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

Namespaces
	checker
	loop_close

Classes
class	InputStreamWithResidueInfo
class	MainChainTorsionSet
class	StepWiseProteinBackboneSampler

Typedefs
typedef utility::pointer::shared_ptr< InputStreamWithResidueInfo >	InputStreamWithResidueInfoOP
typedef utility::pointer::shared_ptr< InputStreamWithResidueInfo const >	InputStreamWithResidueInfoCOP
typedef utility::vector1< MainChainTorsionSet >	MainChainTorsionSetList
typedef std::map< core::Size, core::Size >	ResMap

Functions
import_pose::pose_stream::PoseInputStreamOP	setup_pose_input_stream (utility::options::StringVectorOption const &option_s1, utility::options::StringVectorOption const &option_silent1, utility::options::StringVectorOption const &option_tags1)
void	initialize_input_streams (utility::vector1< protocols::stepwise::modeler::protein::InputStreamWithResidueInfoOP > &input_streams)
void	initialize_input_streams_with_residue_info (utility::vector1< InputStreamWithResidueInfoOP > &input_streams_with_residue_info, utility::vector1< std::string > const &pdb_tags, utility::vector1< std::string > const &silent_files_in, utility::vector1< core::Size > const &input_res, utility::vector1< core::Size > const &input_res2)
void	setup_protein_backbone_atom_id_map (core::pose::Pose const &pose_1, core::pose::Pose const &pose_2, core::Size const base_res, core::Size const base_res2, core::id::AtomID_Map< core::id::AtomID > &atom_ID_map)
void	figure_out_protein_modeling_info (pose::Pose const &pose, core::Size const moving_res, utility::vector1< core::Size > &moving_res_list)
utility::vector1< core::Size >	get_bridge_res (pose::Pose const &pose, utility::vector1< core::Size > const &moving_res_list)
utility::vector1< core::Size >	just_protein (utility::vector1< core::Size > const &res_list, pose::Pose const &pose)
bool	contains_protein (core::pose::Pose const &pose, utility::vector1< core::Size > const &res_list)

Typedef Documentation

InputStreamWithResidueInfoCOP

typedef utility::pointer::shared_ptr< InputStreamWithResidueInfo const > protocols::stepwise::modeler::protein::InputStreamWithResidueInfoCOP

InputStreamWithResidueInfoOP

typedef utility::pointer::shared_ptr< InputStreamWithResidueInfo > protocols::stepwise::modeler::protein::InputStreamWithResidueInfoOP

MainChainTorsionSetList

typedef utility::vector1< MainChainTorsionSet > protocols::stepwise::modeler::protein::MainChainTorsionSetList

ResMap

typedef std::map< core::Size, core::Size > protocols::stepwise::modeler::protein::ResMap

Function Documentation

contains_protein()

bool protocols::stepwise::modeler::protein::contains_protein	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	res_list
	)

References core::chemical::ResidueTypeBase::is_protein(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

Referenced by protocols::stepwise::modeler::packer::StepWiseMasterPacker::add_packer_screeners(), protocols::rna::denovo::movers::RNA_Minimizer::apply(), core::import_pose::libraries::ChunkSet::insert_protein_chunk_into_pose(), protocols::stepwise::modeler::StepWiseMinimizer::output_minimized_pose_list(), and protocols::stepwise::modeler::StepWiseMinimizer::StepWiseMinimizer().

figure_out_protein_modeling_info()

void protocols::stepwise::modeler::protein::figure_out_protein_modeling_info	(	pose::Pose const &	pose,
		core::Size const	moving_res,
		utility::vector1< core::Size > &	moving_res_list
	)

References core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_parent_residue(), core::pose::full_model_info::get_sample_res_for_pose(), core::chemical::ResidueTypeBase::is_protein(), core::conformation::Residue::is_protein(), core::pose::Pose::residue(), and core::pose::Pose::residue_type().

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

get_bridge_res()

utility::vector1< core::Size > protocols::stepwise::modeler::protein::get_bridge_res	(	pose::Pose const &	pose,
		utility::vector1< core::Size > const &	moving_res_list
	)

References core::pose::full_model_info::const_full_model_info(), protocols::stepwise::modeler::figure_out_moving_cutpoints_closed_from_moving_res(), core::pose::full_model_info::get_sample_res_for_pose(), core::chemical::ResidueTypeBase::is_protein(), protocols::stepwise::modeler::merge_vectors(), core::pose::Pose::residue_type(), and core::pose::full_model_info::sub_to_full().

Referenced by protocols::stepwise::modeler::working_parameters::setup_working_parameters_for_swa().

initialize_input_streams()

void protocols::stepwise::modeler::protein::initialize_input_streams

(

utility::vector1< protocols::stepwise::modeler::protein::InputStreamWithResidueInfoOP > &

input_streams

)

References initialize_input_streams_with_residue_info(), and setup_pose_input_stream().

initialize_input_streams_with_residue_info()

void protocols::stepwise::modeler::protein::initialize_input_streams_with_residue_info	(	utility::vector1< InputStreamWithResidueInfoOP > &	input_streams_with_residue_info,
		utility::vector1< std::string > const &	pdb_tags,
		utility::vector1< std::string > const &	silent_files_in,
		utility::vector1< core::Size > const &	input_res,
		utility::vector1< core::Size > const &	input_res2
	)

References protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::input_res(), and protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::InputStreamWithResidueInfo().

Referenced by initialize_input_streams().

just_protein()

utility::vector1< core::Size > protocols::stepwise::modeler::protein::just_protein	(	utility::vector1< core::Size > const &	res_list,
		pose::Pose const &	pose
	)

References core::chemical::ResidueTypeBase::is_protein(), and core::pose::Pose::residue_type().

Referenced by protocols::stepwise::modeler::StepWiseMinimizer::close_chainbreaks(), and protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_checkers().

setup_pose_input_stream()

core::import_pose::pose_stream::PoseInputStreamOP protocols::stepwise::modeler::protein::setup_pose_input_stream	(	utility::options::StringVectorOption const &	option_s1,
		utility::options::StringVectorOption const &	option_silent1,
		utility::options::StringVectorOption const &	option_tags1
	)

Referenced by initialize_input_streams().

setup_protein_backbone_atom_id_map()

void protocols::stepwise::modeler::protein::setup_protein_backbone_atom_id_map	(	core::pose::Pose const &	pose_1,
		core::pose::Pose const &	pose_2,
		core::Size const	base_res,
		core::Size const	base_res2,
		core::id::AtomID_Map< core::id::AtomID > &	atom_ID_map
	)

References core::chemical::ResidueType::has(), core::chemical::ResidueTypeBase::has_variant_type(), core::chemical::ResidueTypeBase::is_protein(), core::pose::named_atom_id_to_atom_id(), core::pose::Pose::residue_type(), core::id::AtomID_Map< T >::set(), and core::chemical::VIRTUAL_RESIDUE_VARIANT.

Referenced by protocols::stepwise::modeler::align::create_alignment_id_map_legacy().