Classes
class	StepWiseProteinConnectionSampler

class	StepWiseProteinMinimizer

class	StepWiseProteinModeler

class	StepWiseProteinMultiPosePacker

class	StepWiseProteinPoseSetup

Typedefs
typedef utility::pointer::owning_ptr < StepWiseProteinConnectionSampler >	StepWiseProteinConnectionSamplerOP

typedef utility::pointer::owning_ptr < StepWiseProteinConnectionSampler const >	StepWiseProteinConnectionSamplerCOP

typedef utility::pointer::owning_ptr < StepWiseProteinMinimizer >	StepWiseProteinMinimizerOP

typedef utility::pointer::owning_ptr < StepWiseProteinMinimizer const >	StepWiseProteinMinimizerCOP

typedef utility::pointer::owning_ptr < StepWiseProteinModeler >	StepWiseProteinModelerOP

typedef utility::pointer::owning_ptr < StepWiseProteinModeler const >	StepWiseProteinModelerCOP

typedef utility::pointer::owning_ptr < StepWiseProteinMultiPosePacker >	StepWiseProteinMultiPosePackerOP

typedef utility::pointer::owning_ptr < StepWiseProteinMultiPosePacker const >	StepWiseProteinMultiPosePackerCOP

typedef utility::pointer::owning_ptr < StepWiseProteinPoseSetup >	StepWiseProteinPoseSetupOP

typedef utility::pointer::owning_ptr < StepWiseProteinPoseSetup const >	StepWiseProteinPoseSetupCOP

Functions
StepWiseProteinWorkingParametersOP	setup_protein_working_parameters_for_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)

utility::vector1< Size >	convert_to_vector1 (ObjexxFCL::FArray1D< Size > farray)

utility::vector1< Size > const	convert_to_working_res (utility::vector1< Size > const &res_vector, utility::vector1< Size > const &working_res)

void	output_pose_list (utility::vector1< core::pose::PoseOP > pose_list, core::pose::PoseCOP native_pose, std::string const &silent_file, utility::vector1< Size > const &working_calc_rms_res)

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)

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)

bool	is_close_chain_break (pose::Pose const &pose)

Typedef Documentation

typedef utility::pointer::owning_ptr< StepWiseProteinConnectionSampler const > protocols::stepwise::legacy::modeler::protein::StepWiseProteinConnectionSamplerCOP

typedef utility::pointer::owning_ptr< StepWiseProteinConnectionSampler > protocols::stepwise::legacy::modeler::protein::StepWiseProteinConnectionSamplerOP

typedef utility::pointer::owning_ptr< StepWiseProteinMinimizer const > protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizerCOP

typedef utility::pointer::owning_ptr< StepWiseProteinMinimizer > protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizerOP

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

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

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

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

typedef utility::pointer::owning_ptr< StepWiseProteinPoseSetup const > protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetupCOP

typedef utility::pointer::owning_ptr< StepWiseProteinPoseSetup > protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetupOP

Function Documentation

utility::vector1< Size > protocols::stepwise::legacy::modeler::protein::convert_to_vector1 ( ObjexxFCL::FArray1D< Size > farray )

Referenced by protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::figure_out_working_sequence_and_mapping().

utility::vector1< core::Size > const protocols::stepwise::legacy::modeler::protein::convert_to_working_res	(	utility::vector1< Size > const &	res_vector,
		utility::vector1< Size > const &	working_res
	)

References full_to_sub().

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

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

Referenced by protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::fix_phi_psi_offsets(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::initialize_phi_psi_offsets(), and protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::save_phi_psi_offsets().

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

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

Referenced by protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::fix_phi_psi_offsets(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::initialize_phi_psi_offsets(), and protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::save_phi_psi_offsets().

bool protocols::stepwise::legacy::modeler::protein::is_close_chain_break ( pose::Pose const & pose )

References protocols::stepwise::modeler::is_cutpoint_closed(), and core::pose::Pose::total_residue().

Referenced by protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::check_close_chain_break().

void protocols::stepwise::legacy::modeler::protein::output_pose_list	(	utility::vector1< core::pose::PoseOP >	pose_list,
		core::pose::PoseCOP	native_pose,
		std::string const &	silent_file,
		utility::vector1< Size > const &	working_calc_rms_res
	)

References output_silent_struct(), and tag.

Referenced by protocols::moves::MoverForPoseList::apply(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::apply(), protocols::stepwise::modeler::StepWiseMinimizer::apply(), protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler::bulge_chain_closure_complete(), protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler::bulge_chain_closure_legacy(), protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler::bulge_chain_minimize_legacy(), protocols::stepwise::modeler::StepWiseMinimizer::do_full_minimizing(), and protocols::stepwise::legacy::modeler::StepWiseLegacyMinimizer::do_protein_minimizing().

void protocols::stepwise::legacy::modeler::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, and output_silent_struct().

Referenced by protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler::do_minimizing().

void protocols::stepwise::legacy::modeler::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 utility::is_nan(), 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().

Referenced by output_pose_list(), and output_silent_struct().

StepWiseProteinWorkingParametersOP protocols::stepwise::legacy::modeler::protein::setup_protein_working_parameters_for_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(), and core::kinematics::FoldTree::jump_nr().

Referenced by protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler::setup_working_parameters_for_stepwise_with_full_model_info().

Classes

Typedefs

Functions

Typedef Documentation

Function Documentation