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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::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< 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 More...
 
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...
 

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::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

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 
)
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, and protocols::forge::build::SegmentInsertConnectionScheme::N.

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 
)
void protocols::backrub::init_backrub_mover_with_options ( BackrubMover &  mover)
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

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