#include <InvrotTreeNode.hh>

Inheritance diagram for protocols::toolbox::match_enzdes_util::InvrotTreeNode:

Public Member Functions
	InvrotTreeNode (InvrotTreeNodeBaseCAP parent)

	~InvrotTreeNode ()

bool	initialize_from_enzcst_io (core::conformation::Residue const &target_residue, EnzConstraintIOCOP enzcst_io, Size invrot_geomcst, core::pose::PoseCOP pose=NULL)
	generate invrots according to an enzdes cstfile returns true if it was possible to build invrots, i.e. geometry correctly defined in cstfile and no clashes with any parent inverse rotamers More...

bool	initialize_from_enzcst_io_and_invrots (std::list< core::conformation::ResidueCOP > const &all_invrots, EnzConstraintIOCOP enzcst_io, Size invrot_geomcst, core::pose::PoseCOP pose=NULL)

core::scoring::constraints::ConstraintCOP	generate_constraints (core::pose::Pose const &pose, AllowedSeqposForGeomCstCOP geomcst_seqpos) const

core::id::AtomID	get_fixed_pt (core::pose::Pose const &pose) const
	this function returns the AtomID for an atom in the pose that's supposed to stay fixed during folding, i.e. the neighbor atom of the first target needed to generate the right backbone_stub constraints 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...

void	remove_invrots_clashing_with_parent_res (std::list< core::conformation::ResidueCOP > &invrots, bool covalent) const

void	collect_all_inverse_rotamers (utility::vector1< InvrotCollectorOP > &invrot_collectors) 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 ()

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 (Size location)

Size	location_in_parent_node () const

Private Types
typedef std::pair< std::list < core::conformation::ResidueCOP > , utility::vector1 < InvrotTreeNodeBaseOP > >	invrots_node_ptrs_pair

typedef core::Size	Size

Private Attributes
Size	geom_cst_

utility::vector1 < invrots_node_ptrs_pair >	invrots_and_next_nodes_

bool	generate_invrot_csts_

Member Typedef Documentation

typedef std::pair< std::list<core::conformation::ResidueCOP >, utility::vector1< InvrotTreeNodeBaseOP > > protocols::toolbox::match_enzdes_util::InvrotTreeNode::invrots_node_ptrs_pair

private

typedef core::Size protocols::toolbox::match_enzdes_util::InvrotTreeNode::Size

private

Constructor & Destructor Documentation

protocols::toolbox::match_enzdes_util::InvrotTreeNode::InvrotTreeNode ( InvrotTreeNodeBaseCAP parent )

References invrots_and_next_nodes_.

Referenced by initialize_from_enzcst_io_and_invrots().

protocols::toolbox::match_enzdes_util::InvrotTreeNode::~InvrotTreeNode ( )

Member Function Documentation

utility::vector1< std::list< core::conformation::ResidueCOP > > protocols::toolbox::match_enzdes_util::InvrotTreeNode::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.

References protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase::get_self_weak_ptr(), invrots_and_next_nodes_, and protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase::parent_node().

void protocols::toolbox::match_enzdes_util::InvrotTreeNode::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.

References geom_cst_, protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase::get_self_ptr(), invrots_and_next_nodes_, and protocols::toolbox::match_enzdes_util::tr().

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

virtual

for each invrots/node pointer pair: a.generate an ambigous constraint for the inverse rots for each node pointer to child nodes (only if there are child nodes, of course) b. call the generate_constraints function on the pointers to child nodes c. package the ambig constraint generated for the inverse rots and the constraints that come from the child nodes into one multicst caveat: if the child nodes send up a multi constraint and not an ambiguous constraint, 'unpackage' those multicst and generate a new multicst containing this nodes ambigcst and the member_csts from the child nodes' multicsts
if there is more than one invrots/node pointer pair, throw all the generated multicsts into one ambig cst
return either the multicst (one pair) or the ambigcst
hope this works

the real meat of this thing see brief description in .hh file

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

References protocols::toolbox::match_enzdes_util::constrain_pose_res_to_invrots(), generate_invrot_csts_, geom_cst_, get_fixed_pt(), and invrots_and_next_nodes_.

core::id::AtomID protocols::toolbox::match_enzdes_util::InvrotTreeNode::get_fixed_pt ( core::pose::Pose const & pose ) const

this function returns the AtomID for an atom in the pose that's supposed to stay fixed during folding, i.e. the neighbor atom of the first target needed to generate the right backbone_stub constraints

approach: get the target residues, then find a residue in the pose that has the same name as the first target residue and a neighbor atom in the same position. this will be the fixed point. exit w error if not found

References core::conformation::Residue::atom(), core::conformation::Residue::atoms(), protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase::get_self_weak_ptr(), core::chemical::ResidueType::name3(), protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase::parent_node(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), and core::conformation::Atom::xyz().

Referenced by generate_constraints().

bool protocols::toolbox::match_enzdes_util::InvrotTreeNode::initialize_from_enzcst_io	(	core::conformation::Residue const &	target_residue,
		EnzConstraintIOCOP	enzcst_io,
		Size	invrot_geomcst,
		core::pose::PoseCOP	pose = `NULL`
	)

generate invrots according to an enzdes cstfile returns true if it was possible to build invrots, i.e. geometry correctly defined in cstfile and no clashes with any parent inverse rotamers

assumptions: this node represents the upstream_res of this geom_cst (invrot_geomcst), and the given target_residue corresponds to the downstream_res of invrot_geomcst

References protocols::toolbox::match_enzdes_util::cst_residue_in_pose(), core::conformation::Residue::get_self_ptr(), initialize_from_enzcst_io_and_invrots(), invrots_and_next_nodes_, remove_invrots_clashing_with_parent_res(), and protocols::toolbox::match_enzdes_util::tr().

bool protocols::toolbox::match_enzdes_util::InvrotTreeNode::initialize_from_enzcst_io_and_invrots	(	std::list< core::conformation::ResidueCOP > const &	all_invrots,
		EnzConstraintIOCOP	enzcst_io,
		Size	invrot_geomcst,
		core::pose::PoseCOP	pose = `NULL`
	)

References geom_cst_, protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase::get_self_weak_ptr(), invrots_and_next_nodes_, InvrotTreeNode(), core::scoring::pair, and protocols::toolbox::match_enzdes_util::tr().

Referenced by initialize_from_enzcst_io().

void protocols::toolbox::match_enzdes_util::InvrotTreeNode::remove_invrots_clashing_with_parent_res	(	std::list< core::conformation::ResidueCOP > &	invrots,
		bool	covalent
	)		const

if covalent is true, clashes will not be checked for the last vector that comes down from the parent. kinda crude, could be made better, i.e. only except the actual constrained atoms from clash check

References core::conformation::Residue::atom(), core::sequence::end, protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase::get_self_weak_ptr(), core::chemical::ResidueType::is_virtual(), core::conformation::Residue::nheavyatoms(), protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase::parent_node(), core::conformation::Residue::type(), and core::conformation::Atom::xyz().

Referenced by initialize_from_enzcst_io().