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Classes | Typedefs | Enumerations | Functions
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. It 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...
 
struct  SingleConstraint
 
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::shared_ptr< AlignPoseToInvrotTreeMover > AlignPoseToInvrotTreeMoverOP
 
typedef utility::pointer::shared_ptr< AlignPoseToInvrotTreeMover const > AlignPoseToInvrotTreeMoverCOP
 
typedef utility::pointer::shared_ptr< AllowedSeqposForGeomCst > AllowedSeqposForGeomCstOP
 
typedef utility::pointer::shared_ptr< AllowedSeqposForGeomCst const > AllowedSeqposForGeomCstCOP
 
typedef utility::pointer::shared_ptr< EnzConstraintParameters > EnzConstraintParametersOP
 
typedef utility::pointer::shared_ptr< EnzConstraintParameters const > EnzConstraintParametersCOP
 
typedef utility::pointer::weak_ptr< EnzConstraintParameters > EnzConstraintParametersAP
 
typedef utility::pointer::weak_ptr< EnzConstraintParameters const > EnzConstraintParametersCAP
 
typedef utility::pointer::shared_ptr< EnzCstTemplateRes > EnzCstTemplateResOP
 
typedef utility::pointer::shared_ptr< EnzCstTemplateRes const > EnzCstTemplateResCOP
 
typedef utility::pointer::shared_ptr< EnzCstTemplateResAtoms > EnzCstTemplateResAtomsOP
 
typedef utility::pointer::shared_ptr< EnzCstTemplateResAtoms const > EnzCstTemplateResAtomsCOP
 
typedef utility::pointer::shared_ptr< EnzConstraintIO > EnzConstraintIOOP
 
typedef utility::pointer::shared_ptr< EnzConstraintIO const > EnzConstraintIOCOP
 
typedef utility::pointer::weak_ptr< EnzConstraintIO const > EnzConstraintIOCAP
 
typedef utility::pointer::weak_ptr< EnzConstraintIO > EnzConstraintIOAP
 
typedef utility::pointer::shared_ptr< CovalentConnectionReplaceInfo > CovalentConnectionReplaceInfoOP
 
typedef utility::pointer::shared_ptr< CovalentConnectionReplaceInfo const > CovalentConnectionReplaceInfoCOP
 
typedef utility::pointer::shared_ptr< EnzdesCacheableObserver > EnzdesCacheableObserverOP
 
typedef utility::pointer::shared_ptr< EnzdesCacheableObserver const > EnzdesCacheableObserverCOP
 
typedef utility::pointer::weak_ptr< EnzdesCacheableObserver const > EnzdesCacheableObserverCAP
 
typedef utility::pointer::weak_ptr< EnzdesCacheableObserver > EnzdesCacheableObserverAP
 
typedef utility::pointer::shared_ptr< EnzdesCstCache > EnzdesCstCacheOP
 
typedef utility::pointer::shared_ptr< EnzdesCstCache const > EnzdesCstCacheCOP
 
typedef utility::pointer::shared_ptr< EnzdesCstParamCache > EnzdesCstParamCacheOP
 
typedef utility::pointer::shared_ptr< EnzdesCstParamCache const > EnzdesCstParamCacheCOP
 
typedef utility::pointer::shared_ptr< EnzCstTemplateResCache > EnzCstTemplateResCacheOP
 
typedef utility::pointer::shared_ptr< EnzCstTemplateResCache const > EnzCstTemplateResCacheCOP
 
typedef utility::pointer::shared_ptr< EnzdesLoopsFile > EnzdesLoopsFileOP
 
typedef utility::pointer::shared_ptr< EnzdesLoopsFile const > EnzdesLoopsFileCOP
 
typedef utility::pointer::shared_ptr< EnzdesLoopInfo > EnzdesLoopInfoOP
 
typedef utility::pointer::shared_ptr< EnzdesLoopInfo const > EnzdesLoopInfoCOP
 
typedef utility::pointer::shared_ptr< EnzdesSeqRecoveryCache > EnzdesSeqRecoveryCacheOP
 
typedef utility::pointer::shared_ptr< EnzdesSeqRecoveryCache const > EnzdesSeqRecoveryCacheCOP
 
typedef utility::pointer::shared_ptr< ExternalGeomSampler > ExternalGeomSamplerOP
 
typedef utility::pointer::shared_ptr< ExternalGeomSampler const > ExternalGeomSamplerCOP
 
typedef utility::pointer::shared_ptr< InvrotTarget > InvrotTargetOP
 
typedef utility::pointer::shared_ptr< InvrotTarget const > InvrotTargetCOP
 
typedef utility::pointer::shared_ptr< SingleResidueInvrotTarget > SingleResidueInvrotTargetOP
 
typedef utility::pointer::shared_ptr< SingleResidueInvrotTarget const > SingleResidueInvrotTargetCOP
 
typedef utility::pointer::shared_ptr< InvrotTree > InvrotTreeOP
 
typedef utility::pointer::shared_ptr< InvrotTree const > InvrotTreeCOP
 
typedef utility::pointer::shared_ptr< InvrotTreeNode > InvrotTreeNodeOP
 
typedef utility::pointer::shared_ptr< InvrotTreeNode const > InvrotTreeNodeCOP
 
typedef utility::pointer::shared_ptr< InvrotTreeNodeBase > InvrotTreeNodeBaseOP
 
typedef utility::pointer::shared_ptr< InvrotTreeNodeBase const > InvrotTreeNodeBaseCOP
 
typedef utility::pointer::weak_ptr< InvrotTreeNodeBase > InvrotTreeNodeBaseAP
 
typedef utility::pointer::weak_ptr< InvrotTreeNodeBase const > InvrotTreeNodeBaseCAP
 
typedef utility::pointer::shared_ptr< InvrotCollector > InvrotCollectorOP
 
typedef utility::pointer::shared_ptr< InvrotCollector const > InvrotCollectorCOP
 
typedef utility::pointer::shared_ptr< LigandConformer > LigandConformerOP
 
typedef utility::pointer::shared_ptr< LigandConformer const > LigandConformerCOP
 
typedef utility::pointer::shared_ptr< GeomSampleInfo > GeomSampleInfoOP
 
typedef utility::pointer::shared_ptr< GeomSampleInfo const > GeomSampleInfoCOP
 
typedef utility::pointer::shared_ptr< MatchConstraintFileInfo > MatchConstraintFileInfoOP
 
typedef utility::pointer::shared_ptr< MatchConstraintFileInfo const > MatchConstraintFileInfoCOP
 
typedef utility::pointer::shared_ptr< MatchConstraintFileInfoList > MatchConstraintFileInfoListOP
 
typedef utility::pointer::shared_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, std::string const &name3, core::chemical::ResidueTypeSetCOP 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...
 
std::string matcher_constraint_name_mangler (std::string const &foo)
 
std::string matcher_constraint_combination_name_mangler (std::string const &foo)
 
void setup_geometric_attribute_list (utility::tag::AttributeList &attlist)
 
void add_subelement_for_constraint_combination (utility::tag::XMLSchemaSimpleSubelementList &ssl, utility::tag::XMLSchemaDefinition &xsd)
 
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::func::FuncOP constraint_func=nullptr)
 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=nullptr)
 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 const &chainA, std::string const &resA, int seqposA, std::string const &chainB, std::string const &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)
 
utility::vector1< core::chemical::ResidueTypeCOP > sort_residue_type_pointers_by_name (utility::vector1< core::chemical::ResidueTypeCOP > const &restype_temp_set)
 

Typedef Documentation

◆ AlignPoseToInvrotTreeMoverCOP

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

◆ AlignPoseToInvrotTreeMoverOP

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

◆ AllowedSeqposForGeomCstCOP

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

◆ AllowedSeqposForGeomCstOP

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

◆ CovalentConnectionReplaceInfoCOP

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

◆ CovalentConnectionReplaceInfoOP

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

◆ EnzConstraintIOAP

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

◆ EnzConstraintIOCAP

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

◆ EnzConstraintIOCOP

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

◆ EnzConstraintIOOP

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

◆ EnzConstraintParametersAP

typedef utility::pointer::weak_ptr< EnzConstraintParameters > protocols::toolbox::match_enzdes_util::EnzConstraintParametersAP

◆ EnzConstraintParametersCAP

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

◆ EnzConstraintParametersCOP

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

◆ EnzConstraintParametersOP

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

◆ EnzCstTemplateResAtomsCOP

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

◆ EnzCstTemplateResAtomsOP

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

◆ EnzCstTemplateResCacheCOP

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

◆ EnzCstTemplateResCacheOP

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

◆ EnzCstTemplateResCOP

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

◆ EnzCstTemplateResOP

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

◆ EnzdesCacheableObserverAP

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

◆ EnzdesCacheableObserverCAP

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

◆ EnzdesCacheableObserverCOP

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

◆ EnzdesCacheableObserverOP

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

◆ EnzdesCstCacheCOP

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

◆ EnzdesCstCacheOP

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

◆ EnzdesCstParamCacheCOP

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

◆ EnzdesCstParamCacheOP

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

◆ EnzdesLoopInfoCOP

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

◆ EnzdesLoopInfoOP

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

◆ EnzdesLoopsFileCOP

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

◆ EnzdesLoopsFileOP

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

◆ EnzdesSeqRecoveryCacheCOP

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

◆ EnzdesSeqRecoveryCacheOP

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

◆ ExternalGeomSamplerCOP

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

◆ ExternalGeomSamplerOP

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

◆ GeomSampleInfoCOP

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

◆ GeomSampleInfoOP

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

◆ InvrotCollectorCOP

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

◆ InvrotCollectorOP

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

◆ InvrotTargetCOP

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

◆ InvrotTargetOP

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

◆ InvrotTreeCOP

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

◆ InvrotTreeNodeBaseAP

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

◆ InvrotTreeNodeBaseCAP

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

◆ InvrotTreeNodeBaseCOP

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

◆ InvrotTreeNodeBaseOP

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

◆ InvrotTreeNodeCOP

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

◆ InvrotTreeNodeOP

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

◆ InvrotTreeOP

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

◆ LigandConformerCOP

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

◆ LigandConformerOP

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

◆ MatchConstraintFileInfoCOP

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

◆ MatchConstraintFileInfoListCOP

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

◆ MatchConstraintFileInfoListOP

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

◆ MatchConstraintFileInfoOP

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

◆ SingleResidueInvrotTargetCOP

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

◆ SingleResidueInvrotTargetOP

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

Enumeration Type Documentation

◆ ExternalTransform

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

◆ add_relevant_restypes_to_subset()

void protocols::toolbox::match_enzdes_util::add_relevant_restypes_to_subset ( std::set< core::chemical::ResidueTypeCOP > &  restype_subset,
std::string const &  name3,
core::chemical::ResidueTypeSetCOP  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

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

◆ add_subelement_for_constraint_combination()

void protocols::toolbox::match_enzdes_util::add_subelement_for_constraint_combination ( utility::tag::XMLSchemaSimpleSubelementList &  ssl,
utility::tag::XMLSchemaDefinition &  xsd 
)

References matcher_constraint_combination_name_mangler(), and setup_geometric_attribute_list().

Referenced by protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::return_complex_type_for_MatcherConstraint().

◆ assemble_remark_line()

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

References core::id::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().

◆ constrain_pose_res_to_invrots() [1/2]

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::conformation::Residue::get_self_ptr(), core::pose::Pose::residue(), and tr().

◆ constrain_pose_res_to_invrots() [2/2]

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().

◆ cst_residue_in_pose()

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

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

◆ get_enzdes_observer() [1/2]

EnzdesCacheableObserverOP protocols::toolbox::match_enzdes_util::get_enzdes_observer ( core::pose::Pose &  pose)

convenience function to get a cacheable observer from a pose

References core::pose::datacache::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::RepackLigandSiteWithoutLigandMover::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::enzdes::AddRigidBodyLigandConfs::apply(), protocols::enzdes::SetCatalyticResPackBehavior::apply(), protocols::hbnet::ConstrainHBondNetwork::apply(), protocols::enzdes::enzutil::catalytic_res(), protocols::enzdes::EnzdesBaseProtocol::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_file(), 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::simple_moves::RepeatPropagationMover::repeat_ligand_constraints(), 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().

◆ get_enzdes_observer() [2/2]

EnzdesCacheableObserverCOP protocols::toolbox::match_enzdes_util::get_enzdes_observer ( core::pose::Pose const &  pose)

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

◆ get_first_protein_residue()

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(), core::pose::Pose::size(), and tr().

◆ get_last_protein_residue()

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(), core::pose::Pose::size(), and tr().

◆ matcher_constraint_combination_name_mangler()

std::string protocols::toolbox::match_enzdes_util::matcher_constraint_combination_name_mangler ( std::string const &  foo)

Referenced by add_subelement_for_constraint_combination().

◆ matcher_constraint_name_mangler()

std::string protocols::toolbox::match_enzdes_util::matcher_constraint_name_mangler ( std::string const &  foo)

Referenced by protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::return_complex_type_for_MatcherConstraint().

◆ replace_residue_keeping_all_atom_positions()

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_is_hydrogen(), core::conformation::Residue::atom_name(), core::pose::Pose::conformation(), core::id::AtomID_Map< T >::empty(), core::conformation::Conformation::fill_missing_atoms(), core::conformation::Residue::is_virtual(), core::conformation::Residue::name3(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::id::AtomID_Map< T >::set(), 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().

◆ setup_geometric_attribute_list()

void protocols::toolbox::match_enzdes_util::setup_geometric_attribute_list ( utility::tag::AttributeList &  attlist)

Referenced by add_subelement_for_constraint_combination().

◆ sort_residue_type_pointers_by_name()

utility::vector1< core::chemical::ResidueTypeCOP > protocols::toolbox::match_enzdes_util::sort_residue_type_pointers_by_name ( utility::vector1< core::chemical::ResidueTypeCOP > const &  restype_temp_set)

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

◆ split_up_remark_line()

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 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().

◆ tr() [1/5]

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::EnzConstraintIO::process_pdb_header(), protocols::toolbox::match_enzdes_util::GeomSampleInfo::read_data(), protocols::toolbox::match_enzdes_util::ResInteractions::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().

◆ TR() [1/3]

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

◆ TR() [2/3]

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(), and protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::set_geomcst_for_superposition_from_enz_io().

◆ TR() [3/3]

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

◆ tr() [2/5]

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

◆ tr() [3/5]

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

◆ tr() [4/5]

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

◆ tr() [5/5]

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