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	EnzConstraintIO
class	CovalentConnectionReplaceInfo
	helper class to allow for removal of covalent constraints More...
class	EnzConstraintParameters
	class that holds all the parameters for one specific constraint More...
class	EnzCstTemplateResAtoms
	helper class for EnzCstTemplateRes, holds atom ids corresponding More...
class	EnzCstTemplateRes
	helper class for class EnzConstraintParameters, gathers information More...
class	EnzdesCacheableObserver
class	EnzdesCstCache
	a simple class to store the pose specific enzdes constraint information in the actual pose More...
class	EnzdesCstParamCache
class	EnzCstTemplateResCache
class	ResInteractions
class	CstResInteractions
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	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	SingleResidueInvrotTarget
class	InvrotTree
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...
class	InvrotTreeNode
class	InvrotCollector
	@ brief helper class for collecting all different definitions of invrots from a tree More...
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	GeomSampleInfo
	class that stores information of one geometric parameter line of the .cst file i.e. angleA or torsionB More...
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...

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

Typedef Documentation

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

Definition at line 28 of file AlignPoseToInvrotTreeMover.fwd.hh.

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

Definition at line 25 of file AlignPoseToInvrotTreeMover.fwd.hh.

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

Definition at line 28 of file AllowedSeqposForGeomCst.fwd.hh.

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

Definition at line 26 of file AllowedSeqposForGeomCst.fwd.hh.

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

Definition at line 47 of file EnzConstraintIO.fwd.hh.

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

Definition at line 46 of file EnzConstraintIO.fwd.hh.

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

Definition at line 44 of file EnzConstraintIO.fwd.hh.

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

Definition at line 43 of file EnzConstraintIO.fwd.hh.

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

Definition at line 42 of file EnzConstraintIO.fwd.hh.

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

Definition at line 41 of file EnzConstraintIO.fwd.hh.

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

Definition at line 33 of file EnzConstraintIO.fwd.hh.

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

Definition at line 32 of file EnzConstraintIO.fwd.hh.

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

Definition at line 29 of file EnzConstraintIO.fwd.hh.

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

Definition at line 39 of file EnzConstraintIO.fwd.hh.

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

Definition at line 38 of file EnzConstraintIO.fwd.hh.

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

Definition at line 34 of file EnzdesCstCache.fwd.hh.

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

Definition at line 33 of file EnzdesCstCache.fwd.hh.

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

Definition at line 36 of file EnzConstraintIO.fwd.hh.

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

Definition at line 35 of file EnzConstraintIO.fwd.hh.

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

Definition at line 29 of file EnzdesCacheableObserver.fwd.hh.

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

Definition at line 28 of file EnzdesCacheableObserver.fwd.hh.

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

Definition at line 27 of file EnzdesCacheableObserver.fwd.hh.

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

Definition at line 24 of file EnzdesCacheableObserver.fwd.hh.

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

Definition at line 28 of file EnzdesCstCache.fwd.hh.

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

Definition at line 25 of file EnzdesCstCache.fwd.hh.

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

Definition at line 31 of file EnzdesCstCache.fwd.hh.

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

Definition at line 30 of file EnzdesCstCache.fwd.hh.

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

Definition at line 37 of file EnzdesLoopsFile.fwd.hh.

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

Definition at line 35 of file EnzdesLoopsFile.fwd.hh.

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

Definition at line 33 of file EnzdesLoopsFile.fwd.hh.

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

Definition at line 31 of file EnzdesLoopsFile.fwd.hh.

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

Definition at line 27 of file EnzdesSeqRecoveryCache.fwd.hh.

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

Definition at line 25 of file EnzdesSeqRecoveryCache.fwd.hh.

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

Definition at line 37 of file ExternalGeomSampler.fwd.hh.

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

Definition at line 34 of file ExternalGeomSampler.fwd.hh.

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

Definition at line 28 of file MatchConstraintFileInfo.fwd.hh.

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

Definition at line 25 of file MatchConstraintFileInfo.fwd.hh.

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

Definition at line 40 of file InvrotTreeNodeBase.fwd.hh.

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

Definition at line 38 of file InvrotTreeNodeBase.fwd.hh.

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

Definition at line 28 of file InvrotTarget.fwd.hh.

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

Definition at line 25 of file InvrotTarget.fwd.hh.

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

Definition at line 28 of file InvrotTree.fwd.hh.

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

Definition at line 31 of file InvrotTreeNodeBase.fwd.hh.

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

Definition at line 32 of file InvrotTreeNodeBase.fwd.hh.

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

Definition at line 29 of file InvrotTreeNodeBase.fwd.hh.

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

Definition at line 26 of file InvrotTreeNodeBase.fwd.hh.

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

Definition at line 28 of file InvrotTreeNode.fwd.hh.

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

Definition at line 25 of file InvrotTreeNode.fwd.hh.

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

Definition at line 25 of file InvrotTree.fwd.hh.

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

Definition at line 28 of file LigandConformer.fwd.hh.

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

Definition at line 25 of file LigandConformer.fwd.hh.

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

Definition at line 32 of file MatchConstraintFileInfo.fwd.hh.

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

Definition at line 36 of file MatchConstraintFileInfo.fwd.hh.

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

Definition at line 34 of file MatchConstraintFileInfo.fwd.hh.

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

Definition at line 30 of file MatchConstraintFileInfo.fwd.hh.

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

Definition at line 33 of file InvrotTarget.fwd.hh.

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

Definition at line 30 of file InvrotTarget.fwd.hh.

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

Definition at line 25 of file ExternalGeomSampler.fwd.hh.

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

Definition at line 79 of file MatchConstraintFileInfo.cc.

References core::chemical::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
	)

Definition at line 174 of file util_functions.cc.

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::constraints::FuncOP	constraint_func
	)

fowarding function for function below

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

Definition at line 89 of file util_functions.cc.

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::constraints::FuncOP	constraint_func
	)

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

Definition at line 102 of file util_functions.cc.

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

Definition at line 153 of file util_functions.cc.

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

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

Definition at line 59 of file EnzdesCacheableObserver.cc.

References 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)

Definition at line 79 of file EnzdesCacheableObserver.cc.

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

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

(

core::pose::Pose const &

pose)

Definition at line 240 of file util_functions.cc.

References core::conformation::Residue::is_protein(), core::pose::Pose::residue(), 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)

Definition at line 260 of file util_functions.cc.

References core::conformation::Residue::is_protein(), core::pose::Pose::residue(), 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
	)

Definition at line 52 of file util_functions.cc.

References core::conformation::Residue::atom_name(), 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
	)

Definition at line 197 of file util_functions.cc.

References 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().

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

static

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

static

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

static

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

static

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

static

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

static

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::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().

static 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().