the 'root' target against which the inverse rotamers are built abstract base class to allow for invrots being built against any sort of entity More...

#include <InvrotTarget.hh>

Inheritance diagram for protocols::toolbox::match_enzdes_util::InvrotTarget:

[legend]

Public Member Functions
	InvrotTarget ()

	~InvrotTarget () override

core::conformation::ResidueCOP	target_res_for_geom_cst (core::Size geom_cst) const

std::list < core::conformation::ResidueCOP >	all_target_res () const

core::scoring::constraints::ConstraintCOP	generate_constraints (core::pose::Pose const &pose, AllowedSeqposForGeomCstCOP geomcst_seqpos) const override
	generate constraints against a certain pose More...

bool	initialize_tree_nodes_from_enzcst_io (EnzConstraintIOCOP enzcst_io)
	can initialize tree nodes according to an enzcst io note that this function presumes that representative_target_res_for_geom_cst_ and all_target_res_ have been set through calling the generate_representative_target_res_for_geom_cst() function as implemented by the child class More...

utility::vector1< std::list < core::conformation::ResidueCOP > >	all_target_residues (InvrotTreeNodeBaseCAP child_node) const override
	this function traverses up the tree and adds the target residue for every geomcst in the branch toward this node used for clash checking, i.e. in case where the interaction is lig<-geomcst1-<geomcst2-<geomcst3, we don't want geomcst2 rots that clash with the ligand, and we don't wand geomcst3 rots that clash with the ligand or geomcst1 res the child node argument usually represents the node that is asking for the target residues, i.e. the node that's calling this function More...

void	collect_all_inverse_rotamers (utility::vector1< InvrotCollectorOP > &invrot_collector) const override
	convenience funtion to get all inverse rotamers in the tree puts all the inverse rotamers associated with this node into vector, and should call this function on daughter nodes uses std:vector because the targets will be put into 0th element needs vector of vector bc there can be different definitions of the tree More...

Public Member Functions inherited from protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase
	InvrotTreeNodeBase (InvrotTreeNodeBaseCAP parent_node)

	~InvrotTreeNodeBase () override

InvrotTreeNodeBaseCOP	get_self_ptr () const
	self pointers More...

InvrotTreeNodeBaseOP	get_self_ptr ()

InvrotTreeNodeBaseCAP	get_self_weak_ptr () const

InvrotTreeNodeBaseAP	get_self_weak_ptr ()

InvrotTreeNodeBaseCAP	parent_node () const

void	set_location_in_parent_node (core::Size location)

core::Size	location_in_parent_node () const

Protected Member Functions
virtual void	generate_representative_target_res_for_geom_cst (core::Size const num_geom_cst)=0
	this function figures out the coordinates (in Residue format) of the target residue for each geomcst. for a ligand, it's simply that ligand More...

void	set_all_target_res (std::list< core::conformation::ResidueCOP > const &all_target_res)

void	set_representative_target_res_for_geom_cst (utility::vector1< core::conformation::ResidueCOP > const &representative_res)

Private Attributes
utility::vector1 < core::conformation::ResidueCOP >	representative_target_res_for_geom_cst_

std::list < core::conformation::ResidueCOP >	all_target_res_

utility::vector1 < InvrotTreeNodeOP >	next_nodes_

Detailed Description

the 'root' target against which the inverse rotamers are built abstract base class to allow for invrots being built against any sort of entity

Constructor & Destructor Documentation

protocols::toolbox::match_enzdes_util::InvrotTarget::InvrotTarget ( )

References all_target_res_, next_nodes_, and representative_target_res_for_geom_cst_.

protocols::toolbox::match_enzdes_util::InvrotTarget::~InvrotTarget ( )

overridedefault

Member Function Documentation

std::list< core::conformation::ResidueCOP > protocols::toolbox::match_enzdes_util::InvrotTarget::all_target_res ( ) const

References all_target_res_.

Referenced by set_all_target_res().

utility::vector1< std::list< core::conformation::ResidueCOP > > protocols::toolbox::match_enzdes_util::InvrotTarget::all_target_residues ( InvrotTreeNodeBaseCAP child_node ) const

overridevirtual

this function traverses up the tree and adds the target residue for every geomcst in the branch toward this node used for clash checking, i.e. in case where the interaction is lig<-geomcst1-<geomcst2-<geomcst3, we don't want geomcst2 rots that clash with the ligand, and we don't wand geomcst3 rots that clash with the ligand or geomcst1 res the child node argument usually represents the node that is asking for the target residues, i.e. the node that's calling this function

Implements protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase.

References all_target_res_.

void protocols::toolbox::match_enzdes_util::InvrotTarget::collect_all_inverse_rotamers ( utility::vector1< InvrotCollectorOP > & invrot_collectors ) const

overridevirtual

convenience funtion to get all inverse rotamers in the tree puts all the inverse rotamers associated with this node into vector, and should call this function on daughter nodes uses std:vector because the targets will be put into 0th element needs vector of vector bc there can be different definitions of the tree

Implements protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase.

References all_target_res_, protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase::get_self_ptr(), next_nodes_, representative_target_res_for_geom_cst_, and core::id::to_string().

core::scoring::constraints::ConstraintCOP protocols::toolbox::match_enzdes_util::InvrotTarget::generate_constraints	(	core::pose::Pose const &	pose,
		AllowedSeqposForGeomCstCOP	geomcst_seqpos
	)		const

overridevirtual

generate constraints against a certain pose

Implements protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase.

References next_nodes_.

virtual void protocols::toolbox::match_enzdes_util::InvrotTarget::generate_representative_target_res_for_geom_cst ( core::Size const num_geom_cst )

protectedpure virtual

this function figures out the coordinates (in Residue format) of the target residue for each geomcst. for a ligand, it's simply that ligand

Implemented in protocols::toolbox::match_enzdes_util::SingleResidueInvrotTarget.

Referenced by initialize_tree_nodes_from_enzcst_io().

bool protocols::toolbox::match_enzdes_util::InvrotTarget::initialize_tree_nodes_from_enzcst_io ( EnzConstraintIOCOP enzcst_io )

can initialize tree nodes according to an enzcst io note that this function presumes that representative_target_res_for_geom_cst_ and all_target_res_ have been set through calling the generate_representative_target_res_for_geom_cst() function as implemented by the child class

the meat...

References generate_representative_target_res_for_geom_cst(), protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase::get_self_weak_ptr(), next_nodes_, representative_target_res_for_geom_cst_, and protocols::toolbox::match_enzdes_util::tr().

void protocols::toolbox::match_enzdes_util::InvrotTarget::set_all_target_res ( std::list< core::conformation::ResidueCOP > const & all_target_res )

protected

References all_target_res(), and all_target_res_.

Referenced by protocols::toolbox::match_enzdes_util::SingleResidueInvrotTarget::SingleResidueInvrotTarget().

void protocols::toolbox::match_enzdes_util::InvrotTarget::set_representative_target_res_for_geom_cst ( utility::vector1< core::conformation::ResidueCOP > const & representative_res )

protected

References representative_target_res_for_geom_cst_.

Referenced by protocols::toolbox::match_enzdes_util::SingleResidueInvrotTarget::generate_representative_target_res_for_geom_cst().

core::conformation::ResidueCOP protocols::toolbox::match_enzdes_util::InvrotTarget::target_res_for_geom_cst ( core::Size geom_cst ) const

References representative_target_res_for_geom_cst_.

Member Data Documentation

std::list< core::conformation::ResidueCOP > protocols::toolbox::match_enzdes_util::InvrotTarget::all_target_res_

private

Referenced by all_target_res(), all_target_residues(), collect_all_inverse_rotamers(), InvrotTarget(), and set_all_target_res().

utility::vector1< InvrotTreeNodeOP > protocols::toolbox::match_enzdes_util::InvrotTarget::next_nodes_

private

Referenced by collect_all_inverse_rotamers(), generate_constraints(), initialize_tree_nodes_from_enzcst_io(), and InvrotTarget().

utility::vector1< core::conformation::ResidueCOP > protocols::toolbox::match_enzdes_util::InvrotTarget::representative_target_res_for_geom_cst_

private

Referenced by collect_all_inverse_rotamers(), initialize_tree_nodes_from_enzcst_io(), InvrotTarget(), set_representative_target_res_for_geom_cst(), and target_res_for_geom_cst().

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

src/protocols/toolbox/match_enzdes_util/InvrotTarget.hh
src/protocols/toolbox/match_enzdes_util/InvrotTarget.cc

Public Member Functions

Protected Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation