protocols::viewer Namespace Reference

Namespaces
	graphics_states_param

Classes
class	GraphicsState
class	SilentObserver
class	triangle
class	triangleIterator

Typedefs
typedef utility::pointer::shared_ptr< ConformationViewer >	ConformationViewerOP
typedef utility::pointer::shared_ptr< SilentObserver >	SilentObserverOP
typedef void *(*	VoidFunc) (void *)

Enumerations
enum	spheremode { SPHERE_MODE_BB , SPHERE_MODE_SC , SPHERE_MODE_LIGAND }

Functions
void	clear_conformation_viewers ()
	Allows for graceful exit of graphics viewers. More...
static std::string	empty_string ("")
void	add_conformation_viewer (core::conformation::Conformation &, std::string const &=empty_string, int const =900, int const =900, bool const =false, bool const =false, core::Vector const =core::Vector(0.0))
void	add_monte_carlo_viewer (moves::MonteCarlo &, std::string const &=empty_string, int const =900, int const =900, bool=false)
int	viewer_main (VoidFunc worker_main)
void	print_node (std::ostream &out, int residue_num, int atom_num, core::conformation::Conformation const &conf, std::string const &extras="")
void	print_node (std::ostream &out, int residue_num, std::string atom_name, core::conformation::Conformation const &conf, std::string const &extras="")
void	print_interres_bond (std::ostream &out, core::conformation::Residue const &rsd1, core::conformation::Residue const &rsd2, core::conformation::Conformation const &conf)
void	dump_residue_kinemage (std::ostream &out, core::conformation::Residue const &rsd, core::conformation::Conformation const &conf)
void	dump_structure_kinemage (std::ostream &out, core::conformation::Conformation const &conf)
	A better way to visualize the structure is use Prekin or KiNG's File | Import | Molecules command. More...
void	dump_foldtree_kinemage (std::ostream &out, core::kinematics::FoldTree const &fold_tree, core::conformation::Conformation const &conf)
void	visit_atomtree_node (std::ostream &out, core::kinematics::tree::Atom const &katom, core::conformation::Conformation const &conf)
void	dump_atomtree_kinemage (std::ostream &out, core::kinematics::AtomTree const &atom_tree, core::conformation::Conformation const &conf)
void	dump_pose_kinemage (std::string const &filename, core::pose::Pose const &pose)

Variables
const int	POLY_CASES [][21]
const int	VERTEX_OFF [][3]
const int	EDGE_NGHBRS [][3]

Typedef Documentation

ConformationViewerOP

typedef utility::pointer::shared_ptr< ConformationViewer > protocols::viewer::ConformationViewerOP

SilentObserverOP

typedef utility::pointer::shared_ptr< SilentObserver > protocols::viewer::SilentObserverOP

VoidFunc

typedef void*(* protocols::viewer::VoidFunc) (void *)

Enumeration Type Documentation

spheremode

enum protocols::viewer::spheremode

Enumerator
SPHERE_MODE_BB
SPHERE_MODE_SC
SPHERE_MODE_LIGAND

Function Documentation

add_conformation_viewer()

void protocols::viewer::add_conformation_viewer ( core::conformation::Conformation &  , std::string const &  = empty_string, int const  = 900, int const  = 900, bool const  = false, bool const  = false, core::Vector const  = core::Vector( 0.0 )  )

inline

Referenced by protocols::abinitio::AbrelaxMover::apply(), protocols::abinitio::MembraneAbinitio::apply(), protocols::antibody::design::AntibodyDesignMover::apply(), protocols::canonical_sampling::CanonicalSamplingMover::apply(), protocols::flexpep_docking::FlexPepDockingProtocol::apply(), protocols::ncbb::oop::OopDockDesignProtocol::apply(), protocols::rbsegment_relax::RBSegmentRelax::apply(), protocols::relax::FastRelax::apply(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::apply(), protocols::symmetric_docking::SymDockProtocol::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::jobdist::not_universal_main(), protocols::rna::movers::ErraserMinimizerMover::process_entire_pose(), protocols::rna::movers::ERRASER2Protocol::resample_full_model(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::run(), and protocols::jd2::JobDistributor::run_one_job().

add_monte_carlo_viewer()

void protocols::viewer::add_monte_carlo_viewer ( moves::MonteCarlo &  , std::string const &  = empty_string, int const  = 900, int const  = 900, bool  = false  )

inline

Referenced by protocols::backrub::BackrubProtocol::apply(), protocols::coupled_moves::CoupledMovesProtocol::apply(), and protocols::simple_moves::rational_mc::RationalMonteCarlo::RationalMonteCarlo().

clear_conformation_viewers()

void protocols::viewer::clear_conformation_viewers

(

)

Allows for graceful exit of graphics viewers.

Referenced by protocols::ncbb::oop::OopDockDesignProtocol::apply(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::apply(), protocols::rna::movers::ERRASER2Protocol::resample_full_model(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::run(), and protocols::rna::movers::write_checkpoint().

dump_atomtree_kinemage()

void protocols::viewer::dump_atomtree_kinemage	(	std::ostream &	out,
		core::kinematics::AtomTree const &	atom_tree,
		core::conformation::Conformation const &	conf
	)

References core::conformation::membrane::out, core::kinematics::AtomTree::root(), and visit_atomtree_node().

Referenced by dump_pose_kinemage().

dump_foldtree_kinemage()

void protocols::viewer::dump_foldtree_kinemage	(	std::ostream &	out,
		core::kinematics::FoldTree const &	fold_tree,
		core::conformation::Conformation const &	conf
	)

References core::kinematics::FoldTree::begin(), core::kinematics::FoldTree::end(), core::conformation::membrane::out, and print_node().

Referenced by dump_pose_kinemage().

dump_pose_kinemage()

void protocols::viewer::dump_pose_kinemage	(	std::string const &	filename,
		core::pose::Pose const &	pose
	)

References core::pose::Pose::atom_tree(), core::pose::Pose::conformation(), dump_atomtree_kinemage(), dump_foldtree_kinemage(), dump_structure_kinemage(), protocols::abinitio::filename(), core::pose::Pose::fold_tree(), and core::conformation::membrane::out.

dump_residue_kinemage()

void protocols::viewer::dump_residue_kinemage	(	std::ostream &	out,
		core::conformation::Residue const &	rsd,
		core::conformation::Conformation const &	conf
	)

References core::conformation::Residue::is_bonded(), core::chemical::ResidueType::n_possible_residue_connections(), core::conformation::Residue::natoms(), core::conformation::Residue::nbrs(), core::conformation::membrane::out, print_interres_bond(), print_node(), core::conformation::Conformation::residue(), core::conformation::Residue::residue_connection_partner(), core::conformation::Residue::seqpos(), core::conformation::Conformation::size(), and core::conformation::Residue::type().

Referenced by dump_structure_kinemage().

dump_structure_kinemage()

void protocols::viewer::dump_structure_kinemage	(	std::ostream &	out,
		core::conformation::Conformation const &	conf
	)

A better way to visualize the structure is use Prekin or KiNG's File | Import | Molecules command.

References dump_residue_kinemage(), core::conformation::membrane::out, core::conformation::Conformation::residue(), and core::conformation::Conformation::size().

Referenced by dump_pose_kinemage().

empty_string()

static std::string protocols::viewer::empty_string ( ""  )

static

Referenced by core::io::silent::SilentStruct::get_string_value().

print_interres_bond()

void protocols::viewer::print_interres_bond	(	std::ostream &	out,
		core::conformation::Residue const &	rsd1,
		core::conformation::Residue const &	rsd2,
		core::conformation::Conformation const &	conf
	)

References core::conformation::Residue::connect_atom(), core::conformation::membrane::out, print_node(), and core::conformation::Residue::seqpos().

Referenced by dump_residue_kinemage().

print_node() [1/2]

void protocols::viewer::print_node	(	std::ostream &	out,
		int	residue_num,
		int	atom_num,
		core::conformation::Conformation const &	conf,
		std::string const &	extras = ""
	)

References core::conformation::Residue::atom(), core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type(), protocols::loops::extras, core::chemical::AtomType::name(), core::chemical::ResidueTypeBase::name3(), core::conformation::membrane::out, core::conformation::Conformation::residue(), core::conformation::Conformation::residue_type(), core::conformation::Residue::seqpos(), and core::conformation::Atom::xyz().

Referenced by dump_foldtree_kinemage(), dump_residue_kinemage(), print_interres_bond(), print_node(), and visit_atomtree_node().

print_node() [2/2]

void protocols::viewer::print_node	(	std::ostream &	out,
		int	residue_num,
		std::string	atom_name,
		core::conformation::Conformation const &	conf,
		std::string const &	extras = ""
	)

References core::conformation::Residue::atom_index(), protocols::loops::extras, core::conformation::membrane::out, print_node(), and core::conformation::Conformation::residue().

viewer_main()

int protocols::viewer::viewer_main ( VoidFunc  worker_main )

inline

visit_atomtree_node()

void protocols::viewer::visit_atomtree_node	(	std::ostream &	out,
		core::kinematics::tree::Atom const &	katom,
		core::conformation::Conformation const &	conf
	)

References core::kinematics::tree::Atom::atom_id(), core::id::AtomID::atomno(), core::kinematics::tree::Atom::atoms_begin(), core::kinematics::tree::Atom::atoms_end(), core::kinematics::tree::Atom::is_jump(), core::conformation::membrane::out, core::kinematics::tree::Atom::parent(), print_node(), and core::id::AtomID::rsd().

Referenced by dump_atomtree_kinemage().

Variable Documentation

EDGE_NGHBRS

const int protocols::viewer::EDGE_NGHBRS

Initial value:

= {
{-1, -1, -1}, 
 
 
{ 1,  2,  0}, 
{ 2,  3,  1}, 
{ 3,  4,  3}, 
{ 4,  1,  4}, 
 
{ 5,  6,  0}, 
{ 6,  7,  1}, 
{ 7,  8,  3}, 
{ 8,  5,  4}, 
 
{ 1,  5,  2}, 
{ 2,  6,  2}, 
{ 4,  8,  2}, 
{ 3,  7,  2}  
}

Referenced by protocols::viewer::triangleIterator::aquireNextQueue().

POLY_CASES

const int protocols::viewer::POLY_CASES

Referenced by protocols::viewer::triangleIterator::aquireNextQueue().

VERTEX_OFF

const int protocols::viewer::VERTEX_OFF

Initial value:

= {
{-1, -1, -1}, 
{0, 0, 0},
{1, 0, 0},
{1, 1, 0},
{0, 1, 0},
{0, 0, 1},
{1, 0, 1},
{1, 1, 1},
{0, 1, 1}
}

Referenced by protocols::viewer::triangleIterator::aquireNextQueue().