP1_atom,
core::kinematics::tree::Atom const *  PP2_atom,
core::kinematics::tree::Atom const *  REF_atom,
utility::vector0< Real > &  constants,
core::Real const  alpha_min,
core::Real const  alpha_max,
numeric::IntervalSet< core::Real > *  tau_intervals 
)
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 protocols::forge::build::SegmentInsertConnectionScheme::C, protocols::frag_picker::CA, protocols::forge::build::SegmentInsertConnectionScheme::N, and core::kinematics::tree::Atom::xyz().

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

void protocols::backrub::backrub_rotation_constants ( core::kinematics::tree::Atom const *  PM2_atom,
core::kinematics::tree::Atom const *  PM1_atom,
core::kinematics::tree::Atom const *  P_atom,
core::kinematics::tree::Atom const *  PP1_atom,
core::kinematics::tree::Atom const *  PP2_atom,
core::kinematics::tree::Atom const *  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

core::Size protocols::backrub::connected_mainchain_atomids ( Pose const &  pose,
core::id::AtomID  atomid,
utility::vector1< core::id::AtomID > &  atomids 
)
void protocols::backrub::init_backrub_mover_with_options ( BackrubMover &  mover)
int protocols::backrub::tree_distance ( kinematics::tree::Atom const *  ancestor,
kinematics::tree::Atom const *  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().

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