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Rosetta
2016.11
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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 |
typedef utility::pointer::shared_ptr< ProteinBetaAntiParallelStepWiseSampler const > protocols::stepwise::sampler::protein::ProteinBetaAntiParallelStepWiseSamplerCOP |
typedef utility::pointer::shared_ptr< ProteinBetaAntiParallelStepWiseSampler > protocols::stepwise::sampler::protein::ProteinBetaAntiParallelStepWiseSamplerOP |
typedef utility::pointer::shared_ptr< ProteinFragmentStepWiseSampler const > protocols::stepwise::sampler::protein::ProteinFragmentStepWiseSamplerCOP |
typedef utility::pointer::shared_ptr< ProteinFragmentStepWiseSampler > protocols::stepwise::sampler::protein::ProteinFragmentStepWiseSamplerOP |
typedef utility::pointer::shared_ptr< ProteinMainChainStepWiseSampler const > protocols::stepwise::sampler::protein::ProteinMainChainStepWiseSamplerCOP |
typedef utility::pointer::shared_ptr< ProteinMainChainStepWiseSampler > protocols::stepwise::sampler::protein::ProteinMainChainStepWiseSamplerOP |
void protocols::stepwise::sampler::protein::do_set_xyz | ( | pose::Pose const & | pose, |
Size const | i, | ||
pose::Pose & | scratch_pose, | ||
Size const | i_scratch, | ||
core::kinematics::Stub const & | stub | ||
) |
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(), protocols::stepwise::modeler::get_file_name(), core::scoring::get_score_function(), core::scoring::hbond, protocols::stepwise::setup::load_s_and_l(), core::chemical::LOWER_TERMINUS_VARIANT, core::pose::make_pose_from_sequence(), core::kinematics::FoldTree::new_jump(), protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::output_silent_file(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), 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(), 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(), and core::chemical::UPPER_TERMINUS_VARIANT.
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(), protocols::stepwise::modeler::get_file_name(), 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(), TR(), and protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::which_torsions().
Referenced by protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_protein_bond_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(), protocols::stepwise::modeler::get_file_name(), 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(), TR(), and protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::which_torsions().
Referenced by protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_protein_bond_sampler().
utility::vector1< std::string > protocols::stepwise::sampler::protein::load_s_and_l | ( | ) |
References protocols::abinitio::filename().