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:

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Collaboration diagram for protocols::toolbox::match_enzdes_util::InvrotTarget:

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Public Member Functions
	InvrotTarget ()

	~InvrotTarget ()

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
	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
	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...

virtual void	collect_all_inverse_rotamers (utility::vector1< InvrotCollectorOP > &invrot_collector) const
	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)

virtual	~InvrotTreeNodeBase ()

InvrotTreeNodeBaseCAP	parent_node () const

void	set_location_in_parent_node (Size location)

Size	location_in_parent_node () const

Protected Member Functions
virtual void	generate_representative_target_res_for_geom_cst (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

Definition at line 47 of file InvrotTarget.hh.

Constructor & Destructor Documentation

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

Definition at line 40 of file InvrotTarget.cc.

References all_target_res_, next_nodes_, and representative_target_res_for_geom_cst_.

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

Definition at line 48 of file InvrotTarget.cc.

Member Function Documentation

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

Definition at line 57 of file InvrotTarget.cc.

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

virtual

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.

Definition at line 114 of file InvrotTarget.cc.

References all_target_res_.

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

virtual

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.

Definition at line 123 of file InvrotTarget.cc.

References all_target_res_, next_nodes_, representative_target_res_for_geom_cst_, and core::io::serialization::size().

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

virtual

generate constraints against a certain pose

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

Definition at line 63 of file InvrotTarget.cc.

References next_nodes_.

virtual void protocols::toolbox::match_enzdes_util::InvrotTarget::generate_representative_target_res_for_geom_cst ( 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...

Definition at line 84 of file InvrotTarget.cc.

References generate_representative_target_res_for_geom_cst(), 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

Definition at line 157 of file InvrotTarget.cc.

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

Definition at line 163 of file InvrotTarget.cc.

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

Definition at line 51 of file InvrotTarget.cc.

References representative_target_res_for_geom_cst_.