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protocols::backbone_moves::local_backbone_mover::FreePeptide Class Reference

FreePeptide represents a free peptide. More...

#include <FreePeptide.hh>

Inheritance diagram for protocols::backbone_moves::local_backbone_mover::FreePeptide:
Inheritance graph
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Public Member Functions

 FreePeptide (core::pose::Pose const &pose, core::Size pivot1, core::Size pivot2)
 
 FreePeptide (FreePeptide const &)=default
 
 ~FreePeptide () override
 
FreePeptideOP clone () const
 
core::Size number_of_atoms ()
 Total number of atoms Only consider atoms in the free peptide, The N of the first residue and C of the last residue are excluded. More...
 
core::Size number_of_residues ()
 Total number of free peptide residues. More...
 
core::Size pivot1 ()
 Getter of the first pivot. More...
 
core::Size pivot2 ()
 Getter of the second pivot. More...
 
Real n_ca_bond (core::Size seqpos)
 Getter of the n_ca_bond. More...
 
void n_ca_bond (core::Size seqpos, Real value)
 Setter of the n_ca_bond. More...
 
Real ca_c_bond (core::Size seqpos)
 Getter of the ca_c_bond. More...
 
void ca_c_bond (core::Size seqpos, Real value)
 Setter of the ca_c_bond. More...
 
Real c_n_bond (core::Size seqpos)
 Getter of the c_n_bond. More...
 
void c_n_bond (core::Size seqpos, Real value)
 Setter of the c_n_bond. More...
 
Real n_ca_c_angle (core::Size seqpos)
 Getter of the n_ca_c_angle. More...
 
void n_ca_c_angle (core::Size seqpos, Real value)
 Setter of the n_ca_c_angle. More...
 
Real ca_c_n_angle (core::Size seqpos)
 Getter of the ca_c_n_angle. More...
 
void ca_c_n_angle (core::Size seqpos, Real value)
 Setter of the ca_c_n_angle. More...
 
Real c_n_ca_angle (core::Size seqpos)
 Getter of the c_n_ca_angle. More...
 
void c_n_ca_angle (core::Size seqpos, Real value)
 Setter of the c_n_ca_angle. More...
 
Real phi (core::Size seqpos)
 Getter of the phi. More...
 
void phi (core::Size seqpos, Real value)
 Setter of the phi. More...
 
Real psi (core::Size seqpos)
 Getter of the psi. More...
 
void psi (core::Size seqpos, Real value)
 Setter of the psi. More...
 
Real omega (core::Size seqpos)
 Getter of the omega. More...
 
void omega (core::Size seqpos, Real value)
 Setter of the omega. More...
 
xyzVector< Real > n_xyz (core::Size seqpos)
 Getter of the xyz coordinates of N. More...
 
xyzVector< Real > ca_xyz (core::Size seqpos)
 Getter of the xyz coordinates of CA. More...
 
xyzVector< Real > c_xyz (core::Size seqpos)
 Getter of the xyz coordinates of C. More...
 
void apply_to_pose (core::pose::Pose &pose)
 Apply the coordinates of the free peptide to a pose. The internal coordinates from pivot1 - 1 to pivot2 + 1 will be apply to the pose. Torsions in the two gaps should be further reset to close the segment. More...
 
void update_xyz_coords ()
 Update the xyz coordinates of the residues. More...
 
void translate (xyzVector< Real > v)
 Translate the free peptide by the vector v. More...
 
void rotate (xyzMatrix< Real > M)
 Rotate the free peptide by the rotation matrix M The center of rotation is the CA atom of the first residue of the free peptide. More...
 
void align ()
 Align the stubs to the old stubs. More...
 

Private Member Functions

core::Size res_id (core::Size seqpos)
 Translate the seqpos to the id within the free peptide. More...
 
core::Size seqpos (core::Size res_id)
 Translate the id of a residue within the free peptide to its seqpos. More...
 

Private Attributes

core::Size pivot1_
 
core::Size pivot2_
 
vector1< Residueresidues_
 
vector1< xyzVector< Real > > old_stubs_
 
xyzVector< Real > old_stub_centor_of_mass_
 
vector1< core::id::AtomIDreference_atom_ids_
 
vector1< xyzVector< Real > > reference_coordinates_
 
bool xyz_updated_ = false
 

Friends

class ::LocalBackboneMoverTests
 

Detailed Description

FreePeptide represents a free peptide.

Constructor & Destructor Documentation

protocols::backbone_moves::local_backbone_mover::FreePeptide::FreePeptide ( core::pose::Pose const &  pose,
core::Size  pivot1,
core::Size  pivot2 
)
protocols::backbone_moves::local_backbone_mover::FreePeptide::FreePeptide ( FreePeptide const &  )
default
protocols::backbone_moves::local_backbone_mover::FreePeptide::~FreePeptide ( )
overridedefault

Member Function Documentation

void protocols::backbone_moves::local_backbone_mover::FreePeptide::align ( )
void protocols::backbone_moves::local_backbone_mover::FreePeptide::apply_to_pose ( core::pose::Pose pose)

Apply the coordinates of the free peptide to a pose. The internal coordinates from pivot1 - 1 to pivot2 + 1 will be apply to the pose. Torsions in the two gaps should be further reset to close the segment.

References pivot1_, pivot2_, res_id(), and residues_.

Referenced by protocols::backbone_moves::local_backbone_mover::GapCloser::apply_closure().

Real protocols::backbone_moves::local_backbone_mover::FreePeptide::c_n_bond ( core::Size  seqpos)
inline
void protocols::backbone_moves::local_backbone_mover::FreePeptide::c_n_bond ( core::Size  seqpos,
Real  value 
)
inline

Setter of the c_n_bond.

References res_id(), residues_, and xyz_updated_.

Real protocols::backbone_moves::local_backbone_mover::FreePeptide::c_n_ca_angle ( core::Size  seqpos)
inline
void protocols::backbone_moves::local_backbone_mover::FreePeptide::c_n_ca_angle ( core::Size  seqpos,
Real  value 
)
inline

Setter of the c_n_ca_angle.

References res_id(), residues_, and xyz_updated_.

xyzVector<Real> protocols::backbone_moves::local_backbone_mover::FreePeptide::c_xyz ( core::Size  seqpos)
inline
Real protocols::backbone_moves::local_backbone_mover::FreePeptide::ca_c_bond ( core::Size  seqpos)
inline
void protocols::backbone_moves::local_backbone_mover::FreePeptide::ca_c_bond ( core::Size  seqpos,
Real  value 
)
inline

Setter of the ca_c_bond.

References res_id(), residues_, and xyz_updated_.

Real protocols::backbone_moves::local_backbone_mover::FreePeptide::ca_c_n_angle ( core::Size  seqpos)
inline
void protocols::backbone_moves::local_backbone_mover::FreePeptide::ca_c_n_angle ( core::Size  seqpos,
Real  value 
)
inline

Setter of the ca_c_n_angle.

References res_id(), residues_, and xyz_updated_.

xyzVector<Real> protocols::backbone_moves::local_backbone_mover::FreePeptide::ca_xyz ( core::Size  seqpos)
inline
FreePeptideOP protocols::backbone_moves::local_backbone_mover::FreePeptide::clone ( ) const
Real protocols::backbone_moves::local_backbone_mover::FreePeptide::n_ca_bond ( core::Size  seqpos)
inline
void protocols::backbone_moves::local_backbone_mover::FreePeptide::n_ca_bond ( core::Size  seqpos,
Real  value 
)
inline

Setter of the n_ca_bond.

References res_id(), residues_, and xyz_updated_.

Real protocols::backbone_moves::local_backbone_mover::FreePeptide::n_ca_c_angle ( core::Size  seqpos)
inline
void protocols::backbone_moves::local_backbone_mover::FreePeptide::n_ca_c_angle ( core::Size  seqpos,
Real  value 
)
inline

Setter of the n_ca_c_angle.

References res_id(), residues_, and xyz_updated_.

xyzVector<Real> protocols::backbone_moves::local_backbone_mover::FreePeptide::n_xyz ( core::Size  seqpos)
inline
core::Size protocols::backbone_moves::local_backbone_mover::FreePeptide::number_of_atoms ( )
inline

Total number of atoms Only consider atoms in the free peptide, The N of the first residue and C of the last residue are excluded.

References pivot1_, and pivot2_.

core::Size protocols::backbone_moves::local_backbone_mover::FreePeptide::number_of_residues ( )
inline

Total number of free peptide residues.

References pivot1_, and pivot2_.

Real protocols::backbone_moves::local_backbone_mover::FreePeptide::omega ( core::Size  seqpos)
inline
void protocols::backbone_moves::local_backbone_mover::FreePeptide::omega ( core::Size  seqpos,
Real  value 
)
inline

Setter of the omega.

References res_id(), residues_, and xyz_updated_.

Real protocols::backbone_moves::local_backbone_mover::FreePeptide::phi ( core::Size  seqpos)
inline
void protocols::backbone_moves::local_backbone_mover::FreePeptide::phi ( core::Size  seqpos,
Real  value 
)
inline

Setter of the phi.

References res_id(), residues_, and xyz_updated_.

core::Size protocols::backbone_moves::local_backbone_mover::FreePeptide::pivot1 ( )
inline
core::Size protocols::backbone_moves::local_backbone_mover::FreePeptide::pivot2 ( )
inline
Real protocols::backbone_moves::local_backbone_mover::FreePeptide::psi ( core::Size  seqpos)
inline
void protocols::backbone_moves::local_backbone_mover::FreePeptide::psi ( core::Size  seqpos,
Real  value 
)
inline

Setter of the psi.

References res_id(), residues_, and xyz_updated_.

core::Size protocols::backbone_moves::local_backbone_mover::FreePeptide::res_id ( core::Size  seqpos)
inlineprivate

Translate the seqpos to the id within the free peptide.

References pivot1_, and pivot2_.

Referenced by apply_to_pose(), c_n_bond(), c_n_ca_angle(), c_xyz(), ca_c_bond(), ca_c_n_angle(), ca_xyz(), n_ca_bond(), n_ca_c_angle(), n_xyz(), omega(), phi(), psi(), and update_xyz_coords().

void protocols::backbone_moves::local_backbone_mover::FreePeptide::rotate ( xyzMatrix< Real >  M)

Rotate the free peptide by the rotation matrix M The center of rotation is the CA atom of the first residue of the free peptide.

References core::conformation::membrane::center, reference_coordinates_, and xyz_updated_.

Referenced by protocols::backbone_moves::local_backbone_mover::free_peptide_movers::LongAxisRotationFreePeptideMover::apply().

core::Size protocols::backbone_moves::local_backbone_mover::FreePeptide::seqpos ( core::Size  res_id)
inlineprivate

Translate the id of a residue within the free peptide to its seqpos.

References pivot1_, and pivot2_.

void protocols::backbone_moves::local_backbone_mover::FreePeptide::translate ( xyzVector< Real >  v)
void protocols::backbone_moves::local_backbone_mover::FreePeptide::update_xyz_coords ( )

Friends And Related Function Documentation

friend class ::LocalBackboneMoverTests
friend

Member Data Documentation

xyzVector<Real> protocols::backbone_moves::local_backbone_mover::FreePeptide::old_stub_centor_of_mass_
private

Referenced by align(), and FreePeptide().

vector1< xyzVector<Real> > protocols::backbone_moves::local_backbone_mover::FreePeptide::old_stubs_
private

Referenced by align(), and FreePeptide().

core::Size protocols::backbone_moves::local_backbone_mover::FreePeptide::pivot1_
private
core::Size protocols::backbone_moves::local_backbone_mover::FreePeptide::pivot2_
private
vector1<core::id::AtomID> protocols::backbone_moves::local_backbone_mover::FreePeptide::reference_atom_ids_
private

Referenced by FreePeptide().

vector1< xyzVector<Real> > protocols::backbone_moves::local_backbone_mover::FreePeptide::reference_coordinates_
private
vector1<Residue> protocols::backbone_moves::local_backbone_mover::FreePeptide::residues_
private
bool protocols::backbone_moves::local_backbone_mover::FreePeptide::xyz_updated_ = false
private

The documentation for this class was generated from the following files: