protocols::denovo_design Namespace Reference

Namespaces
	filters

Classes
class	DisulfidizeMover
class	DisulfidizeMoverCreator

Typedefs
typedef utility::pointer::shared_ptr < DisulfidizerMover >	DisulfidizerMoverOP
typedef utility::pointer::shared_ptr < DisulfidizerMover const >	DisulfidizerMoverCOP
typedef utility::pointer::weak_ptr < DisulfidizerMover >	DisulfidizerMoverAP
typedef utility::pointer::weak_ptr < DisulfidizerMover const >	DisulfidizerMoverCAP

Functions
void	add_to_list (DisulfidizeMover::DisulfideList &disulf_partners, core::Size const r1, core::Size const r2)
bool	same_pose (core::pose::Pose const &pose1, core::pose::Pose const &pose2)
	Tells whether the two given poses are identical based on # resides and dihedrals. More...
void	construct_poly_ala_pose (core::pose::Pose &pose, bool const keep_disulf, std::set< core::Size > const &set1, std::set< core::Size > const &set2)
	creates a poly-ala pose where every non-gly, non-cyd, protein residue except those in the given set are converted to alanine More...
void	construct_poly_ala_pose (core::pose::Pose &pose, bool const keep_disulf, std::set< core::Size > const &res_set)
	creates a poly-ala pose where every non-gly, non-cyd, protein residue except those in the given set are converted to alanine More...
std::ostream &	operator<< (std::ostream &os, numeric::xyzMatrix< core::Real > const &mat)
	Output operators for std classes ///. More...
std::ostream &	operator<< (std::ostream &os, std::set< core::Size > const &set)
	outputs a set More...
std::ostream &	operator<< (std::ostream &os, std::list< std::string > const &list)
	outputs a list of strings More...
std::ostream &	operator<< (std::ostream &os, std::set< std::string > const &set)
	outputs a set More...
std::ostream &	operator<< (std::ostream &os, std::map< core::Size, core::Size > const &map)
	outputs a map More...
std::ostream &	operator<< (std::ostream &os, std::map< std::string, core::Size > const &map)
	outputs a map More...
std::ostream &	operator<< (std::ostream &os, std::map< std::pair< std::string, std::string >, core::Size > const &map)
	outputs a map More...
std::ostream &	operator<< (std::ostream &os, std::map< std::string, core::Real > const &map)
	outputs a map More...

Typedef Documentation

typedef utility::pointer::weak_ptr< DisulfidizerMover > protocols::denovo_design::DisulfidizerMoverAP

typedef utility::pointer::weak_ptr< DisulfidizerMover const > protocols::denovo_design::DisulfidizerMoverCAP

typedef utility::pointer::shared_ptr< DisulfidizerMover const > protocols::denovo_design::DisulfidizerMoverCOP

typedef utility::pointer::shared_ptr< DisulfidizerMover > protocols::denovo_design::DisulfidizerMoverOP

Function Documentation

void protocols::denovo_design::add_to_list	(	DisulfidizeMover::DisulfideList &	disulf_partners,
		core::Size const	r1,
		core::Size const	r2
	)

Referenced by protocols::denovo_design::DisulfidizeMover::find_disulfides_in_the_neighborhood().

void protocols::denovo_design::construct_poly_ala_pose	(	core::pose::Pose &	pose,
		bool const	keep_disulf,
		std::set< core::Size > const &	set1,
		std::set< core::Size > const &	set2
	)

creates a poly-ala pose where every non-gly, non-cyd, protein residue except those in the given set are converted to alanine

Referenced by protocols::forge::components::BDR::centroid_build(), and protocols::denovo_design::DisulfidizeMover::find_disulfides_in_the_neighborhood().

void protocols::denovo_design::construct_poly_ala_pose	(	core::pose::Pose &	pose,
		bool const	keep_disulf,
		std::set< core::Size > const &	res_set
	)

creates a poly-ala pose where every non-gly, non-cyd, protein residue except those in the given set are converted to alanine

References protocols::simple_moves::MutateResidue::apply(), protocols::toolbox::pose_manipulation::construct_poly_ala_pose(), core::conformation::Residue::is_protein(), core::conformation::Residue::name(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

std::ostream& protocols::denovo_design::operator<<	(	std::ostream &	os,
		numeric::xyzMatrix< core::Real > const &	mat
	)

Output operators for std classes ///.

outputs a matrix

std::ostream & protocols::denovo_design::operator<<	(	std::ostream &	os,
		std::set< core::Size > const &	set
	)

outputs a set

Output operators for std template classes ///.

outputs a set

std::ostream & protocols::denovo_design::operator<<	(	std::ostream &	os,
		std::list< std::string > const &	list
	)

outputs a list of strings

References c, and end.

std::ostream & protocols::denovo_design::operator<<	(	std::ostream &	os,
		std::set< std::string > const &	set
	)

outputs a set

std::ostream & protocols::denovo_design::operator<<	(	std::ostream &	os,
		std::map< core::Size, core::Size > const &	map
	)

outputs a map

std::ostream & protocols::denovo_design::operator<<	(	std::ostream &	os,
		std::map< std::string, core::Size > const &	map
	)

outputs a map

std::ostream & protocols::denovo_design::operator<<	(	std::ostream &	os,
		std::map< std::pair< std::string, std::string >, core::Size > const &	map
	)

outputs a map

std::ostream & protocols::denovo_design::operator<<	(	std::ostream &	os,
		std::map< std::string, core::Real > const &	map
	)

outputs a map

bool protocols::denovo_design::same_pose	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2
	)

Tells whether the two given poses are identical based on # resides and dihedrals.

References core::conformation::Residue::is_protein(), core::conformation::Residue::name(), core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().