FreePeptide represents a free peptide. More...

#include <FreePeptide.hh>

Inheritance diagram for protocols::backbone_moves::local_backbone_mover::FreePeptide:

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< Residue >	residues_

vector1< xyzVector< Real > >	old_stubs_

xyzVector< Real >	old_stub_centor_of_mass_

vector1< core::id::AtomID >	reference_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
	)

References old_stub_centor_of_mass_, old_stubs_, reference_atom_ids_, reference_coordinates_, residues_, and core::pose::Pose::xyz().

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 ( )

Align the stubs to the old stubs.

References c_xyz(), ca_xyz(), n_xyz(), old_stub_centor_of_mass_, old_stubs_, pivot1(), pivot2(), reference_coordinates_, protocols::seeded_abinitio::superposition_transform(), and xyz_updated_.

Referenced by protocols::backbone_moves::local_backbone_mover::free_peptide_movers::CircularPermuteFreePeptideMover::apply(), and protocols::backbone_moves::local_backbone_mover::free_peptide_movers::ShearFreePeptideMover::apply().

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

Getter of the c_n_bond.

References res_id(), and residues_.

Referenced by protocols::backbone_moves::local_backbone_mover::GapCloser::solve_a_gap(), and update_xyz_coords().

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

Getter of the c_n_ca_angle.

References res_id(), and residues_.

Referenced by protocols::backbone_moves::local_backbone_mover::GapCloser::solve_a_gap(), and update_xyz_coords().

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

Getter of the xyz coordinates of C.

References res_id(), residues_, update_xyz_coords(), and xyz_updated_.

Referenced by align(), protocols::backbone_moves::local_backbone_mover::GapCloser::solve_a_gap(), and update_xyz_coords().

Real protocols::backbone_moves::local_backbone_mover::FreePeptide::ca_c_bond ( core::Size seqpos )

inline

Getter of the ca_c_bond.

References res_id(), and residues_.

Referenced by protocols::backbone_moves::local_backbone_mover::GapCloser::solve_a_gap(), and update_xyz_coords().

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

Getter of the ca_c_n_angle.

References res_id(), and residues_.

Referenced by protocols::backbone_moves::local_backbone_mover::GapCloser::solve_a_gap(), and update_xyz_coords().

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

Getter of the xyz coordinates of CA.

References res_id(), residues_, update_xyz_coords(), and xyz_updated_.

Referenced by align(), protocols::backbone_moves::local_backbone_mover::free_peptide_movers::LongAxisRotationFreePeptideMover::apply(), protocols::backbone_moves::local_backbone_mover::GapCloser::solve_a_gap(), and update_xyz_coords().

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

Getter of the n_ca_bond.

References res_id(), and residues_.

Referenced by protocols::backbone_moves::local_backbone_mover::GapCloser::solve_a_gap(), and update_xyz_coords().

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

Getter of the n_ca_c_angle.

References res_id(), and residues_.

Referenced by protocols::backbone_moves::local_backbone_mover::GapCloser::solve_a_gap(), and update_xyz_coords().

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

Getter of the xyz coordinates of N.

References res_id(), residues_, update_xyz_coords(), and xyz_updated_.

Referenced by align(), protocols::backbone_moves::local_backbone_mover::GapCloser::solve_a_gap(), and update_xyz_coords().

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

Getter of the omega.

References res_id(), and residues_.

Referenced by protocols::backbone_moves::local_backbone_mover::free_peptide_movers::CircularPermuteFreePeptideMover::apply(), protocols::backbone_moves::local_backbone_mover::GapCloser::solve_a_gap(), and update_xyz_coords().

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

Getter of the phi.

References res_id(), and residues_.

Referenced by protocols::backbone_moves::local_backbone_mover::free_peptide_movers::CircularPermuteFreePeptideMover::apply(), protocols::backbone_moves::local_backbone_mover::free_peptide_movers::ShearFreePeptideMover::apply(), and update_xyz_coords().

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

Getter of the first pivot.

References pivot1_.

Referenced by align(), protocols::backbone_moves::local_backbone_mover::free_peptide_movers::CircularPermuteFreePeptideMover::apply(), protocols::backbone_moves::local_backbone_mover::free_peptide_movers::LongAxisRotationFreePeptideMover::apply(), protocols::backbone_moves::local_backbone_mover::GapCloser::apply_closure(), protocols::backbone_moves::local_backbone_mover::GapCloser::pick_solutions(), and protocols::backbone_moves::local_backbone_mover::GapCloser::solve_gaps().

core::Size protocols::backbone_moves::local_backbone_mover::FreePeptide::pivot2 ( )

inline

Getter of the second pivot.

References pivot2_.

Referenced by align(), protocols::backbone_moves::local_backbone_mover::free_peptide_movers::CircularPermuteFreePeptideMover::apply(), protocols::backbone_moves::local_backbone_mover::free_peptide_movers::LongAxisRotationFreePeptideMover::apply(), protocols::backbone_moves::local_backbone_mover::GapCloser::apply_closure(), protocols::backbone_moves::local_backbone_mover::GapCloser::pick_solutions(), and protocols::backbone_moves::local_backbone_mover::GapCloser::solve_gaps().

Real protocols::backbone_moves::local_backbone_mover::FreePeptide::psi ( core::Size seqpos )

inline

Getter of the psi.

References res_id(), and residues_.

Referenced by protocols::backbone_moves::local_backbone_mover::free_peptide_movers::CircularPermuteFreePeptideMover::apply(), protocols::backbone_moves::local_backbone_mover::free_peptide_movers::ShearFreePeptideMover::apply(), and update_xyz_coords().

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 )

Translate the free peptide by the vector v.

References reference_coordinates_, and xyz_updated_.

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

void protocols::backbone_moves::local_backbone_mover::FreePeptide::update_xyz_coords ( )

Update the xyz coordinates of the residues.

References 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(), pivot2_, psi(), reference_coordinates_, res_id(), residues_, protocols::backbone_moves::local_backbone_mover::xyz_from_internal_coords(), and xyz_updated_.

Referenced by c_xyz(), ca_xyz(), and n_xyz().

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

Referenced by apply_to_pose(), number_of_atoms(), number_of_residues(), pivot1(), res_id(), and seqpos().

core::Size protocols::backbone_moves::local_backbone_mover::FreePeptide::pivot2_

private

Referenced by apply_to_pose(), number_of_atoms(), number_of_residues(), pivot2(), res_id(), seqpos(), and update_xyz_coords().

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

Referenced by align(), FreePeptide(), rotate(), translate(), and update_xyz_coords().

vector1<Residue> protocols::backbone_moves::local_backbone_mover::FreePeptide::residues_

private

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

bool protocols::backbone_moves::local_backbone_mover::FreePeptide::xyz_updated_ = false

private

Referenced by align(), 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(), rotate(), translate(), and update_xyz_coords().

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

src/protocols/backbone_moves/local_backbone_mover/FreePeptide.hh
src/protocols/backbone_moves/local_backbone_mover/FreePeptide.cc

Public Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation