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Rosetta 3.5
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Rosetta 3.5
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Functions | |
| static basic::Tracer | tr ("protocols.enzdes.enzdes_util") |
| bool | is_catalytic_seqpos (core::pose::Pose const &pose, core::Size const seqpos) |
| queries whether a certain position is considered catalytic, i.e. if the residue is constrained according to the enzdes constraint file More... | |
| utility::vector1< core::Size > | catalytic_res (core::pose::Pose const &pose) |
| core::Real | sum_constraint_scoreterms (core::pose::Pose const &pose, int which_res) |
| sums up coordinate, atom_pair, angle, and dihedral constraint scores for the residue in question. in case which_res is -1, the scores for the whole pose will be taken More... | |
| void | read_pose_from_pdb (core::pose::Pose &pose, std::string const &filename) |
| convenience function to read in a pose for enzdes this function basically just calls pose_from_pdb, but it will create an enzdes cacheable observer in the pose, also, 1, if a multimodel pdb is requested, if there are different ligand positions, these will be saved in the enzdes cacheable observer and 2, if option additional_packing_ligand_rb_confs is active, random ligand rigid body confs will be generated and added to the cacheable observer More... | |
| void | make_continuous_true_regions_in_bool_vector (utility::vector1< bool > &the_vector, core::Size const min_number_continuous_trues) |
| core::pack::task::PackerTaskOP | recreate_task (core::pose::Pose const &pose, core::pack::task::PackerTask const &orig_task) |
| toolbox::match_enzdes_util::EnzConstraintIOCOP | get_enzcst_io (core::pose::Pose const &pose) |
| convenience function to get enzdes cst io out of cst cache. note: may return empty pointer in case cst cache wasn't set yet More... | |
| void | remove_remark_header_for_geomcst (core::pose::Pose &pose, core::Size geomcst) |
| void | create_remark_headers_from_cstcache (core::pose::Pose &pose) |
| function to write proper remark headers from whatever is found in the pose cstcache More... | |
| std::string | get_pdb_code_from_pose_tag (core::pose::Pose const &pose) |
| bool | is_digit (char *cha) |
| delete and use cctype functions More... | |
| bool | is_uppercase_letter (char *cha) |
| delete and use cctype functions More... | |
| bool | is_lowercase_letter (char *cha) |
| delete and use cctype functions More... | |
| void | disable_constraint_scoreterms (core::scoring::ScoreFunctionOP scorefxn) |
| void | enable_constraint_scoreterms (core::scoring::ScoreFunctionOP scorefxn) |
| bool | is_scofx_cstfied (core::scoring::ScoreFunctionCOP scorefxn) |
| void | scorefxn_update_from_options (core::scoring::ScoreFunctionOP scorefxn) |
| void | remove_all_enzdes_constraints (core::pose::Pose &pose) |
| void | get_resnum_from_cstid_list (std::string const &cstidlist, core::pose::Pose const &pose, utility::vector1< core::Size > &resnums) |
| core::Size | get_resnum_from_cstid (std::string const &cstid, core::pose::Pose const &pose) |
| Extracts residue number from cstid string Expects cstid string to be of format [0-9]+[A-Z], where the number is constraint number and trailing letter is temlplate id i.e. either A or B. More... | |
| utility::vector1< core::Size > protocols::enzdes::enzutil::catalytic_res | ( | core::pose::Pose const & | pose) |
Definition at line 98 of file enzdes_util.cc.
References protocols::toolbox::match_enzdes_util::get_enzdes_observer(), core::chemical::ResidueType::is_ligand(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().
Referenced by protocols::enzdes::EnzdesScorefileFilter::examine_pose(), and protocols::enzdes::EnzdesScorefileFilter::setup_pose_metric_calculators().
| void protocols::enzdes::enzutil::create_remark_headers_from_cstcache | ( | core::pose::Pose & | pose) |
function to write proper remark headers from whatever is found in the pose cstcache
Definition at line 404 of file enzdes_util.cc.
References protocols::toolbox::match_enzdes_util::assemble_remark_line(), protocols::toolbox::match_enzdes_util::get_enzdes_observer(), protocols::toolbox::match_enzdes_util::EnzdesCstParamCache::missing_in_pose(), core::conformation::Residue::name3(), core::pose::RemarkInfo::num, core::pose::Pose::pdb_info(), core::pose::Pose::residue(), protocols::toolbox::match_enzdes_util::split_up_remark_line(), protocols::toolbox::match_enzdes_util::EnzdesCstParamCache::template_res_cache(), protocols::toolbox::match_enzdes_util::EnzdesCstParamCache::template_res_cache_size(), and core::pose::RemarkInfo::value.
| void protocols::enzdes::enzutil::disable_constraint_scoreterms | ( | core::scoring::ScoreFunctionOP | scorefxn) |
Definition at line 616 of file enzdes_util.cc.
References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, core::scoring::coordinate_constraint, core::scoring::dihedral_constraint, and core::scoring::res_type_constraint.
Referenced by protocols::enzdes::RepackWithoutLigandFilter::compute().
| void protocols::enzdes::enzutil::enable_constraint_scoreterms | ( | core::scoring::ScoreFunctionOP | scorefxn) |
Definition at line 626 of file enzdes_util.cc.
References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, core::scoring::coordinate_constraint, core::scoring::dihedral_constraint, and core::scoring::res_type_constraint.
Referenced by protocols::enzdes::LigInterfaceEnergyFilter::compute(), protocols::enzdes::EnzScoreFilter::compute(), protocols::enzdes::EnzRepackMinimize::ensure_scofx_cstfication(), and protocols::enzdes::LigInterfaceEnergyFilter::LigInterfaceEnergyFilter().
| toolbox::match_enzdes_util::EnzConstraintIOCOP protocols::enzdes::enzutil::get_enzcst_io | ( | core::pose::Pose const & | pose) |
convenience function to get enzdes cst io out of cst cache. note: may return empty pointer in case cst cache wasn't set yet
Definition at line 372 of file enzdes_util.cc.
References protocols::toolbox::match_enzdes_util::get_enzdes_observer().
Referenced by protocols::enzdes::SecondaryMatchProtocol::do_matching(), and protocols::enzdes::EnzdesBaseProtocol::enzdes_pack().
| std::string protocols::enzdes::enzutil::get_pdb_code_from_pose_tag | ( | core::pose::Pose const & | pose) |
function not implemented very slick at the moment, need to find way to compile boost regex library :(( to extract the pdb code from the pose tag without a regular expression module, some explicit functions have been written below
Definition at line 457 of file enzdes_util.cc.
References core::pose::Pose::data(), is_digit(), is_lowercase_letter(), is_uppercase_letter(), and protocols::kinmatch::str().
Referenced by protocols::enzdes::DesignVsNativeComparison::compare_to_native().
| core::Size protocols::enzdes::enzutil::get_resnum_from_cstid | ( | std::string const & | cstid, |
| core::pose::Pose const & | pose | ||
| ) |
Extracts residue number from cstid string Expects cstid string to be of format [0-9]+[A-Z], where the number is constraint number and trailing letter is temlplate id i.e. either A or B.
Definition at line 679 of file enzdes_util.cc.
References protocols::toolbox::match_enzdes_util::get_enzdes_observer(), and core::pose::Pose::total_residue().
Referenced by protocols::enzdes::EnzScoreFilter::compute(), and get_resnum_from_cstid_list().
| void protocols::enzdes::enzutil::get_resnum_from_cstid_list | ( | std::string const & | cstidlist, |
| core::pose::Pose const & | pose, | ||
| utility::vector1< core::Size > & | resnums | ||
| ) |
Definition at line 662 of file enzdes_util.cc.
References get_resnum_from_cstid(), and core::pose::Pose::total_residue().
Referenced by protocols::enzdes::PackRotamersMoverPartGreedy::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), and protocols::enzdes::RepackWithoutLigandFilter::compute().
| bool protocols::enzdes::enzutil::is_catalytic_seqpos | ( | core::pose::Pose const & | pose, |
| core::Size const | seqpos | ||
| ) |
queries whether a certain position is considered catalytic, i.e. if the residue is constrained according to the enzdes constraint file
Definition at line 81 of file enzdes_util.cc.
References protocols::toolbox::match_enzdes_util::get_enzdes_observer().
Referenced by protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::enzdes::ProteinLigandInterfaceUpweighter::apply(), protocols::enzdes::EnzdesBaseProtocol::design_targets(), and protocols::enzdes::EnzdesBaseProtocol::is_catalytic_position().
| bool protocols::enzdes::enzutil::is_digit | ( | char * | cha) |
delete and use cctype functions
Definition at line 527 of file enzdes_util.cc.
Referenced by get_pdb_code_from_pose_tag().
| bool protocols::enzdes::enzutil::is_lowercase_letter | ( | char * | cha) |
delete and use cctype functions
Definition at line 583 of file enzdes_util.cc.
Referenced by get_pdb_code_from_pose_tag().
| bool protocols::enzdes::enzutil::is_scofx_cstfied | ( | core::scoring::ScoreFunctionCOP | scorefxn) |
Definition at line 637 of file enzdes_util.cc.
References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, core::scoring::coordinate_constraint, and core::scoring::dihedral_constraint.
Referenced by protocols::enzdes::EnzRepackMinimize::ensure_scofx_cstfication().
| bool protocols::enzdes::enzutil::is_uppercase_letter | ( | char * | cha) |
delete and use cctype functions
Definition at line 548 of file enzdes_util.cc.
Referenced by get_pdb_code_from_pose_tag().
| void protocols::enzdes::enzutil::make_continuous_true_regions_in_bool_vector | ( | utility::vector1< bool > & | the_vector, |
| core::Size const | min_number_continuous_trues | ||
| ) |
Definition at line 200 of file enzdes_util.cc.
Referenced by protocols::enzdes::EnzdesBaseProtocol::create_enzdes_movemap(), and protocols::enzdes::EnzdesFlexBBProtocol::determine_flexible_regions().
| void protocols::enzdes::enzutil::read_pose_from_pdb | ( | core::pose::Pose & | pose, |
| std::string const & | filename | ||
| ) |
convenience function to read in a pose for enzdes this function basically just calls pose_from_pdb, but it will create an enzdes cacheable observer in the pose, also, 1, if a multimodel pdb is requested, if there are different ligand positions, these will be saved in the enzdes cacheable observer and 2, if option additional_packing_ligand_rb_confs is active, random ligand rigid body confs will be generated and added to the cacheable observer
Definition at line 151 of file enzdes_util.cc.
References protocols::enzdes::GenerateStoredRBConfs::apply(), core::io::serialization::clone(), protocols::toolbox::match_enzdes_util::get_enzdes_observer(), core::import_pose::pose_from_pdb(), and core::io::serialization::size().
Referenced by protocols::enzdes::EnzdesJobInputter::pose_from_job().
| core::pack::task::PackerTaskOP protocols::enzdes::enzutil::recreate_task | ( | core::pose::Pose const & | pose, |
| core::pack::task::PackerTask const & | orig_task | ||
| ) |
Definition at line 323 of file enzdes_util.cc.
References core::pack::task::ResidueLevelTask::allowed_residue_types_begin(), core::pack::task::ResidueLevelTask::allowed_residue_types_end(), core::pack::task::ResidueLevelTask::being_designed(), core::pack::task::ResidueLevelTask::being_packed(), core::pack::task::PackerTask::IGEdgeReweights(), core::chemical::num_canonical_aas, core::pack::task::PackerTask::residue_task(), core::pack::task::ResidueLevelTask::rotamer_operations(), core::pack::task::ResidueLevelTask::rotamer_set_operation_begin(), core::pack::task::ResidueLevelTask::rotamer_set_operation_end(), core::pack::task::PackerTask::total_residue(), and core::pose::Pose::total_residue().
Referenced by protocols::enzdes::EnzdesFlexBBProtocol::apply(), protocols::enzdes::EnzdesBaseProtocol::enzdes_pack(), and protocols::enzdes::EnzdesFlexibleRegion::sort_ensemble_by_designability().
| void protocols::enzdes::enzutil::remove_all_enzdes_constraints | ( | core::pose::Pose & | pose) |
Definition at line 653 of file enzdes_util.cc.
References protocols::toolbox::match_enzdes_util::get_enzdes_observer().
Referenced by protocols::enzdes::RepackWithoutLigandFilter::compute().
| void protocols::enzdes::enzutil::remove_remark_header_for_geomcst | ( | core::pose::Pose & | pose, |
| core::Size | geomcst | ||
| ) |
Definition at line 382 of file enzdes_util.cc.
References core::pose::Pose::pdb_info(), and protocols::toolbox::match_enzdes_util::split_up_remark_line().
| void protocols::enzdes::enzutil::scorefxn_update_from_options | ( | core::scoring::ScoreFunctionOP | scorefxn) |
Definition at line 643 of file enzdes_util.cc.
References core::scoring::methods::EnergyMethodOptions::exclude_protein_protein_hack_elec().
Referenced by protocols::enzdes::EnzRepackMinimize::ensure_scofx_cstfication().
| core::Real protocols::enzdes::enzutil::sum_constraint_scoreterms | ( | core::pose::Pose const & | pose, |
| int | which_res | ||
| ) |
sums up coordinate, atom_pair, angle, and dihedral constraint scores for the residue in question. in case which_res is -1, the scores for the whole pose will be taken
Definition at line 120 of file enzdes_util.cc.
References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, core::scoring::coordinate_constraint, core::scoring::dihedral_constraint, core::pose::Pose::energies(), core::scoring::Energies::residue_total_energies(), core::scoring::Energies::total_energies(), and core::scoring::Energies::weights().
Referenced by protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose(), protocols::enzdes::EnzdesScorefileFilter::compute_metrics_for_residue_subset(), and protocols::enzdes::EnzdesScorefileFilter::examine_pose().
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1.8.4