#include <InvrotTree.hh>

Inheritance diagram for protocols::toolbox::match_enzdes_util::InvrotTree:

Collaboration diagram for protocols::toolbox::match_enzdes_util::InvrotTree:

Public Types
typedef core::Size	Size

Public Member Functions
	InvrotTree ()

virtual	~InvrotTree ()

core::scoring::constraints::ConstraintCOP	get_constraint_for_target_state (Size target_state) const

void	generate_inverse_rotamer_constraints (core::pose::Pose const &pose, AllowedSeqposForGeomCstCOP geomcst_seqpos)
	the main function, generate the constraints More...

utility::vector1 < InvrotCollectorCOP >	collect_all_inverse_rotamers () const
	convenience access function to the inverse rotamers in the tree note: the returned invrots can contain duplications, as every unique definition of the tree is returned More...

void	dump_invrots_tree_as_multimodel_pdbs (std::string filename_base) const
	visualization this can lead to several files being written, depending on the ambiguities in the tree More...

virtual void	generate_targets_and_inverse_rotamers ()=0
	important function 1: populate the tree should be called before folding a chain obviously see TheozymeInvrotTree below for example More...

virtual bool	check_pose_tree_compatibility (core::pose::Pose &pose) const =0
	important function 2: after a chain/pose has been generated, check whether it's compatible with the inverse rotamers in the tree this can change the pose again More...

Size	num_target_states () const

Protected Member Functions
void	clear_target_states ()

void	add_to_targets (InvrotTargetOP invrot_target)

Private Attributes
utility::vector1< InvrotTargetOP >	invrot_targets_

utility::vector1 < core::scoring::constraints::ConstraintCOP >	invrot_tree_constraints_

Detailed Description

abstract base class for the inverse rotamer tree is abstract so that in the future inverse rots could be generated in different ways than throug the enz cst machinery

Member Typedef Documentation

typedef core::Size protocols::toolbox::match_enzdes_util::InvrotTree::Size

Constructor & Destructor Documentation

protocols::toolbox::match_enzdes_util::InvrotTree::InvrotTree ( )

References invrot_targets_, and invrot_tree_constraints_.

protocols::toolbox::match_enzdes_util::InvrotTree::~InvrotTree ( )

virtual

Member Function Documentation

void protocols::toolbox::match_enzdes_util::InvrotTree::add_to_targets ( InvrotTargetOP invrot_target)

protected

References invrot_targets_.

Referenced by protocols::toolbox::match_enzdes_util::TheozymeInvrotTree::generate_targets_and_inverse_rotamers().

virtual bool protocols::toolbox::match_enzdes_util::InvrotTree::check_pose_tree_compatibility ( core::pose::Pose & pose) const

pure virtual

important function 2: after a chain/pose has been generated, check whether it's compatible with the inverse rotamers in the tree this can change the pose again

Implemented in protocols::toolbox::match_enzdes_util::TheozymeInvrotTree.

void protocols::toolbox::match_enzdes_util::InvrotTree::clear_target_states ( )

protected

References invrot_targets_.

Referenced by protocols::toolbox::match_enzdes_util::TheozymeInvrotTree::generate_targets_and_inverse_rotamers().

utility::vector1< InvrotCollectorCOP > protocols::toolbox::match_enzdes_util::InvrotTree::collect_all_inverse_rotamers ( ) const

convenience access function to the inverse rotamers in the tree note: the returned invrots can contain duplications, as every unique definition of the tree is returned

References invrot_targets_.

Referenced by dump_invrots_tree_as_multimodel_pdbs().

void protocols::toolbox::match_enzdes_util::InvrotTree::dump_invrots_tree_as_multimodel_pdbs ( std::string filename_base) const

visualization this can lead to several files being written, depending on the ambiguities in the tree

References collect_all_inverse_rotamers(), core::io::pdb::dump_pdb_residue(), core::sequence::end, protocols::abinitio::filename(), and protocols::toolbox::match_enzdes_util::tr().

void protocols::toolbox::match_enzdes_util::InvrotTree::generate_inverse_rotamer_constraints	(	core::pose::Pose const &	pose,
		AllowedSeqposForGeomCstCOP	geomcst_seqpos
	)

the main function, generate the constraints

References invrot_targets_, and invrot_tree_constraints_.

virtual void protocols::toolbox::match_enzdes_util::InvrotTree::generate_targets_and_inverse_rotamers ( )

pure virtual

important function 1: populate the tree should be called before folding a chain obviously see TheozymeInvrotTree below for example

Implemented in protocols::toolbox::match_enzdes_util::TheozymeInvrotTree.

core::scoring::constraints::ConstraintCOP protocols::toolbox::match_enzdes_util::InvrotTree::get_constraint_for_target_state ( Size target_state) const

References invrot_tree_constraints_.

Size protocols::toolbox::match_enzdes_util::InvrotTree::num_target_states ( ) const

inline

References invrot_targets_.

Referenced by protocols::toolbox::match_enzdes_util::TheozymeInvrotTree::generate_targets_and_inverse_rotamers().