protocols::stepwise::sampler::protein Namespace Reference

Classes
class	ProteinBetaAntiParallelStepWiseSampler
class	ProteinFragmentStepWiseSampler
class	ProteinMainChainStepWiseSampler

Typedefs
typedef utility::pointer::shared_ptr< ProteinBetaAntiParallelStepWiseSampler >	ProteinBetaAntiParallelStepWiseSamplerOP
typedef utility::pointer::shared_ptr< ProteinBetaAntiParallelStepWiseSampler const >	ProteinBetaAntiParallelStepWiseSamplerCOP
typedef utility::pointer::shared_ptr< ProteinFragmentStepWiseSampler >	ProteinFragmentStepWiseSamplerOP
typedef utility::pointer::shared_ptr< ProteinFragmentStepWiseSampler const >	ProteinFragmentStepWiseSamplerCOP
typedef utility::pointer::shared_ptr< ProteinMainChainStepWiseSampler >	ProteinMainChainStepWiseSamplerOP
typedef utility::pointer::shared_ptr< ProteinMainChainStepWiseSampler const >	ProteinMainChainStepWiseSamplerCOP

Functions
StepWiseSamplerSizedOP	get_basic_protein_sampler (core::pose::Pose const &pose, utility::vector1< core::Size > const &moving_res_list, protocols::stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP working_parameters, protocols::stepwise::modeler::options::StepWiseModelerOptionsCOP options, utility::vector1< protocols::stepwise::modeler::protein::InputStreamWithResidueInfoOP > &input_streams)
void	do_set_xyz (pose::Pose const &pose, core::Size const i, pose::Pose &scratch_pose, core::Size const i_scratch, core::kinematics::Stub const &stub)
void	generate_beta_database_test ()

Typedef Documentation

ProteinBetaAntiParallelStepWiseSamplerCOP

typedef utility::pointer::shared_ptr< ProteinBetaAntiParallelStepWiseSampler const > protocols::stepwise::sampler::protein::ProteinBetaAntiParallelStepWiseSamplerCOP

ProteinBetaAntiParallelStepWiseSamplerOP

typedef utility::pointer::shared_ptr< ProteinBetaAntiParallelStepWiseSampler > protocols::stepwise::sampler::protein::ProteinBetaAntiParallelStepWiseSamplerOP

ProteinFragmentStepWiseSamplerCOP

typedef utility::pointer::shared_ptr< ProteinFragmentStepWiseSampler const > protocols::stepwise::sampler::protein::ProteinFragmentStepWiseSamplerCOP

ProteinFragmentStepWiseSamplerOP

typedef utility::pointer::shared_ptr< ProteinFragmentStepWiseSampler > protocols::stepwise::sampler::protein::ProteinFragmentStepWiseSamplerOP

ProteinMainChainStepWiseSamplerCOP

typedef utility::pointer::shared_ptr< ProteinMainChainStepWiseSampler const > protocols::stepwise::sampler::protein::ProteinMainChainStepWiseSamplerCOP

ProteinMainChainStepWiseSamplerOP

typedef utility::pointer::shared_ptr< ProteinMainChainStepWiseSampler > protocols::stepwise::sampler::protein::ProteinMainChainStepWiseSamplerOP

Function Documentation

do_set_xyz()

void protocols::stepwise::sampler::protein::do_set_xyz	(	pose::Pose const &	pose,
		core::Size const	i,
		pose::Pose &	scratch_pose,
		core::Size const	i_scratch,
		core::kinematics::Stub const &	stub
	)

References core::kinematics::Stub::global2local(), core::chemical::ResidueType::has(), core::pose::Pose::residue_type(), core::pose::Pose::set_xyz(), and core::pose::Pose::xyz().

Referenced by generate_beta_database_test().

generate_beta_database_test()

void protocols::stepwise::sampler::protein::generate_beta_database_test

(

)

References protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::cluster(), protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::clustered_pose_list(), do_set_xyz(), core::chemical::FA_STANDARD, core::scoring::hbonds::fill_hbond_set(), core::pose::Pose::fold_tree(), core::io::silent::get_outfile_name_with_tag(), core::scoring::get_score_function(), core::scoring::hbond, protocols::jd2::input_pdb_files_from_command_line(), core::chemical::LOWER_TERMINUS_VARIANT, core::pose::make_pose_from_sequence(), core::kinematics::FoldTree::new_jump(), core::conformation::membrane::out, protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::output_silent_file(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), core::kinematics::FoldTree::reassign_atoms_for_intra_residue_stubs(), core::pose::remove_variant_type_from_pose_residue(), protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_calc_rms_res(), protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_cluster_radius(), core::kinematics::FoldTree::set_jump_atoms(), protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_max_decoys(), protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_rename_tags(), protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_score_diff_cut(), core::pose::Pose::size(), core::chemical::UPPER_TERMINUS_VARIANT, and core::pose::Pose::xyz().

get_basic_protein_sampler()

StepWiseSamplerSizedOP protocols::stepwise::sampler::protein::get_basic_protein_sampler	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	moving_res_list,
		protocols::stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP	working_parameters,
		protocols::stepwise::modeler::options::StepWiseModelerOptionsCOP	options,
		utility::vector1< protocols::stepwise::modeler::protein::InputStreamWithResidueInfoOP > &	input_streams
	)

References protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::apply(), core::io::silent::get_outfile_name_with_tag(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::main_chain_torsion_set_lists_real(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_expand_loop_takeoff(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_filter_native_big_bins(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_n_sample(), protocols::moves::Mover::set_native_pose(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_silent_file(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::setup_centroid_screen(), core::pose::TR(), and protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::which_torsions().

Referenced by protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_protein_bond_sampler().