Rosetta 3.4
Classes | Typedefs | Enumerations | Functions
protocols::toolbox::match_enzdes_util Namespace Reference

Classes

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  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
< 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
< 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.enzdes.EnzdesCacheableObserver")
EnzdesCacheableObserverOP get_enzdes_observer (core::pose::Pose &pose)
 convenience function to get a cacheable observer from a pose
EnzdesCacheableObserverCOP get_enzdes_observer (core::pose::Pose const &pose)
static basic::Tracer TR ("protocols.enzdes.EnzdesSeqRecoveryCache")
void add_relevant_restypes_to_subset (std::set< core::chemical::ResidueTypeCAP > &restype_subset, utility::vector1< core::chemical::ResidueTypeCAP > 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
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)
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)

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::ResidueTypeCAP > &  restype_subset,
utility::vector1< core::chemical::ResidueTypeCAP > 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 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 
)
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::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::EnzConstraintParameters::allowed_res_name3_at_position(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::allowed_res_name3_at_position(), protocols::forge::remodel::RemodelMover::apply(), protocols::forge::remodel::RemodelEnzdesCstModule::apply(), protocols::enzdes::AddRigidBodyLigandConfs::apply(), protocols::enzdes::SetCatalyticResPackBehavior::apply(), protocols::enzdes::RepackLigandSiteWithoutLigandMover::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(), 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::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::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)
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 
)
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.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::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::EnzCstTemplateRes::find_in_pose_if_missing_from_header(), protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::generate_ss_strings_from_blueprint(), protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList::inverse_rotamers_against_residue(), protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::inverse_rotamers_against_residue(), protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::process_algorithm_info(), protocols::toolbox::match_enzdes_util::ResInteractions::process_input_line_tokens(), protocols::toolbox::match_enzdes_util::GeomSampleInfo::read_data(), protocols::toolbox::match_enzdes_util::CstResInteractions::read_data(), protocols::toolbox::match_enzdes_util::ResInteractions::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::CstResInteractions::write_data(), and protocols::toolbox::match_enzdes_util::ResInteractions::write_data().

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