protocols::stepwise::sampling::rna::legacy Namespace Reference

Namespaces
	rigid_body
	suite

Classes
class	RNA_AnalyticLoopCloser
	The RNA de novo structure modeling protocol. More...
class	StepWiseRNA_JobParametersSetup
class	StepWiseRNA_PoseSetup

Typedefs
typedef utility::pointer::owning_ptr < RNA_AnalyticLoopCloser >	RNA_AnalyticLoopCloserOP
typedef utility::pointer::owning_ptr < StepWiseRNA_PoseSetup >	StepWiseRNA_PoseSetupOP
typedef utility::pointer::owning_ptr < StepWiseRNA_PoseSetup const >	StepWiseRNA_PoseSetupCOP

Functions
void	apply_chi_cst (core::pose::Pose &pose, core::pose::Pose const &ref_pose)
std::string	get_working_directory ()
utility::vector1< core::Size >	get_fixed_res (core::Size const nres)
bool	is_nonempty_input_silent_file (std::string const input_silent_file, std::string const exit_key_string)
utility::vector1< core::Size >	get_input_res (core::Size const nres, std::string const pose_num)
utility::vector1< std::string >	get_silent_file_tags ()
core::scoring::ScoreFunctionOP	create_scorefxn ()
StepWiseRNA_JobParametersOP	setup_simple_full_length_rna_job_parameters ()
StepWiseRNA_JobParametersOP	setup_rna_job_parameters (bool check_for_previously_closed_cutpoint_with_input_pose)
void	setup_copy_DOF_input (StepWiseRNA_PoseSetupOP &stepwise_rna_pose_setup)
StepWiseRNA_PoseSetupOP	setup_pose_setup_class (StepWiseRNA_JobParametersOP &job_parameters, bool const copy_DOF)
void	check_if_silent_file_exists ()
bool	get_tag_and_silent_file_for_struct (std::string &swa_silent_file, std::string &out_tag, Size const &n, bool const &multiple_shots, std::string const &silent_file)
void	ensure_directory_for_out_silent_file_exists ()

Typedef Documentation

typedef utility::pointer::owning_ptr< RNA_AnalyticLoopCloser > protocols::stepwise::sampling::rna::legacy::RNA_AnalyticLoopCloserOP

typedef utility::pointer::owning_ptr< StepWiseRNA_PoseSetup const > protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetupCOP

typedef utility::pointer::owning_ptr< StepWiseRNA_PoseSetup > protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetupOP

Function Documentation

void protocols::stepwise::sampling::rna::legacy::apply_chi_cst	(	core::pose::Pose &	pose,
		core::pose::Pose const &	ref_pose
	)

References core::conformation::Residue::aa(), core::conformation::Residue::atom_index(), core::id::CHI, core::pose::Pose::constraint_set(), is_purine(), core::conformation::Residue::is_RNA(), na_rad, na_rgu, nres, numeric::conversions::radians(), core::pose::Pose::residue(), core::pose::Pose::torsion(), and core::pose::Pose::total_residue().

void protocols::stepwise::sampling::rna::legacy::check_if_silent_file_exists

(

)

References utility::file::file_exists(), option, out::file::silent, TR, and utility_exit_with_message.

core::scoring::ScoreFunctionOP protocols::stepwise::sampling::rna::legacy::create_scorefxn

(

)

References getScoreFunction(), option, rna_sugar_close, TR, user, utility_exit_with_message, and basic::options::OptionKeys::score::weights.

void protocols::stepwise::sampling::rna::legacy::ensure_directory_for_out_silent_file_exists

(

)

References option, out::file::silent, TR, user, and utility_exit_with_message.

utility::vector1< core::Size > protocols::stepwise::sampling::rna::legacy::get_fixed_res

(

core::Size const

nres

)

References in::file::input_res, option, TR, and utility_exit_with_message.

Referenced by setup_rna_job_parameters(), and setup_simple_full_length_rna_job_parameters().

utility::vector1< core::Size > protocols::stepwise::sampling::rna::legacy::get_input_res	(	core::Size const	nres,
		std::string const	pose_num
	)

References in::file::input_res, option, TR, and utility_exit_with_message.

Referenced by setup_rna_job_parameters().

utility::vector1< std::string > protocols::stepwise::sampling::rna::legacy::get_silent_file_tags

(

)

References getline(), option, protocols::stepwise::sampling::rna::output_title_text(), runtime_assert, in::file::tags, protocols::stepwise::sampling::rna::tokenize(), TR, user, and utility_exit_with_message.

Referenced by setup_copy_DOF_input(), and setup_rna_job_parameters().

bool protocols::stepwise::sampling::rna::legacy::get_tag_and_silent_file_for_struct	(	std::string &	swa_silent_file,
		std::string &	out_tag,
		Size const &	n,
		bool const &	multiple_shots,
		std::string const &	silent_file
	)

References core::io::silent::initialize_tag_is_done(), option, runtime_assert, and TR.

std::string protocols::stepwise::sampling::rna::legacy::get_working_directory

(

)

References GetCurrentDir, ss, and utility_exit_with_message.

bool protocols::stepwise::sampling::rna::legacy::is_nonempty_input_silent_file	(	std::string const	input_silent_file,
		std::string const	exit_key_string
	)

References getline(), runtime_assert, TR, and utility_exit_with_message.

void protocols::stepwise::sampling::rna::legacy::setup_copy_DOF_input

(

StepWiseRNA_PoseSetupOP &

stepwise_rna_pose_setup

)

References get_silent_file_tags(), option, in::file::s, in::file::silent, TR, user, and utility_exit_with_message.

Referenced by setup_pose_setup_class().

StepWiseRNA_PoseSetupOP protocols::stepwise::sampling::rna::legacy::setup_pose_setup_class	(	StepWiseRNA_JobParametersOP &	job_parameters,
		bool const	copy_DOF
	)

References basic::options::OptionKeys::stepwise::rna::bulge_res, basic::options::OptionKeys::rna::corrected_geo, core::chemical::ChemicalManager::get_instance(), protocols::farna::make_phosphate_nomenclature_matches_mini(), in::file::native, basic::options::OptionKeys::stepwise::rna::native_virtual_res, option, core::import_pose::pose_from_pdb(), core::chemical::ChemicalManager::residue_type_set(), RNA, setup_copy_DOF_input(), TR, user, and basic::options::OptionKeys::full_model::virtual_res.

StepWiseRNA_JobParametersOP protocols::stepwise::sampling::rna::legacy::setup_rna_job_parameters

(

bool

check_for_previously_closed_cutpoint_with_input_pose

)

References in::file::fasta, get_fixed_res(), get_input_res(), get_silent_file_tags(), nres, option, core::sequence::read_fasta_file(), basic::options::OptionKeys::stepwise::rna::rebuild_bulge_mode, runtime_assert, basic::options::OptionKeys::stepwise::rna::sample_both_sugar_base_rotamer, in::file::silent, TR, user, and utility_exit_with_message.

StepWiseRNA_JobParametersOP protocols::stepwise::sampling::rna::legacy::setup_simple_full_length_rna_job_parameters

(

)

Oct 28, 2011:This function is an alternative way to setup the job_parameters//////////////////////////////////////////////////// The original job_parameters was designed primarily for use during the SWA building step///////////////////////////////////////// However since then, many other other SWA and FARFAR class make use of it especially the full pose length version//////////////// Hence the original job_parameters setup has become clumbersome for most usage (containing many options and independencies)////// The new job_parameter setup function is a work in progress and will be updated as needed./////////////////////////////////////// For example right now (Oct 28, 2011), it only contains parameters needed by output_data()///////////////////////////////////////

References protocols::stepwise::sampling::rna::apply_virtual_rna_residue_variant_type(), in::file::fasta, full_to_sub(), get_fixed_res(), core::chemical::ChemicalManager::get_instance(), input_res, input_res2, protocols::farna::make_phosphate_nomenclature_matches_mini(), in::file::native, nres, option, core::import_pose::pose_from_pdb(), protocols::stepwise::sampling::rna::print_JobParameters_info(), core::sequence::read_fasta_file(), core::chemical::ChemicalManager::residue_type_set(), RNA, protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_is_simple_full_length_job_params(), string_to_int(), protocols::stepwise::sampling::rna::tokenize(), TR, user, and utility_exit_with_message.