protocols::stepwise::legacy::modeler::protein Namespace Reference

Classes
class	StepWiseProteinMinimizer
class	StepWiseProteinPoseSetup

Typedefs
typedef utility::pointer::shared_ptr < StepWiseProteinMinimizer >	StepWiseProteinMinimizerOP
typedef utility::pointer::shared_ptr < StepWiseProteinMinimizer const >	StepWiseProteinMinimizerCOP
typedef utility::pointer::shared_ptr < StepWiseProteinPoseSetup >	StepWiseProteinPoseSetupOP
typedef utility::pointer::shared_ptr < StepWiseProteinPoseSetup const >	StepWiseProteinPoseSetupCOP

Functions
utility::vector1< core::Size >	convert_to_vector1 (ObjexxFCL::FArray1D< core::Size > farray)
utility::vector1< core::Size > const	convert_to_working_res (utility::vector1< core::Size > const &res_vector, utility::vector1< core::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< core::Size > const &working_calc_rms_res, bool const overwrite)
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, core::Size const &res)
Real	get_pretend_phi_explicit (core::pose::Pose const &pose, core::Size const &res)
bool	is_close_chain_break (core::pose::Pose const &pose)

Typedef Documentation

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

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

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

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

Function Documentation

utility::vector1< core::Size > protocols::stepwise::legacy::modeler::protein::convert_to_vector1

(

ObjexxFCL::FArray1D< core::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< core::Size > const &	res_vector,
		utility::vector1< core::Size > const &	working_res
	)

References core::pose::full_model_info::full_to_sub().

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

References core::conformation::Residue::has(), 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,
		core::Size const &	res
	)

References 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

(

core::pose::Pose const &

pose

)

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

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< core::Size > const &	working_calc_rms_res,
		bool const	overwrite
	)

References output_silent_struct(), and core::io::silent::remove_silent_file_if_it_exists().

Referenced by protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::apply(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::bulge_chain_closure_complete(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::bulge_chain_closure_legacy(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::bulge_chain_minimize_legacy(), protocols::stepwise::modeler::StepWiseMinimizer::do_full_minimizing(), and protocols::stepwise::modeler::StepWiseMinimizer::output_minimized_pose_list().

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 output_silent_struct().

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 core::io::silent::SilentStruct::add_energy(), core::scoring::rms_at_corresponding_atoms(), core::scoring::rms_at_corresponding_atoms_no_super(), core::scoring::setup_matching_CA_atoms(), core::scoring::setup_matching_heavy_atoms(), core::scoring::setup_matching_protein_backbone_heavy_atoms(), and core::io::silent::SilentFileData::write_silent_struct().

Referenced by output_pose_list(), and output_silent_struct().