protocols::stepwise::sampling::protein Namespace Reference

Namespaces
	checker

Classes
class	InputStreamWithResidueInfo
class	MainChainTorsionSet
class	StepWiseBetaAntiParallelJumpSampleGenerator
class	StepWisePoseSetup
class	StepWiseProteinBackboneSampler
class	StepWiseProteinCCD_Closer
class	StepWiseProteinJobParameters
class	StepWiseProteinLoopBridger
class	StepWiseProteinModeler
class	StepWiseProteinModelerOptions
class	StepWiseProteinMultiPosePacker
class	StepWiseProteinPacker
class	StepWiseProteinPoseMinimizer
class	StepWiseProteinResidueSampler

Typedefs
typedef utility::pointer::owning_ptr < InputStreamWithResidueInfo >	InputStreamWithResidueInfoOP
typedef utility::pointer::owning_ptr < InputStreamWithResidueInfo const >	InputStreamWithResidueInfoCOP
typedef utility::pointer::owning_ptr < StepWiseProteinMultiPosePacker >	StepWiseProteinMultiPosePackerOP
typedef utility::pointer::owning_ptr < StepWiseProteinMultiPosePacker const >	StepWiseProteinMultiPosePackerCOP
typedef utility::vector1 < MainChainTorsionSet >	MainChainTorsionSetList
typedef utility::pointer::owning_ptr < StepWisePoseSetup >	StepWisePoseSetupOP
typedef utility::pointer::owning_ptr < StepWisePoseSetup const >	StepWisePoseSetupCOP
typedef std::map< core::Size, core::Size >	ResMap
typedef utility::pointer::owning_ptr < StepWiseProteinJobParameters >	StepWiseProteinJobParametersOP
typedef utility::pointer::owning_ptr < StepWiseProteinJobParameters const >	StepWiseProteinJobParametersCOP
typedef utility::pointer::owning_ptr < StepWiseProteinJobParametersUtil >	StepWiseProteinJobParametersUtilOP
typedef utility::pointer::owning_ptr < StepWiseProteinJobParametersUtil const >	StepWiseProteinJobParametersUtilCOP
typedef utility::pointer::owning_ptr < StepWiseProteinModeler >	StepWiseProteinModelerOP
typedef utility::pointer::owning_ptr < StepWiseProteinModeler const >	StepWiseProteinModelerCOP
typedef utility::pointer::owning_ptr < StepWiseProteinModelerOptions >	StepWiseProteinModelerOptionsOP
typedef utility::pointer::owning_ptr < StepWiseProteinModelerOptions const >	StepWiseProteinModelerOptionsCOP
typedef utility::pointer::owning_ptr < StepWiseProteinPacker >	StepWiseProteinPackerOP
typedef utility::pointer::owning_ptr < StepWiseProteinPacker const >	StepWiseProteinPackerCOP
typedef utility::pointer::owning_ptr < StepWiseProteinPoseMinimizer >	StepWiseProteinPoseMinimizerOP
typedef utility::pointer::owning_ptr < StepWiseProteinPoseMinimizer const >	StepWiseProteinPoseMinimizerCOP
typedef utility::pointer::owning_ptr < StepWiseProteinResidueSampler >	StepWiseProteinResidueSamplerOP
typedef utility::pointer::owning_ptr < StepWiseProteinResidueSampler const >	StepWiseProteinResidueSamplerCOP

Functions
import_pose::pose_stream::PoseInputStreamOP	setup_pose_input_stream (utility::options::StringVectorOption const &option_s1, utility::options::StringVectorOption const &option_silent1, utility::options::StringVectorOption const &option_tags1)
void	initialize_input_streams (utility::vector1< protocols::stepwise::sampling::protein::InputStreamWithResidueInfoOP > &input_streams)
void	initialize_input_streams_with_residue_info (utility::vector1< InputStreamWithResidueInfoOP > &input_streams_with_residue_info, utility::vector1< std::string > const &pdb_tags, utility::vector1< std::string > const &silent_files_in, utility::vector1< Size > const &input_res, utility::vector1< Size > const &input_res2)
	MainChainTorsionSet (core::Real const &phi, core::Real const &psi, core::Real const &omega)
	MainChainTorsionSet (core::Real const &phi, core::Real const &psi)
	~MainChainTorsionSet ()
core::Real const	phi () const
core::Real const	psi () const
core::Real const	omega () const
StepWiseProteinJobParametersOP	setup_job_parameters_for_protein_swa (utility::vector1< Size > const &moving_res_list, pose::Pose const &pose, pose::PoseCOP native_pose, utility::vector1< Size > const &bridge_res, utility::vector1< Size > const &working_minimize_res)
Real	get_rotamer_angle (core::Size const &i, core::Size const &N_SAMPLE)
void	output_silent_struct (core::pose::Pose const &pose, core::pose::PoseCOP const &native_pose_op, std::string const &silent_file, std::string const &tag, core::io::silent::SilentFileDataOP sfd_in)
void	output_silent_struct (core::pose::Pose const &pose, core::pose::PoseCOP const &native_pose_op, std::string const &silent_file, std::string const &tag, core::io::silent::SilentFileDataOP sfd_in, utility::vector1< core::Size > const &calc_rms_res)
void	remove_end_variants (core::pose::Pose &pose)
Real	get_pretend_psi_explicit (core::pose::Pose const &pose, Size const &res)
Real	get_pretend_phi_explicit (core::pose::Pose const &pose, Size const &res)
void	setup_protein_CA_atom_id_map (core::pose::Pose const &pose_1, core::pose::Pose const &pose_2, Size const base_res, core::id::AtomID_Map< core::id::AtomID > &atom_ID_map)
void	setup_protein_backbone_atom_id_map (core::pose::Pose const &pose_1, core::pose::Pose const &pose_2, Size const base_res, core::id::AtomID_Map< core::id::AtomID > &atom_ID_map)
void	setup_protein_backbone_atom_id_map (core::pose::Pose const &pose_1, core::pose::Pose const &pose_2, Size const base_res, Size const base_res2, core::id::AtomID_Map< core::id::AtomID > &atom_ID_map)

Typedef Documentation

typedef utility::pointer::owning_ptr< InputStreamWithResidueInfo const > protocols::stepwise::sampling::protein::InputStreamWithResidueInfoCOP

typedef utility::pointer::owning_ptr< InputStreamWithResidueInfo > protocols::stepwise::sampling::protein::InputStreamWithResidueInfoOP

typedef utility::vector1< MainChainTorsionSet > protocols::stepwise::sampling::protein::MainChainTorsionSetList

typedef std::map< core::Size, core::Size > protocols::stepwise::sampling::protein::ResMap

typedef utility::pointer::owning_ptr< StepWisePoseSetup const > protocols::stepwise::sampling::protein::StepWisePoseSetupCOP

typedef utility::pointer::owning_ptr< StepWisePoseSetup > protocols::stepwise::sampling::protein::StepWisePoseSetupOP

typedef utility::pointer::owning_ptr< StepWiseProteinJobParameters const > protocols::stepwise::sampling::protein::StepWiseProteinJobParametersCOP

typedef utility::pointer::owning_ptr< StepWiseProteinJobParameters > protocols::stepwise::sampling::protein::StepWiseProteinJobParametersOP

typedef utility::pointer::owning_ptr< StepWiseProteinJobParametersUtil const > protocols::stepwise::sampling::protein::StepWiseProteinJobParametersUtilCOP

typedef utility::pointer::owning_ptr< StepWiseProteinJobParametersUtil > protocols::stepwise::sampling::protein::StepWiseProteinJobParametersUtilOP

typedef utility::pointer::owning_ptr< StepWiseProteinModeler const > protocols::stepwise::sampling::protein::StepWiseProteinModelerCOP

typedef utility::pointer::owning_ptr< StepWiseProteinModeler > protocols::stepwise::sampling::protein::StepWiseProteinModelerOP

typedef utility::pointer::owning_ptr< StepWiseProteinModelerOptions const > protocols::stepwise::sampling::protein::StepWiseProteinModelerOptionsCOP

typedef utility::pointer::owning_ptr< StepWiseProteinModelerOptions > protocols::stepwise::sampling::protein::StepWiseProteinModelerOptionsOP

typedef utility::pointer::owning_ptr< StepWiseProteinMultiPosePacker const > protocols::stepwise::sampling::protein::StepWiseProteinMultiPosePackerCOP

typedef utility::pointer::owning_ptr< StepWiseProteinMultiPosePacker > protocols::stepwise::sampling::protein::StepWiseProteinMultiPosePackerOP

typedef utility::pointer::owning_ptr< StepWiseProteinPacker const > protocols::stepwise::sampling::protein::StepWiseProteinPackerCOP

typedef utility::pointer::owning_ptr< StepWiseProteinPacker > protocols::stepwise::sampling::protein::StepWiseProteinPackerOP

typedef utility::pointer::owning_ptr< StepWiseProteinPoseMinimizer const > protocols::stepwise::sampling::protein::StepWiseProteinPoseMinimizerCOP

typedef utility::pointer::owning_ptr< StepWiseProteinPoseMinimizer > protocols::stepwise::sampling::protein::StepWiseProteinPoseMinimizerOP

typedef utility::pointer::owning_ptr< StepWiseProteinResidueSampler const > protocols::stepwise::sampling::protein::StepWiseProteinResidueSamplerCOP

typedef utility::pointer::owning_ptr< StepWiseProteinResidueSampler > protocols::stepwise::sampling::protein::StepWiseProteinResidueSamplerOP

Function Documentation

core::Real protocols::stepwise::sampling::protein::get_pretend_phi_explicit	(	core::pose::Pose const &	pose,
		Size const &	res
	)

References numeric::conversions::degrees(), numeric::dihedral_radians(), core::conformation::Residue::has(), phi(), numeric::principal_angle_degrees(), core::pose::Pose::residue(), and core::pose::Pose::xyz().

Referenced by protocols::stepwise::sampling::protein::StepWisePoseSetup::fix_phi_psi_offsets(), protocols::stepwise::sampling::protein::StepWisePoseSetup::initialize_phi_psi_offsets(), and protocols::stepwise::sampling::protein::StepWisePoseSetup::save_phi_psi_offsets().

core::Real protocols::stepwise::sampling::protein::get_pretend_psi_explicit	(	core::pose::Pose const &	pose,
		Size const &	res
	)

References numeric::conversions::degrees(), numeric::dihedral_radians(), numeric::principal_angle_degrees(), psi(), and core::pose::Pose::xyz().

Referenced by protocols::stepwise::sampling::protein::StepWisePoseSetup::fix_phi_psi_offsets(), protocols::stepwise::sampling::protein::StepWisePoseSetup::initialize_phi_psi_offsets(), and protocols::stepwise::sampling::protein::StepWisePoseSetup::save_phi_psi_offsets().

core::Real protocols::stepwise::sampling::protein::get_rotamer_angle	(	core::Size const &	i,
		core::Size const &	N_SAMPLE
	)

Referenced by protocols::stepwise::sampling::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_c_terminus(), protocols::stepwise::sampling::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_full(), protocols::stepwise::sampling::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_n_terminus(), protocols::stepwise::sampling::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_sample_phi_only(), and protocols::stepwise::sampling::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_sample_psi_only().

void protocols::stepwise::sampling::protein::initialize_input_streams

(

utility::vector1< protocols::stepwise::sampling::protein::InputStreamWithResidueInfoOP > &

input_streams

)

References backbone_only1, backbone_only2, initialize_input_streams_with_residue_info(), in::file::input_res, input_res1, input_res2, option, in::file::s, s1, s2, setup_pose_input_stream(), in::file::silent, silent1, silent2, slice_res1, slice_res2, in::file::tags, tags1, tags2, and user.

void protocols::stepwise::sampling::protein::initialize_input_streams_with_residue_info	(	utility::vector1< InputStreamWithResidueInfoOP > &	input_streams_with_residue_info,
		utility::vector1< std::string > const &	pdb_tags,
		utility::vector1< std::string > const &	silent_files_in,
		utility::vector1< Size > const &	input_res,
		utility::vector1< Size > const &	input_res2
	)

References protocols::stepwise::sampling::protein::InputStreamWithResidueInfo::InputStreamWithResidueInfo().

Referenced by initialize_input_streams().

protocols::stepwise::sampling::protein::MainChainTorsionSet	(	core::Real const &	phi,
		core::Real const &	psi,
		core::Real const &	omega
	)

Referenced by protocols::stepwise::sampling::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_c_terminus(), protocols::stepwise::sampling::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_coarse(), protocols::stepwise::sampling::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_full(), protocols::stepwise::sampling::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_n_terminus(), protocols::stepwise::sampling::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_sample_phi_only(), protocols::stepwise::sampling::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_sample_psi_only(), protocols::stepwise::sampling::protein::StepWiseProteinBackboneSampler::sample_cis_omega(), and protocols::stepwise::sampling::protein::StepWiseProteinBackboneSampler::setup_torsion_sets().

protocols::stepwise::sampling::protein::MainChainTorsionSet	(	core::Real const &	phi,
		core::Real const &	psi
	)

core::Real const protocols::stepwise::sampling::protein::omega

(

)

const

Referenced by protocols::forge::remodel::RemodelGlobalFrame::align_segment(), protocols::analysis::LoopAnalyzerMover::apply(), protocols::evaluation::PCA::calc_fit_R(), protocols::toolbox::calc_fit_R(), protocols::simple_filters::GeometryFilter::compute(), protocols::sasa_scores::compute_avge_scores(), protocols::features::LoopAnchorFeatures::compute_transform_and_write_to_db(), protocols::frag_picker::scores::LAMBEGO_Similarity::do_caching(), protocols::frag_picker::scores::TorsionBinSimilarity::do_caching(), protocols::sic_dock::dump_loophash_linkers(), protocols::anchored_design::AnchoredDesignMover::filter(), protocols::anchored_design::AnchorMoversData::fix_anchor(), protocols::relax::fix_worst_bad_ramas(), protocols::canonical_sampling::CanonicalSamplingMover::get_ABGEO_string(), protocols::loophash::BackboneDB::get_backbone_segment(), protocols::frags::RMSVallData::get_frags(), protocols::forge::remodel::RemodelGlobalFrame::get_helical_params(), protocols::stepwise::sampling::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_sample_phi_only(), protocols::frag_picker::FragmentPicker::getFragSet(), protocols::environment::EnvClaimBroker::grant_access(), protocols::features::ResidueConformationFeatures::load_conformation(), protocols::features::ProteinResidueConformationFeatures::load_conformation(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), protocols::stepwise::sampling::protein::StepWiseProteinBackboneSampler::main_chain_torsion_set_lists_real(), protocols::ligand_docking::LigandBaseProtocol::make_tweaked_scorefxn(), OPT_1GRP_KEY(), protocols::optimize_weights::IterativeOptEDriver::print_energies(), protocols::simple_filters::SymmetricMotifFilter::process_motifs(), protocols::frags::RMSVallData::read_file(), protocols::antibody::H3CterInsert::read_H3_cter_fragment(), protocols::antibody_legacy::read_H3_cter_fragment(), protocols::anchored_design::AnchoredDesignMover::read_options(), protocols::features::ResidueConformationFeatures::report_features(), protocols::features::ProteinResidueConformationFeatures::report_features(), protocols::features::ProteinBackboneTorsionAngleFeatures::report_features(), protocols::grafting::AnchoredGraftMover::set_default_cen_scorefunction(), protocols::analysis::LoopAnalyzerMover::set_sf(), protocols::kinematic_closure::BalancedKicMover::torsion_id_ranges(), protocols::comparative_modeling::features::TorsionFeature::values_from_pose(), protocols::features::LoopAnchorFeatures::write_loop_anchor_transforms_table_schema(), protocols::features::LoopAnchorFeatures::write_loop_anchor_transforms_three_res_table_schema(), protocols::features::ProteinBackboneTorsionAngleFeatures::write_protein_backbone_torsion_angles_table_schema(), protocols::features::ProteinResidueConformationFeatures::write_schema_to_db(), and protocols::features::ResidueConformationFeatures::write_schema_to_db().

void protocols::stepwise::sampling::protein::output_silent_struct	(	core::pose::Pose const &	pose,
		core::pose::PoseCOP const &	native_pose_op,
		std::string const &	silent_file,
		std::string const &	tag,
		core::io::silent::SilentFileDataOP	sfd_in
	)

References calc_rms_res.

Referenced by protocols::stepwise::sampling::protein::StepWiseProteinModeler::do_minimizing(), and protocols::stepwise::sampling::protein::StepWiseProteinBackboneSampler::filter_and_output().

void protocols::stepwise::sampling::protein::output_silent_struct	(	core::pose::Pose const &	pose,
		core::pose::PoseCOP const &	native_pose_op,
		std::string const &	silent_file,
		std::string const &	tag,
		core::io::silent::SilentFileDataOP	sfd_in,
		utility::vector1< core::Size > const &	calc_rms_res
	)

References rms_at_corresponding_atoms(), rms_at_corresponding_atoms_no_super(), rmsd, s, setup_matching_CA_atoms(), setup_matching_heavy_atoms(), setup_matching_protein_backbone_heavy_atoms(), and core::io::silent::SilentFileData::write_silent_struct().

core::Real const protocols::stepwise::sampling::protein::phi

(

)

const

Referenced by protocols::loop_modeling::openers::RamachandranOpener::apply(), protocols::protein_interface_design::filters::Torsion::apply(), protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::build_rotamer_list(), protocols::frag_picker::scores::MidPhiOut::cached_score(), protocols::frag_picker::scores::ProlinePhiScore::describe_score(), protocols::frag_picker::scores::RamaScore::do_caching(), protocols::frag_picker::scores::LAMBEGO_Similarity::do_caching(), protocols::frag_picker::scores::TorsionBinSimilarity::do_caching(), protocols::cartesian::MolecularDynamics::doDihedralDerivatives(), protocols::sic_dock::dump_loophash_linkers(), protocols::MakeRotLib::dunbrack_print(), protocols::stepwise::sampling::protein::StepWiseProteinBackboneSampler::filter_big_bin(), protocols::canonical_sampling::CanonicalSamplingMover::get_ABGEO_string(), protocols::loophash::BackboneDB::get_backbone_segment(), protocols::frags::RMSVallData::get_frags(), protocols::stepwise::sampling::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_c_terminus(), protocols::stepwise::sampling::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_full(), protocols::stepwise::sampling::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_n_terminus(), protocols::stepwise::sampling::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_sample_phi_only(), protocols::stepwise::sampling::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_sample_psi_only(), protocols::qsar::scoring_grid::ShapeGrid::get_point_score(), get_pretend_phi_explicit(), protocols::sic_dock::get_xform_stats(), protocols::frag_picker::FragmentPicker::getFragSet(), protocols::sparta::Sparta::SpartaLib::getResInfo(), protocols::environment::EnvClaimBroker::grant_access(), protocols::sparta::Sparta::SpartaLib::init_PredErrorSurface(), protocols::antibody::clusters::CDRClusterMatcher::load_center_data(), protocols::features::ResidueConformationFeatures::load_conformation(), protocols::features::ProteinResidueConformationFeatures::load_conformation(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), protocols::stepwise::sampling::protein::StepWiseProteinBackboneSampler::main_chain_torsion_set_lists_real(), protocols::simple_moves::sidechain_moves::SidechainMover::make_move(), OPT_1GRP_KEY(), protocols::kinematic_closure::perturbers::RamaPerturber::perturb_subset(), protocols::kinematic_closure::perturbers::WalkingPerturber::perturb_subset(), protocols::kinematic_closure::perturbers::RamaPerturber::perturb_subset_with_balance(), protocols::kinematic_closure::perturbers::VicinityPerturber::perturb_subset_with_balance(), protocols::simple_moves::sidechain_moves::SidechainMover::proposal_density(), protocols::geometry::random_reorientation_matrix(), protocols::frags::RMSVallData::read_file(), protocols::antibody::H3CterInsert::read_H3_cter_fragment(), protocols::antibody_legacy::read_H3_cter_fragment(), protocols::frag_picker::FragmentPicker::read_spine_x(), protocols::features::ResidueConformationFeatures::report_features(), protocols::features::ProteinResidueConformationFeatures::report_features(), protocols::features::ProteinBackboneTorsionAngleFeatures::report_features(), protocols::features::strand_assembly::SandwichFeatures::report_features(), protocols::stepwise::sampling::protein::StepWiseProteinBackboneSampler::sample_cis_omega(), protocols::frag_picker::scores::ProlinePhiScore::score(), protocols::fldsgn::potentials::sspot::HSPairPotential::score(), protocols::fldsgn::potentials::sspot::SSPairPotential::score(), protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::score(), protocols::cartesian::MolecularDynamics::setDihedralDerivatives(), protocols::kinematic_closure::BalancedKicMover::torsion_id_ranges(), protocols::comparative_modeling::features::TorsionFeature::values_from_pose(), protocols::features::LoopAnchorFeatures::write_loop_anchor_transforms_table_schema(), protocols::features::LoopAnchorFeatures::write_loop_anchor_transforms_three_res_table_schema(), protocols::features::ProteinBackboneTorsionAngleFeatures::write_protein_backbone_torsion_angles_table_schema(), protocols::features::ProteinResidueConformationFeatures::write_schema_to_db(), protocols::features::ResidueConformationFeatures::write_schema_to_db(), and protocols::motif_hash::Xfres::Xfres().

core::Real const protocols::stepwise::sampling::protein::psi

(

)

const

Referenced by protocols::loop_modeling::openers::RamachandranOpener::apply(), protocols::protein_interface_design::filters::Torsion::apply(), protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::build_rotamer_list(), protocols::frag_picker::scores::MidPsiOut::cached_score(), protocols::frag_picker::scores::RamaScore::do_caching(), protocols::frag_picker::scores::LAMBEGO_Similarity::do_caching(), protocols::frag_picker::scores::TorsionBinSimilarity::do_caching(), protocols::sic_dock::dump_loophash_linkers(), protocols::MakeRotLib::dunbrack_print(), protocols::stepwise::sampling::protein::StepWiseProteinBackboneSampler::filter_big_bin(), protocols::canonical_sampling::CanonicalSamplingMover::get_ABGEO_string(), protocols::loophash::BackboneDB::get_backbone_segment(), protocols::frags::RMSVallData::get_frags(), protocols::stepwise::sampling::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_c_terminus(), protocols::stepwise::sampling::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_full(), protocols::stepwise::sampling::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_n_terminus(), protocols::stepwise::sampling::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_sample_phi_only(), protocols::stepwise::sampling::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_sample_psi_only(), get_pretend_psi_explicit(), protocols::sic_dock::get_xform_stats(), protocols::frag_picker::FragmentPicker::getFragSet(), protocols::sparta::Sparta::SpartaLib::getResInfo(), protocols::environment::EnvClaimBroker::grant_access(), protocols::sparta::Sparta::SpartaLib::init_PredErrorSurface(), protocols::frags::TorsionFragment::insert(), protocols::antibody::clusters::CDRClusterMatcher::load_center_data(), protocols::features::ResidueConformationFeatures::load_conformation(), protocols::features::ProteinResidueConformationFeatures::load_conformation(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), protocols::stepwise::sampling::protein::StepWiseProteinBackboneSampler::main_chain_torsion_set_lists_real(), protocols::simple_moves::sidechain_moves::SidechainMover::make_move(), OPT_1GRP_KEY(), protocols::kinematic_closure::perturbers::RamaPerturber::perturb_subset(), protocols::kinematic_closure::perturbers::WalkingPerturber::perturb_subset(), protocols::kinematic_closure::perturbers::RamaPerturber::perturb_subset_with_balance(), protocols::kinematic_closure::perturbers::VicinityPerturber::perturb_subset_with_balance(), protocols::simple_moves::sidechain_moves::SidechainMover::proposal_density(), protocols::geometry::random_reorientation_matrix(), protocols::frags::RMSVallData::read_file(), protocols::antibody::H3CterInsert::read_H3_cter_fragment(), protocols::antibody_legacy::read_H3_cter_fragment(), protocols::frag_picker::FragmentPicker::read_spine_x(), protocols::features::ProteinResidueConformationFeatures::report_features(), protocols::features::ResidueConformationFeatures::report_features(), protocols::features::ProteinBackboneTorsionAngleFeatures::report_features(), protocols::features::SaltBridgeFeatures::report_features(), protocols::features::strand_assembly::SandwichFeatures::report_features(), protocols::stepwise::sampling::protein::StepWiseProteinBackboneSampler::sample_cis_omega(), protocols::frag_picker::scores::ProlinePhiScore::score(), protocols::kinematic_closure::BalancedKicMover::torsion_id_ranges(), protocols::comparative_modeling::features::TorsionFeature::values_from_pose(), protocols::features::LoopAnchorFeatures::write_loop_anchor_transforms_table_schema(), protocols::features::LoopAnchorFeatures::write_loop_anchor_transforms_three_res_table_schema(), protocols::features::ProteinBackboneTorsionAngleFeatures::write_protein_backbone_torsion_angles_table_schema(), protocols::features::SaltBridgeFeatures::write_salt_bridges_table_schema(), protocols::features::ResidueConformationFeatures::write_schema_to_db(), protocols::features::ProteinResidueConformationFeatures::write_schema_to_db(), and protocols::motif_hash::Xfres::Xfres().

void protocols::stepwise::sampling::protein::remove_end_variants

(

core::pose::Pose &

pose

)

References core::pose::remove_variant_type_from_pose_residue(), and core::pose::Pose::total_residue().

StepWiseProteinJobParametersOP protocols::stepwise::sampling::protein::setup_job_parameters_for_protein_swa	(	utility::vector1< Size > const &	moving_res_list,
		pose::Pose const &	pose,
		pose::PoseCOP	native_pose,
		utility::vector1< Size > const &	bridge_res,
		utility::vector1< Size > const &	working_minimize_res
	)

References CALC_RMS, const_full_model_info(), core::pose::full_model_info::FullModelInfo::extra_minimize_res(), fixed_res, core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_parent_residue(), utility::vector1< T, class >::has_value(), core::kinematics::FoldTree::jump_nr(), protocols::stepwise::pdbslice(), and protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::set_full_to_sub().

Referenced by protocols::stepwise::sampling::protein::StepWiseProteinModeler::setup_job_parameters_for_stepwise_with_full_model_info().

import_pose::pose_stream::PoseInputStreamOP protocols::stepwise::sampling::protein::setup_pose_input_stream	(	utility::options::StringVectorOption const &	option_s1,
		utility::options::StringVectorOption const &	option_silent1,
		utility::options::StringVectorOption const &	option_tags1
	)

References utility::options::StringVectorOption::size(), and utility::options::StringVectorOption::user().

Referenced by initialize_input_streams().

void protocols::stepwise::sampling::protein::setup_protein_backbone_atom_id_map	(	core::pose::Pose const &	pose_1,
		core::pose::Pose const &	pose_2,
		Size const	base_res,
		core::id::AtomID_Map< core::id::AtomID > &	atom_ID_map
	)

Referenced by protocols::stepwise::create_alignment_id_map().

void protocols::stepwise::sampling::protein::setup_protein_backbone_atom_id_map	(	core::pose::Pose const &	pose_1,
		core::pose::Pose const &	pose_2,
		Size const	base_res,
		Size const	base_res2,
		core::id::AtomID_Map< core::id::AtomID > &	atom_ID_map
	)

References core::chemical::ResidueType::has_variant_type(), core::chemical::ResidueType::is_protein(), core::pose::named_atom_id_to_atom_id(), core::pose::Pose::residue_type(), and core::id::AtomID_Map< T >::set().

void protocols::stepwise::sampling::protein::setup_protein_CA_atom_id_map	(	core::pose::Pose const &	pose_1,
		core::pose::Pose const &	pose_2,
		Size const	base_res,
		core::id::AtomID_Map< core::id::AtomID > &	atom_ID_map
	)

References core::chemical::ResidueType::is_protein(), core::pose::named_atom_id_to_atom_id(), core::pose::Pose::residue_type(), and core::id::AtomID_Map< T >::set().

protocols::stepwise::sampling::protein::~MainChainTorsionSet

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