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

Classes
class	StepWiseBasicWorkingParameters
class	StepWiseWorkingParameters

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

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

Typedef Documentation

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

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

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

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

Function Documentation

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

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

Referenced by setup_working_parameters_explicit().

bool protocols::stepwise::modeler::working_parameters::figure_out_sample_both_sugar_base_rotamer	(	pose::Pose const &	pose,
		bool const	floating_base,
		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(), and core::pose::Pose::residue().

Referenced by setup_working_parameters_explicit().

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

References calc_rms_res, chemical, const_full_model_info(), cutpoint_closed, cutpoint_open, protocols::stepwise::modeler::figure_out_moving_chain_breaks(), figure_out_rebuild_bulge_mode(), figure_out_sample_both_sugar_base_rotamer(), floating_base, floating_base_anchor_res, core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_parent_residue(), protocols::stepwise::modeler::get_partition_definition(), protocols::stepwise::modeler::rna::get_partition_definition_floating_base(), input_res1, input_res2, core::kinematics::FoldTree::is_cutpoint(), make_vector1(), nres, runtime_assert, protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_output_extra_RMSDs(), terminal_res, core::pose::Pose::total_residue(), and TR.

Referenced by setup_working_parameters_for_swa().

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

References bridge_res, BRIDGE_RES, CALC_RMS, const_full_model_info(), core::pose::full_model_info::FullModelInfo::extra_minimize_res(), protocols::stepwise::sampler::rigid_body::figure_out_moving_partition_res(), fixed_res, core::pose::Pose::fold_tree(), protocols::stepwise::modeler::protein::get_bridge_res(), core::kinematics::FoldTree::get_parent_residue(), get_res_list_from_full_model_info(), utility::vector1< T, class >::has_value(), utility::vector1< T, class >::index(), core::kinematics::FoldTree::jump_nr(), MOVING_RES, core::pose::pdbslice(), core::pose::full_model_info::FullModelInfo::sample_res(), sample_res, setup_working_parameters_explicit(), and core::pose::Pose::total_residue().

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