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protocols::toolbox::match_enzdes_util::InvrotTarget Class Referenceabstract

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:
Inheritance graph
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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 ( )
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
void protocols::toolbox::match_enzdes_util::InvrotTarget::set_representative_target_res_for_geom_cst ( utility::vector1< core::conformation::ResidueCOP > const &  representative_res)
protected
core::conformation::ResidueCOP protocols::toolbox::match_enzdes_util::InvrotTarget::target_res_for_geom_cst ( core::Size  geom_cst) const

Member Data Documentation

std::list< core::conformation::ResidueCOP > protocols::toolbox::match_enzdes_util::InvrotTarget::all_target_res_
private
utility::vector1< InvrotTreeNodeOP > protocols::toolbox::match_enzdes_util::InvrotTarget::next_nodes_
private
utility::vector1< core::conformation::ResidueCOP > protocols::toolbox::match_enzdes_util::InvrotTarget::representative_target_res_for_geom_cst_
private

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