protocols::toolbox::match_enzdes_util Namespace Reference

Classes
class	AlignPoseToInvrotTreeMover
	small mover that takes an invrot tree More...
class	AllowedSeqposForGeomCst
	a simple helper class that holds a list of what sequence positions each geom cst is allowd to be at not sure about the ideal home of this class yet, the matcher task could use it too More...
class	CovalentConnectionReplaceInfo
	helper class to allow for removal of covalent constraints More...
class	CstResInteractions
class	EnzConstraintIO
class	EnzConstraintParameters
	class that holds all the parameters for one specific constraint More...
class	EnzCstTemplateRes
	helper class for class EnzConstraintParameters, gathers information More...
class	EnzCstTemplateResAtoms
	helper class for EnzCstTemplateRes, holds atom ids corresponding More...
class	EnzCstTemplateResCache
class	EnzdesCacheableObserver
class	EnzdesCstCache
	a simple class to store the pose specific enzdes constraint information in the actual pose More...
class	EnzdesCstParamCache
class	EnzdesLoopInfo
class	EnzdesLoopsFile
	class to process an enzdes loops file More...
class	EnzdesSeqRecoveryCache
class	ExternalGeomSampler
	The external geom sampler is a class that manages the data necessary to construct the coordinates of the three atoms in the downstream partner. More...
class	GeomSampleInfo
	class that stores information of one geometric parameter line of the .cst file i.e. angleA or torsionB More...
class	InvrotCollector
	@ brief helper class for collecting all different definitions of invrots from a tree More...
class	InvrotTarget
	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...
class	InvrotTree
class	InvrotTreeNode
class	InvrotTreeNodeBase
	abstract base class for an inverse rotamer tree node. Exists so that the target node (InvrotTreeTarget) and the different geom cst nodes (InvrotTreeNode) have a common base class. This is necessary so that a node can point at its parent node in a tree without having to worry about whether that is a target or a regular node More...
class	LigandConformer
class	MatchConstraintFileInfo
class	MatchConstraintFileInfoList
	a simple container class to contain several MatchConstraintFileInfo instances. this can also query the MatchConstraintFileInfos for common upstream restypes and put all their geomsamples into one list More...
class	ResInteractions
class	SingleResidueInvrotTarget
class	TheozymeInvrotTree
	This class takes an EnzConstraintIO object and generates a 3D model of the theozyme in it, where inverse rotamers are generated for every block in the cstfile. Shit gets complicated when ambiguous interactions are specified and other residues are interacting (possibly in ambiguous fashion) with these ambiguous residues... More...

Typedefs
typedef utility::pointer::owning_ptr < AlignPoseToInvrotTreeMover >	AlignPoseToInvrotTreeMoverOP
typedef utility::pointer::owning_ptr < AlignPoseToInvrotTreeMover const >	AlignPoseToInvrotTreeMoverCOP
typedef utility::pointer::owning_ptr < AllowedSeqposForGeomCst >	AllowedSeqposForGeomCstOP
typedef utility::pointer::owning_ptr < AllowedSeqposForGeomCst const >	AllowedSeqposForGeomCstCOP
typedef utility::pointer::owning_ptr < EnzConstraintParameters >	EnzConstraintParametersOP
typedef utility::pointer::owning_ptr < EnzConstraintParameters const >	EnzConstraintParametersCOP
typedef utility::pointer::access_ptr < EnzConstraintParameters const >	EnzConstraintParametersCAP
typedef utility::pointer::owning_ptr < EnzCstTemplateRes >	EnzCstTemplateResOP
typedef utility::pointer::owning_ptr < EnzCstTemplateRes const >	EnzCstTemplateResCOP
typedef utility::pointer::owning_ptr < EnzCstTemplateResAtoms >	EnzCstTemplateResAtomsOP
typedef utility::pointer::owning_ptr < EnzCstTemplateResAtoms const >	EnzCstTemplateResAtomsCOP
typedef utility::pointer::owning_ptr < EnzConstraintIO >	EnzConstraintIOOP
typedef utility::pointer::owning_ptr < EnzConstraintIO const >	EnzConstraintIOCOP
typedef utility::pointer::access_ptr < EnzConstraintIO const >	EnzConstraintIOCAP
typedef utility::pointer::access_ptr < EnzConstraintIO >	EnzConstraintIOAP
typedef utility::pointer::owning_ptr < CovalentConnectionReplaceInfo >	CovalentConnectionReplaceInfoOP
typedef utility::pointer::owning_ptr < CovalentConnectionReplaceInfo const >	CovalentConnectionReplaceInfoCOP
typedef utility::pointer::owning_ptr < EnzdesCacheableObserver >	EnzdesCacheableObserverOP
typedef utility::pointer::owning_ptr < EnzdesCacheableObserver const >	EnzdesCacheableObserverCOP
typedef utility::pointer::access_ptr < EnzdesCacheableObserver const >	EnzdesCacheableObserverCAP
typedef utility::pointer::access_ptr < EnzdesCacheableObserver >	EnzdesCacheableObserverAP
typedef utility::pointer::owning_ptr < EnzdesCstCache >	EnzdesCstCacheOP
typedef utility::pointer::owning_ptr < EnzdesCstCache const >	EnzdesCstCacheCOP
typedef utility::pointer::owning_ptr < EnzdesCstParamCache >	EnzdesCstParamCacheOP
typedef utility::pointer::owning_ptr < EnzdesCstParamCache const >	EnzdesCstParamCacheCOP
typedef utility::pointer::owning_ptr < EnzCstTemplateResCache >	EnzCstTemplateResCacheOP
typedef utility::pointer::owning_ptr < EnzCstTemplateResCache const >	EnzCstTemplateResCacheCOP
typedef utility::pointer::owning_ptr < EnzdesLoopsFile >	EnzdesLoopsFileOP
typedef utility::pointer::owning_ptr < EnzdesLoopsFile const >	EnzdesLoopsFileCOP
typedef utility::pointer::owning_ptr < EnzdesLoopInfo >	EnzdesLoopInfoOP
typedef utility::pointer::owning_ptr < EnzdesLoopInfo const >	EnzdesLoopInfoCOP
typedef utility::pointer::owning_ptr < EnzdesSeqRecoveryCache >	EnzdesSeqRecoveryCacheOP
typedef utility::pointer::owning_ptr < EnzdesSeqRecoveryCache const >	EnzdesSeqRecoveryCacheCOP
typedef utility::pointer::owning_ptr < ExternalGeomSampler >	ExternalGeomSamplerOP
typedef utility::pointer::owning_ptr < ExternalGeomSampler const >	ExternalGeomSamplerCOP
typedef utility::pointer::owning_ptr < InvrotTarget >	InvrotTargetOP
typedef utility::pointer::owning_ptr < InvrotTarget const >	InvrotTargetCOP
typedef utility::pointer::owning_ptr < SingleResidueInvrotTarget >	SingleResidueInvrotTargetOP
typedef utility::pointer::owning_ptr < SingleResidueInvrotTarget const >	SingleResidueInvrotTargetCOP
typedef utility::pointer::owning_ptr < InvrotTree >	InvrotTreeOP
typedef utility::pointer::owning_ptr < InvrotTree const >	InvrotTreeCOP
typedef utility::pointer::owning_ptr < InvrotTreeNode >	InvrotTreeNodeOP
typedef utility::pointer::owning_ptr < InvrotTreeNode const >	InvrotTreeNodeCOP
typedef utility::pointer::owning_ptr < InvrotTreeNodeBase >	InvrotTreeNodeBaseOP
typedef utility::pointer::owning_ptr < InvrotTreeNodeBase const >	InvrotTreeNodeBaseCOP
typedef utility::pointer::access_ptr < InvrotTreeNodeBase >	InvrotTreeNodeBaseAP
typedef utility::pointer::access_ptr < InvrotTreeNodeBase const >	InvrotTreeNodeBaseCAP
typedef utility::pointer::owning_ptr < InvrotCollector >	InvrotCollectorOP
typedef utility::pointer::owning_ptr < InvrotCollector const >	InvrotCollectorCOP
typedef utility::pointer::owning_ptr < LigandConformer >	LigandConformerOP
typedef utility::pointer::owning_ptr < LigandConformer const >	LigandConformerCOP
typedef utility::pointer::owning_ptr < GeomSampleInfo >	GeomSampleInfoOP
typedef utility::pointer::owning_ptr < GeomSampleInfo const >	GeomSampleInfoCOP
typedef utility::pointer::owning_ptr < MatchConstraintFileInfo >	MatchConstraintFileInfoOP
typedef utility::pointer::owning_ptr < MatchConstraintFileInfo const >	MatchConstraintFileInfoCOP
typedef utility::pointer::owning_ptr < MatchConstraintFileInfoList >	MatchConstraintFileInfoListOP
typedef utility::pointer::owning_ptr < MatchConstraintFileInfoList const >	MatchConstraintFileInfoListCOP

Enumerations
enum	ExternalTransform {   HT_tor_U3D1 = 1, HT_ang_U2D1, HT_tor_U2D2, HT_ang_U1D2,   HT_tor_U1D3, n_external_transforms = HT_tor_U1D3 }

Functions
EnzdesCacheableObserverOP	get_enzdes_observer (core::pose::Pose &pose)
	convenience function to get a cacheable observer from a pose More...
EnzdesCacheableObserverCOP	get_enzdes_observer (core::pose::Pose const &pose)
void	add_relevant_restypes_to_subset (std::set< core::chemical::ResidueTypeCOP > &restype_subset, utility::vector1< core::chemical::ResidueTypeCOP > const &restypes, core::chemical::ResidueTypeSetCAP restype_set)
	function to go through a list of restypes and reduce them to chemically identical ones based on the same base_name i.e. this function gets rid of the variant redundancy More...
void	replace_residue_keeping_all_atom_positions (core::pose::Pose &pose, core::conformation::Residue new_res, core::Size res_pos)
core::scoring::constraints::AmbiguousConstraintCOP	constrain_pose_res_to_invrots (std::list< core::conformation::ResidueCOP > const &invrots, utility::vector1< core::Size > const &seqpos, core::pose::Pose const &pose, core::scoring::func::FuncOP constraint_func=NULL)
	fowarding function for function below More...
core::scoring::constraints::AmbiguousConstraintCOP	constrain_pose_res_to_invrots (std::list< core::conformation::ResidueCOP > const &invrots, utility::vector1< core::Size > const &seqpos, core::pose::Pose const &pose, core::id::AtomID const &fixed_pt, core::scoring::func::FuncOP constraint_func=NULL)
	constraints each invrot to the backbone of each seqpos and throws all those constraints into one ambiguous constraint. More...
core::conformation::ResidueCOP	cst_residue_in_pose (core::pose::Pose const &pose, core::Size geomcst, core::Size geomcst_template_res)
	convenience function that returns a residue of the desired cst interaction in case there are no constraints in the pose, returns null pointer More...
std::string	assemble_remark_line (std::string chainA, std::string resA, int seqposA, std::string chainB, std::string resB, int seqposB, core::Size cst_block, core::Size ex_geom_id)
bool	split_up_remark_line (std::string line, std::string &chainA, std::string &resA, int &seqposA, std::string &chainB, std::string &resB, int &seqposB, core::Size &cst_block, core::Size &ex_geom_id)
core::Size	get_first_protein_residue (core::pose::Pose const &pose)
core::Size	get_last_protein_residue (core::pose::Pose const &pose)

Variables
static basic::Tracer	TR ("protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover")
static basic::Tracer	TR ("protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst")
static basic::Tracer	tr ("protocols.enzdes.EnzdesCacheableObserver")
static basic::Tracer	TR ("protocols.enzdes.EnzdesSeqRecoveryCache")
static basic::Tracer	tr ("protocols.toolbox.match_enzdes_util.InvrotTarget")
static basic::Tracer	tr ("protocols.toolbox.match_enzdes_util.InvrotTree")
static basic::Tracer	tr ("protocols.toolbox.match_enzdes_util.InvrotTreeNode")
static basic::Tracer	tr ("protocols.toolbox.match_enzdes_util.util_functions")

Typedef Documentation

typedef utility::pointer::owning_ptr< AlignPoseToInvrotTreeMover const > protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMoverCOP

typedef utility::pointer::owning_ptr< AlignPoseToInvrotTreeMover > protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMoverOP

typedef utility::pointer::owning_ptr< AllowedSeqposForGeomCst const > protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCstCOP

typedef utility::pointer::owning_ptr< AllowedSeqposForGeomCst > protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCstOP

typedef utility::pointer::owning_ptr< CovalentConnectionReplaceInfo const > protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfoCOP

typedef utility::pointer::owning_ptr< CovalentConnectionReplaceInfo > protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfoOP

typedef utility::pointer::access_ptr< EnzConstraintIO > protocols::toolbox::match_enzdes_util::EnzConstraintIOAP

typedef utility::pointer::access_ptr< EnzConstraintIO const > protocols::toolbox::match_enzdes_util::EnzConstraintIOCAP

typedef utility::pointer::owning_ptr< EnzConstraintIO const > protocols::toolbox::match_enzdes_util::EnzConstraintIOCOP

typedef utility::pointer::owning_ptr< EnzConstraintIO > protocols::toolbox::match_enzdes_util::EnzConstraintIOOP

typedef utility::pointer::access_ptr< EnzConstraintParameters const > protocols::toolbox::match_enzdes_util::EnzConstraintParametersCAP

typedef utility::pointer::owning_ptr< EnzConstraintParameters const > protocols::toolbox::match_enzdes_util::EnzConstraintParametersCOP

typedef utility::pointer::owning_ptr< EnzConstraintParameters > protocols::toolbox::match_enzdes_util::EnzConstraintParametersOP

typedef utility::pointer::owning_ptr< EnzCstTemplateResAtoms const > protocols::toolbox::match_enzdes_util::EnzCstTemplateResAtomsCOP

typedef utility::pointer::owning_ptr< EnzCstTemplateResAtoms > protocols::toolbox::match_enzdes_util::EnzCstTemplateResAtomsOP

typedef utility::pointer::owning_ptr< EnzCstTemplateResCache const > protocols::toolbox::match_enzdes_util::EnzCstTemplateResCacheCOP

typedef utility::pointer::owning_ptr< EnzCstTemplateResCache > protocols::toolbox::match_enzdes_util::EnzCstTemplateResCacheOP

typedef utility::pointer::owning_ptr< EnzCstTemplateRes const > protocols::toolbox::match_enzdes_util::EnzCstTemplateResCOP

typedef utility::pointer::owning_ptr< EnzCstTemplateRes > protocols::toolbox::match_enzdes_util::EnzCstTemplateResOP

typedef utility::pointer::access_ptr< EnzdesCacheableObserver > protocols::toolbox::match_enzdes_util::EnzdesCacheableObserverAP

typedef utility::pointer::access_ptr< EnzdesCacheableObserver const > protocols::toolbox::match_enzdes_util::EnzdesCacheableObserverCAP

typedef utility::pointer::owning_ptr< EnzdesCacheableObserver const > protocols::toolbox::match_enzdes_util::EnzdesCacheableObserverCOP

typedef utility::pointer::owning_ptr< EnzdesCacheableObserver > protocols::toolbox::match_enzdes_util::EnzdesCacheableObserverOP

typedef utility::pointer::owning_ptr< EnzdesCstCache const > protocols::toolbox::match_enzdes_util::EnzdesCstCacheCOP

typedef utility::pointer::owning_ptr< EnzdesCstCache > protocols::toolbox::match_enzdes_util::EnzdesCstCacheOP

typedef utility::pointer::owning_ptr< EnzdesCstParamCache const > protocols::toolbox::match_enzdes_util::EnzdesCstParamCacheCOP

typedef utility::pointer::owning_ptr< EnzdesCstParamCache > protocols::toolbox::match_enzdes_util::EnzdesCstParamCacheOP

typedef utility::pointer::owning_ptr< EnzdesLoopInfo const > protocols::toolbox::match_enzdes_util::EnzdesLoopInfoCOP

typedef utility::pointer::owning_ptr< EnzdesLoopInfo > protocols::toolbox::match_enzdes_util::EnzdesLoopInfoOP

typedef utility::pointer::owning_ptr< EnzdesLoopsFile const > protocols::toolbox::match_enzdes_util::EnzdesLoopsFileCOP

typedef utility::pointer::owning_ptr< EnzdesLoopsFile > protocols::toolbox::match_enzdes_util::EnzdesLoopsFileOP

typedef utility::pointer::owning_ptr< EnzdesSeqRecoveryCache const > protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCacheCOP

typedef utility::pointer::owning_ptr< EnzdesSeqRecoveryCache > protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCacheOP

typedef utility::pointer::owning_ptr< ExternalGeomSampler const > protocols::toolbox::match_enzdes_util::ExternalGeomSamplerCOP

typedef utility::pointer::owning_ptr< ExternalGeomSampler > protocols::toolbox::match_enzdes_util::ExternalGeomSamplerOP

typedef utility::pointer::owning_ptr< GeomSampleInfo const > protocols::toolbox::match_enzdes_util::GeomSampleInfoCOP

typedef utility::pointer::owning_ptr< GeomSampleInfo > protocols::toolbox::match_enzdes_util::GeomSampleInfoOP

typedef utility::pointer::owning_ptr< InvrotCollector const > protocols::toolbox::match_enzdes_util::InvrotCollectorCOP

typedef utility::pointer::owning_ptr< InvrotCollector > protocols::toolbox::match_enzdes_util::InvrotCollectorOP

typedef utility::pointer::owning_ptr< InvrotTarget const > protocols::toolbox::match_enzdes_util::InvrotTargetCOP

typedef utility::pointer::owning_ptr< InvrotTarget > protocols::toolbox::match_enzdes_util::InvrotTargetOP

typedef utility::pointer::owning_ptr< InvrotTree const > protocols::toolbox::match_enzdes_util::InvrotTreeCOP

typedef utility::pointer::access_ptr< InvrotTreeNodeBase > protocols::toolbox::match_enzdes_util::InvrotTreeNodeBaseAP

typedef utility::pointer::access_ptr< InvrotTreeNodeBase const > protocols::toolbox::match_enzdes_util::InvrotTreeNodeBaseCAP

typedef utility::pointer::owning_ptr< InvrotTreeNodeBase const > protocols::toolbox::match_enzdes_util::InvrotTreeNodeBaseCOP

typedef utility::pointer::owning_ptr< InvrotTreeNodeBase > protocols::toolbox::match_enzdes_util::InvrotTreeNodeBaseOP

typedef utility::pointer::owning_ptr< InvrotTreeNode const > protocols::toolbox::match_enzdes_util::InvrotTreeNodeCOP

typedef utility::pointer::owning_ptr< InvrotTreeNode > protocols::toolbox::match_enzdes_util::InvrotTreeNodeOP

typedef utility::pointer::owning_ptr< InvrotTree > protocols::toolbox::match_enzdes_util::InvrotTreeOP

typedef utility::pointer::owning_ptr< LigandConformer const > protocols::toolbox::match_enzdes_util::LigandConformerCOP

typedef utility::pointer::owning_ptr< LigandConformer > protocols::toolbox::match_enzdes_util::LigandConformerOP

typedef utility::pointer::owning_ptr< MatchConstraintFileInfo const > protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoCOP

typedef utility::pointer::owning_ptr< MatchConstraintFileInfoList const > protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoListCOP

typedef utility::pointer::owning_ptr< MatchConstraintFileInfoList > protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoListOP

typedef utility::pointer::owning_ptr< MatchConstraintFileInfo > protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoOP

typedef utility::pointer::owning_ptr< SingleResidueInvrotTarget const > protocols::toolbox::match_enzdes_util::SingleResidueInvrotTargetCOP

typedef utility::pointer::owning_ptr< SingleResidueInvrotTarget > protocols::toolbox::match_enzdes_util::SingleResidueInvrotTargetOP

Enumeration Type Documentation

enum protocols::toolbox::match_enzdes_util::ExternalTransform

Enumerator
HT_tor_U3D1
HT_ang_U2D1
HT_tor_U2D2
HT_ang_U1D2
HT_tor_U1D3
n_external_transforms

Function Documentation

void protocols::toolbox::match_enzdes_util::add_relevant_restypes_to_subset	(	std::set< core::chemical::ResidueTypeCOP > &	restype_subset,
		utility::vector1< core::chemical::ResidueTypeCOP > const &	restypes,
		core::chemical::ResidueTypeSetCAP	restype_set
	)

function to go through a list of restypes and reduce them to chemically identical ones based on the same base_name i.e. this function gets rid of the variant redundancy

References basename, and residue_type_base_name().

Referenced by protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList::determine_upstream_restypes(), and protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::process_data().

std::string protocols::toolbox::match_enzdes_util::assemble_remark_line	(	std::string	chainA,
		std::string	resA,
		int	seqposA,
		std::string	chainB,
		std::string	resB,
		int	seqposB,
		core::Size	cst_block,
		core::Size	ex_geom_id
	)

References utility::add_spaces_right_align(), and utility::to_string().

Referenced by protocols::match::output::PDBWriter::assemble_remark_lines(), protocols::enzdes::PoseFoundResiduesCombination::construct_and_dump_outpose(), protocols::enzdes::enzutil::create_remark_headers_from_cstcache(), protocols::enzdes::EnzdesBaseProtocol::exchange_ligands_in_pose(), and protocols::toolbox::match_enzdes_util::EnzConstraintParameters::update_pdb_remarks().

core::scoring::constraints::AmbiguousConstraintCOP protocols::toolbox::match_enzdes_util::constrain_pose_res_to_invrots	(	std::list< core::conformation::ResidueCOP > const &	invrots,
		utility::vector1< core::Size > const &	seqpos,
		core::pose::Pose const &	pose,
		core::scoring::func::FuncOP	constraint_func
	)

fowarding function for function below

forwarding function, allows stuff to call this functionality without caller having to specify root

References core::pose::Pose::atom_tree(), and core::kinematics::AtomTree::root().

Referenced by protocols::toolbox::match_enzdes_util::InvrotTreeNode::generate_constraints(), and protocols::forge::constraints::InverseRotamersRCG::generate_remodel_constraints().

core::scoring::constraints::AmbiguousConstraintCOP protocols::toolbox::match_enzdes_util::constrain_pose_res_to_invrots	(	std::list< core::conformation::ResidueCOP > const &	invrots,
		utility::vector1< core::Size > const &	seqpos,
		core::pose::Pose const &	pose,
		core::id::AtomID const &	fixed_pt,
		core::scoring::func::FuncOP	constraint_func
	)

constraints each invrot to the backbone of each seqpos and throws all those constraints into one ambiguous constraint.

References core::pose::Pose::residue(), and tr.

core::conformation::ResidueCOP protocols::toolbox::match_enzdes_util::cst_residue_in_pose	(	core::pose::Pose const &	pose,
		core::Size	geomcst,
		core::Size	geomcst_template_res
	)

convenience function that returns a residue of the desired cst interaction in case there are no constraints in the pose, returns null pointer

References get_enzdes_observer(), core::pose::Pose::residue(), and runtime_assert.

Referenced by protocols::toolbox::match_enzdes_util::InvrotTreeNode::initialize_from_enzcst_io().

EnzdesCacheableObserverOP protocols::toolbox::match_enzdes_util::get_enzdes_observer

(

core::pose::Pose &

pose

)

convenience function to get a cacheable observer from a pose

References utility::pointer::dynamic_pointer_cast(), core::pose::datacache::CacheableObserverType::ENZDES_OBSERVER, core::pose::Pose::observer_cache(), and core::pose::datacache::ObserverCache::set().

Referenced by protocols::toolbox::match_enzdes_util::EnzConstraintIO::add_constraints_to_pose(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::add_constraints_to_pose_for_block_without_clearing_and_header_processing(), protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::add_pregenerated_constraints_to_pose(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::allowed_res_name3_at_position(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::allowed_res_name3_at_position(), protocols::forge::remodel::RemodelEnzdesCstModule::apply(), protocols::enzdes::SetCatalyticResPackBehavior::apply(), protocols::enzdes::RepackLigandSiteWithoutLigandMover::apply(), protocols::enzdes::AddRigidBodyLigandConfs::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::enzdes::EnzdesBaseProtocol::catalytic_res(), protocols::enzdes::enzutil::catalytic_res(), protocols::forge::components::VarLengthBuild::centroid_build(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::clear_active_pose_constraints_for_block(), protocols::enzdes::PoseFoundResiduesCombination::construct_and_dump_outpose(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::contains_position(), protocols::enzdes::EnzdesBaseProtocol::create_enzdes_pack_task(), protocols::enzdes::enzutil::create_remark_headers_from_cstcache(), cst_residue_in_pose(), protocols::enzdes::EnzdesFlexBBProtocol::determine_flexible_regions(), protocols::enzdes::EnzRepackMinimize::ensure_scofx_cstfication(), protocols::enzdes::EnzdesBaseProtocol::enzdes_pack(), protocols::enzdes::EnzdesScorefileFilter::examine_pose(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::find_in_pose_if_missing_from_header(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::generate_active_pose_constraints(), protocols::enzdes::enzutil::get_enzcst_io(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::get_missing_template_other_res(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::get_missing_template_res(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::get_pose_data(), protocols::enzdes::enzutil::get_resnum_from_cstid(), protocols::enzdes::ModifyStoredRBConfs::get_rigid_body_confs(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::get_template_atoms_at_pos(), protocols::match::output::PoseMatchOutputWriter::insert_match_into_pose(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::is_backbone_only_cst(), protocols::enzdes::enzutil::is_catalytic_seqpos(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::missing_in_pose(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::ordered_constrained_positions(), protocols::enzdes::EnzdesJobInputter::pose_from_job(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::process_pdb_header(), protocols::enzdes::enzutil::read_pose_from_pdb(), protocols::enzdes::enzutil::remove_all_enzdes_constraints(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::remove_constraints_from_pose(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::remove_constraints_from_pose_for_block(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::remove_covalent_connections_from_pose(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::remove_position_from_template_res(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::remove_position_from_template_res_for_block(), protocols::enzdes::EnzdesJobOutputter::scorefile(), protocols::enzdes::PredesignPerturbMover::set_docking_pose(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::set_position_for_missing_res_in_parameter_block(), protocols::enzdes::ModifyStoredRBConfs::set_rigid_body_confs_for_seqpos(), protocols::enzdes::EnzdesBaseProtocol::setup_sequence_recovery_cache(), and protocols::toolbox::match_enzdes_util::EnzConstraintParameters::update_pdb_remarks().

EnzdesCacheableObserverCOP protocols::toolbox::match_enzdes_util::get_enzdes_observer

(

core::pose::Pose const &

pose

)

References core::pose::datacache::CacheableObserverType::ENZDES_OBSERVER, core::pose::Pose::observer_cache(), and utility::pointer::static_pointer_cast().

core::Size protocols::toolbox::match_enzdes_util::get_first_protein_residue

(

core::pose::Pose const &

pose

)

References core::conformation::Residue::is_protein(), core::pose::Pose::residue(), runtime_assert, core::pose::Pose::total_residue(), and tr.

Referenced by protocols::forge::constraints::NtoC_RCG::generate_remodel_constraints().

core::Size protocols::toolbox::match_enzdes_util::get_last_protein_residue

(

core::pose::Pose const &

pose

)

References core::conformation::Residue::is_protein(), core::pose::Pose::residue(), runtime_assert, core::pose::Pose::total_residue(), and tr.

Referenced by protocols::forge::constraints::NtoC_RCG::generate_remodel_constraints().

void protocols::toolbox::match_enzdes_util::replace_residue_keeping_all_atom_positions	(	core::pose::Pose &	pose,
		core::conformation::Residue	new_res,
		core::Size	res_pos
	)

References core::conformation::Residue::atom_name(), utility::exit(), core::conformation::Residue::name3(), core::conformation::Residue::natoms(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::set_xyz(), and core::conformation::Residue::xyz().

Referenced by protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent_helper(), and protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo::remove_covalent_connection_from_pose().

bool protocols::toolbox::match_enzdes_util::split_up_remark_line	(	std::string	line,
		std::string &	chainA,
		std::string &	resA,
		int &	seqposA,
		std::string &	chainB,
		std::string &	resB,
		int &	seqposB,
		core::Size &	cst_block,
		core::Size &	ex_geom_id
	)

References tag, and tr.

Referenced by protocols::enzdes::enzutil::create_remark_headers_from_cstcache(), protocols::enzdes::EnzdesBaseProtocol::exchange_ligands_in_pose(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::process_pdb_header(), protocols::enzdes::enzutil::remove_remark_header_for_geomcst(), protocols::match::MatcherTask::set_active_site_residue_list_to_preexisting_partial_match(), and protocols::toolbox::match_enzdes_util::EnzConstraintParameters::update_pdb_remarks().

Variable Documentation

basic::Tracer protocols::toolbox::match_enzdes_util::tr("protocols.toolbox.match_enzdes_util.InvrotTarget")

static

basic::Tracer protocols::toolbox::match_enzdes_util::TR("protocols.enzdes.EnzdesSeqRecoveryCache")

static

basic::Tracer protocols::toolbox::match_enzdes_util::TR("protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst")

static

basic::Tracer protocols::toolbox::match_enzdes_util::tr("protocols.toolbox.match_enzdes_util.InvrotTreeNode")

static

basic::Tracer protocols::toolbox::match_enzdes_util::tr("protocols.toolbox.match_enzdes_util.InvrotTree")

static

basic::Tracer protocols::toolbox::match_enzdes_util::tr("protocols.toolbox.match_enzdes_util.util_functions")

static

basic::Tracer protocols::toolbox::match_enzdes_util::tr("protocols.enzdes.EnzdesCacheableObserver")

static

Referenced by protocols::toolbox::match_enzdes_util::EnzConstraintIO::add_constraints_to_pose(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::add_pregenerated_constraints_to_pose(), protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::check_data_consistency(), protocols::toolbox::match_enzdes_util::InvrotTreeNode::collect_all_inverse_rotamers(), constrain_pose_res_to_invrots(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::convert_GeomSampleInfo_to_FuncOP(), protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::create_exgs(), protocols::toolbox::match_enzdes_util::GeomSampleInfo::create_sample_vector(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::determine_atom_inds_for_restype(), protocols::toolbox::match_enzdes_util::InvrotTree::dump_invrots_tree_as_multimodel_pdbs(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::find_in_pose_if_missing_from_header(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::generate_active_pose_constraints(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::generate_pose_specific_data_for_block(), protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::generate_ss_strings_from_blueprint(), protocols::toolbox::match_enzdes_util::TheozymeInvrotTree::generate_targets_and_inverse_rotamers(), get_first_protein_residue(), get_last_protein_residue(), protocols::toolbox::match_enzdes_util::InvrotTreeNode::initialize_from_enzcst_io(), protocols::toolbox::match_enzdes_util::InvrotTreeNode::initialize_from_enzcst_io_and_invrots(), protocols::toolbox::match_enzdes_util::InvrotTarget::initialize_tree_nodes_from_enzcst_io(), protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::inverse_rotamers_against_residue(), protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList::inverse_rotamers_against_residue(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent(), protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::process_algorithm_info(), protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::process_data(), protocols::toolbox::match_enzdes_util::ResInteractions::process_input_line_tokens(), protocols::toolbox::match_enzdes_util::ResInteractions::read_data(), protocols::toolbox::match_enzdes_util::GeomSampleInfo::read_data(), protocols::toolbox::match_enzdes_util::CstResInteractions::read_data(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::read_enzyme_cstfile(), protocols::toolbox::match_enzdes_util::EnzdesLoopsFile::read_loops_file(), protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::read_loops_file_block(), protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver::remove_favor_native_constraints(), protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver::setup_favor_native_constraints(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::show_cst_definitions(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::show_definitions(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::show_params(), split_up_remark_line(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::update_pdb_remarks(), protocols::toolbox::match_enzdes_util::ResInteractions::write_data(), and protocols::toolbox::match_enzdes_util::CstResInteractions::write_data().

basic::Tracer protocols::toolbox::match_enzdes_util::TR("protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover")

static

Referenced by protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst::initialize_from_command_line().