Rosetta Protocols  2014.35
Classes | Typedefs | Enumerations | Functions | Variables
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

Enumeration Type Documentation

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 
)
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)
core::Size protocols::toolbox::match_enzdes_util::get_first_protein_residue ( core::pose::Pose const &  pose)
core::Size protocols::toolbox::match_enzdes_util::get_last_protein_residue ( core::pose::Pose const &  pose)
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 
)
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 
)

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