protocols::stepwise::modeler::working_parameters Namespace Reference

Classes
class	StepWiseBasicWorkingParameters
class	StepWiseWorkingParameters

Typedefs
typedef utility::pointer::shared_ptr< StepWiseBasicWorkingParameters >	StepWiseBasicWorkingParametersOP
typedef utility::pointer::shared_ptr< StepWiseBasicWorkingParameters const >	StepWiseBasicWorkingParametersCOP
typedef utility::pointer::shared_ptr< StepWiseWorkingParameters >	StepWiseWorkingParametersOP
typedef utility::pointer::shared_ptr< StepWiseWorkingParameters const >	StepWiseWorkingParametersCOP

Functions
StepWiseWorkingParametersOP	setup_working_parameters_for_swa (utility::vector1< core::Size > const &moving_res_list, pose::Pose const &pose, pose::PoseCOP native_pose, utility::vector1< core::Size > const &user_defined_bridge_res, utility::vector1< core::Size > const &working_minimize_res)
StepWiseWorkingParametersOP	setup_working_parameters_explicit (core::Size const rebuild_res, pose::Pose const &pose, pose::PoseCOP native_pose)
bool	figure_out_rebuild_bulge_mode (pose::Pose const &pose, core::Size const rebuild_res)
bool	figure_out_sample_both_sugar_base_rotamer (pose::Pose const &pose, bool const floating_base, core::Size const rebuild_suite)

Typedef Documentation

StepWiseBasicWorkingParametersCOP

typedef utility::pointer::shared_ptr< StepWiseBasicWorkingParameters const > protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParametersCOP

StepWiseBasicWorkingParametersOP

typedef utility::pointer::shared_ptr< StepWiseBasicWorkingParameters > protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParametersOP

StepWiseWorkingParametersCOP

typedef utility::pointer::shared_ptr< StepWiseWorkingParameters const > protocols::stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP

StepWiseWorkingParametersOP

typedef utility::pointer::shared_ptr< StepWiseWorkingParameters > protocols::stepwise::modeler::working_parameters::StepWiseWorkingParametersOP

Function Documentation

figure_out_rebuild_bulge_mode()

bool protocols::stepwise::modeler::working_parameters::figure_out_rebuild_bulge_mode	(	pose::Pose const &	pose,
		core::Size const	rebuild_res
	)

References core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), protocols::stepwise::modeler::is_cutpoint_closed(), core::kinematics::FoldTree::jump_nr(), core::kinematics::FoldTree::num_jump(), core::pose::Pose::residue(), core::pose::Pose::size(), core::kinematics::FoldTree::upstream_jump_residue(), and core::chemical::VIRTUAL_RIBOSE.

Referenced by setup_working_parameters_explicit().

figure_out_sample_both_sugar_base_rotamer()

bool protocols::stepwise::modeler::working_parameters::figure_out_sample_both_sugar_base_rotamer	(	pose::Pose const &	pose,
		bool const	floating_base,
		core::Size const	rebuild_suite
	)

References core::conformation::Residue::has_variant_type(), protocols::stepwise::sampler::rna::modeler_sugar_at_five_prime(), protocols::stepwise::sampler::rna::modeler_sugar_at_three_prime(), core::pose::Pose::residue(), and core::chemical::VIRTUAL_RIBOSE.

Referenced by setup_working_parameters_explicit().

setup_working_parameters_explicit()

StepWiseWorkingParametersOP protocols::stepwise::modeler::working_parameters::setup_working_parameters_explicit	(	core::Size const	rebuild_res,
		pose::Pose const &	pose,
		pose::PoseCOP	native_pose
	)

References core::pose::full_model_info::FullModelInfo::calc_rms_res(), core::pose::full_model_info::const_full_model_info(), protocols::stepwise::modeler::figure_out_moving_chain_breaks(), figure_out_rebuild_bulge_mode(), figure_out_sample_both_sugar_base_rotamer(), core::pose::Pose::fold_tree(), core::pose::full_model_info::FullModelInfo::full_model_parameters(), core::pose::full_model_info::FullModelInfo::full_sequence(), core::pose::full_model_info::FullModelInfo::full_to_sub(), core::kinematics::FoldTree::get_parent_residue(), protocols::stepwise::modeler::get_partition_definition(), protocols::stepwise::modeler::rna::get_partition_definition_floating_base(), core::kinematics::FoldTree::is_cutpoint(), core::pose::full_model_info::FullModelInfo::res_list(), core::pose::full_model_info::FullModelInfo::rna_anti_chi_res(), core::pose::full_model_info::FullModelInfo::rna_block_stack_above_res(), core::pose::full_model_info::FullModelInfo::rna_block_stack_below_res(), core::pose::full_model_info::RNA_NORTH_SUGAR, core::pose::full_model_info::RNA_SOUTH_SUGAR, core::pose::full_model_info::FullModelInfo::rna_syn_chi_res(), core::pose::full_model_info::FullModelInfo::rna_terminal_res(), core::pose::Pose::size(), core::pose::full_model_info::FullModelInfo::sub_to_full(), and TR().

Referenced by setup_working_parameters_for_swa().

setup_working_parameters_for_swa()

StepWiseWorkingParametersOP protocols::stepwise::modeler::working_parameters::setup_working_parameters_for_swa	(	utility::vector1< core::Size > const &	moving_res_list,
		pose::Pose const &	pose,
		pose::PoseCOP	native_pose,
		utility::vector1< core::Size > const &	user_defined_bridge_res,
		utility::vector1< core::Size > const &	working_minimize_res
	)

References BRIDGE_RES, core::pose::full_model_info::CALC_RMS, core::pose::full_model_info::const_full_model_info(), core::pose::full_model_info::FullModelInfo::extra_minimize_res(), protocols::toolbox::rigid_body::figure_out_moving_partition_res(), core::pose::full_model_info::FullModelInfo::fixed_domain_map(), core::pose::Pose::fold_tree(), core::pose::full_model_info::FullModelInfo::full_model_parameters(), core::pose::full_model_info::FullModelInfo::full_sequence(), core::pose::full_model_info::FullModelInfo::full_to_sub(), protocols::stepwise::modeler::protein::get_bridge_res(), core::kinematics::FoldTree::get_parent_residue(), core::pose::full_model_info::get_res_list_from_full_model_info(), core::kinematics::FoldTree::jump_nr(), protocols::mean_field::min(), MOVING_RES, core::pose::pdbslice(), core::pose::full_model_info::FullModelInfo::res_list(), core::pose::full_model_info::FullModelInfo::sample_res(), setup_working_parameters_explicit(), core::pose::Pose::size(), and core::pose::full_model_info::FullModelInfo::sub_to_full().

Referenced by protocols::stepwise::modeler::StepWiseModeler::initialize_working_parameters_and_root().