protocols::hybridization::HybridizeSetup Class Reference

#include <HybridizeSetup.hh>

Public Member Functions
	HybridizeSetup ()
void	init ()
void	add_template (std::string template_fn, std::string cst_fn, std::string symmdef_file="NULL", core::Real weight=1., core::Real domain_assembly_weight=0., utility::vector1< core::Size > cst_reses=utility::vector1< core::Size >(0))
void	add_template (core::pose::PoseOP template_pose, std::string cst_fn, std::string symmdef_file="NULL", core::Real weight=1., core::Real domain_assembly_weight=0., utility::vector1< core::Size > cst_reses=utility::vector1< core::Size >(0), std::string name="default")
void	add_starting_templates (core::Size t)
void	pick_starting_template ()
utility::vector1< Loops >	expand_domains_to_full_length (utility::vector1< utility::vector1< Loops > > all_domains, Size ref_domains_index, Size n_residues)
void	align_by_domain (utility::vector1< core::pose::PoseOP > &poses, utility::vector1< Loops > domains, core::pose::PoseCOP &ref_pose)
void	align_by_domain (core::pose::Pose &pose, core::pose::Pose const &ref_pose, utility::vector1< Loops > domains)
void	realign_templates (core::pose::PoseCOP ref_pose)
void	run_domain_assembly ()
void	check_and_create_fragments (core::pose::Pose const &)
void	add_big_fragments (core::fragment::FragSetOP newval)
void	add_small_fragments (core::fragment::FragSetOP newval)
core::Size	initial_template_index () const
utility::vector1< std::string >	template_file_names ()
utility::vector1 < core::pose::PoseOP >	template_poses () const
utility::vector1< std::string >	template_cst_fn () const
utility::vector1< core::Real >	template_wts () const
utility::vector1< core::Real >	domain_assembly_weights () const
utility::vector1< std::string >	symmdef_files () const
utility::vector1 < protocols::loops::Loops >	template_chunks () const
utility::vector1 < protocols::loops::Loops >	template_contigs () const
utility::vector1 < core::fragment::FragSetOP >	fragments_big () const
utility::vector1 < core::fragment::FragSetOP >	fragments_small () const
bool	domain_assembly () const
void	set_domain_assembly (bool v)
void	set_align_domains_to_template (bool v)
void	set_align_domains_to_pose (bool v)
void	add_fragments_small (core::fragment::FragSetOP v)
void	add_fragments_big (core::fragment::FragSetOP v)
void	set_domain_hcut (core::Real v)
void	set_domain_pcut (core::Real v)
void	set_domain_length (core::Size v)
core::Size	nres_tgt_asu () const
core::Size	nres_protein_asu () const
void	set_nres_tgt (core::Size nres_tgt_in)
void	set_nres_protein (core::Size nres_protein_tgt_in)
void	set_add_hetatm (bool v)
void	set_hetatm_self_cst_weight (core::Real v)
void	set_hetatm_prot_cst_weight (core::Real v)
bool	add_hetatm () const
core::Real	hetatm_self_cst_weight () const
core::Real	hetatm_prot_cst_weight () const
virtual HybridizeSetupOP	clone () const

Private Attributes
utility::vector1< core::Size >	starting_templates_
core::Size	initial_template_index_
core::Real	frag_1mer_insertion_weight_
core::Real	small_frag_insertion_weight_
core::Real	big_frag_insertion_weight_
core::Real	frag_weight_aligned_
bool	auto_frag_insertion_weight_
core::Size	max_registry_shift_
bool	domain_assembly_
bool	add_hetatm_
bool	align_domains_to_template_
bool	align_domains_to_pose_
bool	add_non_init_chunks_
core::Real	hetatm_self_cst_weight_
core::Real	hetatm_prot_cst_weight_
std::string	disulf_file_
core::Size	cartfrag_overlap_
core::Real	pcut_
core::Real	hcut_
core::Size	length_
utility::vector1 < core::fragment::FragSetOP >	fragments_big_
utility::vector1 < core::fragment::FragSetOP >	fragments_small_
core::pose::PoseOP	native_
core::sequence::SequenceAlignmentOP	aln_
utility::vector1 < core::pose::PoseOP >	templates_
utility::vector1< std::string >	template_fn_
utility::vector1< std::string >	template_cst_fn_
utility::vector1< std::string >	symmdef_files_
utility::vector1< core::Real >	template_weights_
utility::vector1< core::Real >	domain_assembly_weights_
utility::vector1 < protocols::loops::Loops >	template_chunks_
utility::vector1 < protocols::loops::Loops >	template_contigs_
utility::vector1 < utility::vector1< core::Size > >	template_cst_reses_
core::Real	template_weights_sum_
utility::vector1 < protocols::loops::Loops >	domains_
std::string	pairings_file_
utility::vector1< core::Size >	sheets_
utility::vector1< core::Size >	random_sheets_
bool	filter_templates_
utility::vector1< std::pair < core::Size, core::Size > >	strand_pairs_
core::Size	nres_tgt_
core::Size	nres_protein_tgt_

Constructor & Destructor Documentation

protocols::hybridization::HybridizeSetup::HybridizeSetup

(

)

References init().

Referenced by clone().

Member Function Documentation

void protocols::hybridization::HybridizeSetup::add_big_fragments ( core::fragment::FragSetOP  newval )

inline

References fragments_big_.

void protocols::hybridization::HybridizeSetup::add_fragments_big ( core::fragment::FragSetOP  v )

inline

References fragments_big_.

void protocols::hybridization::HybridizeSetup::add_fragments_small ( core::fragment::FragSetOP  v )

inline

References fragments_small_.

bool protocols::hybridization::HybridizeSetup::add_hetatm ( ) const

inline

References add_hetatm_.

void protocols::hybridization::HybridizeSetup::add_small_fragments ( core::fragment::FragSetOP  newval )

inline

References fragments_small_.

void protocols::hybridization::HybridizeSetup::add_starting_templates ( core::Size  t )

inline

References starting_templates_.

void protocols::hybridization::HybridizeSetup::add_template	(	std::string	template_fn,
		std::string	cst_fn,
		std::string	symmdef_file = "NULL",
		core::Real	weight = 1.,
		core::Real	domain_assembly_weight = 0.,
		utility::vector1< core::Size >	cst_reses = utility::vector1<core::Size>(0)
	)

References core::chemical::ChemicalManager::get_instance(), core::import_pose::pose_from_pdb(), and core::chemical::ChemicalManager::residue_type_set().

void protocols::hybridization::HybridizeSetup::add_template	(	core::pose::PoseOP	template_pose,
		std::string	cst_fn,
		std::string	symmdef_file = "NULL",
		core::Real	weight = 1.,
		core::Real	domain_assembly_weight = 0.,
		utility::vector1< core::Size >	cst_reses = utility::vector1<core::Size>(0),
		std::string	name = "default"
	)

References chunks, domain_assembly_weights_, protocols::loops::extract_continuous_chunks(), protocols::loops::extract_secondary_structure_chunks(), core::scoring::dssp::Dssp::insert_ss_into_pose(), protocols::loops::Loops::num_loop(), core::pose::Pose::pdb_info(), symmdef_files_, template_chunks_, template_contigs_, template_cst_fn_, template_cst_reses_, template_fn_, template_weights_, templates_, core::pose::Pose::total_residue(), and protocols::hybridization::TR.

void protocols::hybridization::HybridizeSetup::align_by_domain	(	utility::vector1< core::pose::PoseOP > &	poses,
		utility::vector1< Loops >	domains,
		core::pose::PoseCOP &	ref_pose
	)

Referenced by realign_templates().

void protocols::hybridization::HybridizeSetup::align_by_domain	(	core::pose::Pose &	pose,
		core::pose::Pose const &	ref_pose,
		utility::vector1< Loops >	domains
	)

References protocols::hybridization::TMalign::alignment2AtomMap(), protocols::hybridization::TMalign::alignment2strings(), protocols::hybridization::TMalign::apply(), core::id::BOGUS_ATOM_ID, F, core::pose::initialize_atomid_map(), core::chemical::ResidueType::is_protein(), protocols::hybridization::partial_align(), core::pose::Pose::pdb_info(), core::pose::Pose::residue_type(), protocols::loops::Loop::set_start(), protocols::loops::Loop::set_stop(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), protocols::loops::stop, protocols::hybridization::TMalign::TMscore(), core::pose::Pose::total_residue(), and protocols::hybridization::TR.

void protocols::hybridization::HybridizeSetup::check_and_create_fragments

(

core::pose::Pose const &

pose

)

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::fragment::Frame::add_fragment(), core::fragment::chop_fragments(), core::pose::Pose::conformation(), fragments_big_, fragments_small_, frags, frame(), core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), option, core::fragment::picking_old::vall::pick_fragments_by_ss_plus_aa(), read_psipred_ss2_file(), residue, core::pose::Pose::residue(), runtime_assert, core::pose::Pose::sequence(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), templates_, core::pose::Pose::total_residue(), and user.

HybridizeSetupOP protocols::hybridization::HybridizeSetup::clone ( ) const

virtual

References HybridizeSetup().

bool protocols::hybridization::HybridizeSetup::domain_assembly ( ) const

inline

References domain_assembly_.

Referenced by run_domain_assembly().

utility::vector1< core::Real > protocols::hybridization::HybridizeSetup::domain_assembly_weights ( ) const

inline

References domain_assembly_weights_.

utility::vector1< Loops > protocols::hybridization::HybridizeSetup::expand_domains_to_full_length	(	utility::vector1< utility::vector1< Loops > >	all_domains,
		Size	ref_domains_index,
		Size	n_residues
	)

References numeric::random::RandomGenerator::random_range(), protocols::hybridization::RG, size(), and protocols::loops::start.

Referenced by realign_templates().

utility::vector1<core::fragment::FragSetOP> protocols::hybridization::HybridizeSetup::fragments_big ( ) const

inline

References fragments_big_.

utility::vector1<core::fragment::FragSetOP> protocols::hybridization::HybridizeSetup::fragments_small ( ) const

inline

References fragments_small_.

core::Real protocols::hybridization::HybridizeSetup::hetatm_prot_cst_weight ( ) const

inline

References hetatm_prot_cst_weight_.

core::Real protocols::hybridization::HybridizeSetup::hetatm_self_cst_weight ( ) const

inline

References hetatm_self_cst_weight_.

void protocols::hybridization::HybridizeSetup::init

(

void

)

References add_hetatm_, cm::hybridize::add_non_init_chunks, add_non_init_chunks_, cm::hybridize::auto_frag_insertion_weight, auto_frag_insertion_weight_, cm::hybridize::big_frag_insertion_weight, big_frag_insertion_weight_, domain_assembly_, cm::hybridize::frag_1mer_insertion_weight, frag_1mer_insertion_weight_, cm::hybridize::frag_weight_aligned, frag_weight_aligned_, hetatm_prot_cst_weight_, hetatm_self_cst_weight_, option, cm::hybridize::small_frag_insertion_weight, and small_frag_insertion_weight_.

Referenced by HybridizeSetup().

core::Size protocols::hybridization::HybridizeSetup::initial_template_index ( ) const

inline

References initial_template_index_.

Referenced by realign_templates().

core::Size protocols::hybridization::HybridizeSetup::nres_protein_asu ( ) const

inline

References nres_protein_tgt_.

core::Size protocols::hybridization::HybridizeSetup::nres_tgt_asu ( ) const

inline

References nres_tgt_.

void protocols::hybridization::HybridizeSetup::pick_starting_template

(

)

References numeric::random::WeightedSampler::add_weight(), initial_template_index_, numeric::random::WeightedSampler::random_sample(), protocols::hybridization::RG, starting_templates_, template_weights_, and numeric::random::WeightedSampler::weights().

void protocols::hybridization::HybridizeSetup::realign_templates

(

core::pose::PoseCOP

ref_pose

)

References align_by_domain(), domains_, expand_domains_to_full_length(), protocols::loops::extract_continuous_chunks(), protocols::loops::extract_secondary_structure_chunks(), hcut_, initial_template_index(), length_, nres_tgt_, pcut_, protocols::hybridization::DDomainParse::split(), protocols::loops::start, protocols::loops::stop, template_chunks_, template_contigs_, template_fn_, templates_, and protocols::hybridization::TR.

void protocols::hybridization::HybridizeSetup::run_domain_assembly

(

)

References domain_assembly(), domain_assembly_weights_, protocols::hybridization::DomainAssembly::run(), and templates_.

void protocols::hybridization::HybridizeSetup::set_add_hetatm ( bool  v )

inline

References add_hetatm_.

void protocols::hybridization::HybridizeSetup::set_align_domains_to_pose ( bool  v )

inline

References align_domains_to_pose_.

void protocols::hybridization::HybridizeSetup::set_align_domains_to_template ( bool  v )

inline

References align_domains_to_template_.

void protocols::hybridization::HybridizeSetup::set_domain_assembly ( bool  v )

inline

References domain_assembly_.

void protocols::hybridization::HybridizeSetup::set_domain_hcut ( core::Real  v )

inline

References hcut_.

void protocols::hybridization::HybridizeSetup::set_domain_length ( core::Size  v )

inline

References length_.

void protocols::hybridization::HybridizeSetup::set_domain_pcut ( core::Real  v )

inline

References pcut_.

void protocols::hybridization::HybridizeSetup::set_hetatm_prot_cst_weight ( core::Real  v )

inline

References hetatm_prot_cst_weight_.

void protocols::hybridization::HybridizeSetup::set_hetatm_self_cst_weight ( core::Real  v )

inline

References hetatm_self_cst_weight_.

void protocols::hybridization::HybridizeSetup::set_nres_protein ( core::Size  nres_protein_tgt_in )

inline

References nres_protein_tgt_.

void protocols::hybridization::HybridizeSetup::set_nres_tgt ( core::Size  nres_tgt_in )

inline

References nres_tgt_.

utility::vector1< std::string > protocols::hybridization::HybridizeSetup::symmdef_files ( ) const

inline

References symmdef_files_.

utility::vector1< protocols::loops::Loops > protocols::hybridization::HybridizeSetup::template_chunks ( ) const

inline

References template_chunks_.

utility::vector1< protocols::loops::Loops > protocols::hybridization::HybridizeSetup::template_contigs ( ) const

inline

References template_contigs_.

utility::vector1< std::string > protocols::hybridization::HybridizeSetup::template_cst_fn ( ) const

inline

References template_cst_fn_.

utility::vector1< std::string > protocols::hybridization::HybridizeSetup::template_file_names ( )

inline

References template_fn_.

utility::vector1< core::pose::PoseOP > protocols::hybridization::HybridizeSetup::template_poses ( ) const

inline

References templates_.

utility::vector1< core::Real > protocols::hybridization::HybridizeSetup::template_wts ( ) const

inline

References template_weights_.

Member Data Documentation

bool protocols::hybridization::HybridizeSetup::add_hetatm_

private

Referenced by add_hetatm(), init(), and set_add_hetatm().

bool protocols::hybridization::HybridizeSetup::add_non_init_chunks_

private

Referenced by init().

bool protocols::hybridization::HybridizeSetup::align_domains_to_pose_

private

Referenced by set_align_domains_to_pose().

bool protocols::hybridization::HybridizeSetup::align_domains_to_template_

private

Referenced by set_align_domains_to_template().

core::sequence::SequenceAlignmentOP protocols::hybridization::HybridizeSetup::aln_

private

bool protocols::hybridization::HybridizeSetup::auto_frag_insertion_weight_

private

Referenced by init().

core::Real protocols::hybridization::HybridizeSetup::big_frag_insertion_weight_

private

Referenced by init().

core::Size protocols::hybridization::HybridizeSetup::cartfrag_overlap_

private

std::string protocols::hybridization::HybridizeSetup::disulf_file_

private

bool protocols::hybridization::HybridizeSetup::domain_assembly_

private

Referenced by domain_assembly(), init(), and set_domain_assembly().

utility::vector1< core::Real > protocols::hybridization::HybridizeSetup::domain_assembly_weights_

private

Referenced by add_template(), domain_assembly_weights(), and run_domain_assembly().

utility::vector1< protocols::loops::Loops > protocols::hybridization::HybridizeSetup::domains_

private

Referenced by realign_templates().

bool protocols::hybridization::HybridizeSetup::filter_templates_

private

core::Real protocols::hybridization::HybridizeSetup::frag_1mer_insertion_weight_

private

Referenced by init().

core::Real protocols::hybridization::HybridizeSetup::frag_weight_aligned_

private

Referenced by init().

utility::vector1<core::fragment::FragSetOP> protocols::hybridization::HybridizeSetup::fragments_big_

private

Referenced by add_big_fragments(), add_fragments_big(), check_and_create_fragments(), and fragments_big().

utility::vector1<core::fragment::FragSetOP> protocols::hybridization::HybridizeSetup::fragments_small_

private

Referenced by add_fragments_small(), add_small_fragments(), check_and_create_fragments(), and fragments_small().

core::Real protocols::hybridization::HybridizeSetup::hcut_

private

Referenced by realign_templates(), and set_domain_hcut().

core::Real protocols::hybridization::HybridizeSetup::hetatm_prot_cst_weight_

private

Referenced by hetatm_prot_cst_weight(), init(), and set_hetatm_prot_cst_weight().

core::Real protocols::hybridization::HybridizeSetup::hetatm_self_cst_weight_

private

Referenced by hetatm_self_cst_weight(), init(), and set_hetatm_self_cst_weight().

core::Size protocols::hybridization::HybridizeSetup::initial_template_index_

private

Referenced by initial_template_index(), and pick_starting_template().

core::Size protocols::hybridization::HybridizeSetup::length_

private

Referenced by realign_templates(), and set_domain_length().

core::Size protocols::hybridization::HybridizeSetup::max_registry_shift_

private

core::pose::PoseOP protocols::hybridization::HybridizeSetup::native_

private

core::Size protocols::hybridization::HybridizeSetup::nres_protein_tgt_

private

Referenced by nres_protein_asu(), and set_nres_protein().

core::Size protocols::hybridization::HybridizeSetup::nres_tgt_

private

Referenced by nres_tgt_asu(), realign_templates(), and set_nres_tgt().

std::string protocols::hybridization::HybridizeSetup::pairings_file_

private

core::Real protocols::hybridization::HybridizeSetup::pcut_

private

Referenced by realign_templates(), and set_domain_pcut().

utility::vector1<core::Size> protocols::hybridization::HybridizeSetup::random_sheets_

private

utility::vector1<core::Size> protocols::hybridization::HybridizeSetup::sheets_

private

core::Real protocols::hybridization::HybridizeSetup::small_frag_insertion_weight_

private

Referenced by init().

utility::vector1< core::Size > protocols::hybridization::HybridizeSetup::starting_templates_

private

Referenced by add_starting_templates(), and pick_starting_template().

utility::vector1< std::pair< core::Size, core::Size > > protocols::hybridization::HybridizeSetup::strand_pairs_

private

utility::vector1< std::string > protocols::hybridization::HybridizeSetup::symmdef_files_

private

Referenced by add_template(), and symmdef_files().

utility::vector1< protocols::loops::Loops > protocols::hybridization::HybridizeSetup::template_chunks_

private

Referenced by add_template(), realign_templates(), and template_chunks().

utility::vector1< protocols::loops::Loops > protocols::hybridization::HybridizeSetup::template_contigs_

private

Referenced by add_template(), realign_templates(), and template_contigs().

utility::vector1< std::string > protocols::hybridization::HybridizeSetup::template_cst_fn_

private

Referenced by add_template(), and template_cst_fn().

utility::vector1< utility::vector1<core::Size> > protocols::hybridization::HybridizeSetup::template_cst_reses_

private

Referenced by add_template().

utility::vector1< std::string > protocols::hybridization::HybridizeSetup::template_fn_

private

Referenced by add_template(), realign_templates(), and template_file_names().

utility::vector1< core::Real > protocols::hybridization::HybridizeSetup::template_weights_

private

Referenced by add_template(), pick_starting_template(), and template_wts().

core::Real protocols::hybridization::HybridizeSetup::template_weights_sum_

private

utility::vector1< core::pose::PoseOP > protocols::hybridization::HybridizeSetup::templates_

private

Referenced by add_template(), check_and_create_fragments(), realign_templates(), run_domain_assembly(), and template_poses().

---

The documentation for this class was generated from the following files:

• src/protocols/hybridization/HybridizeSetup.hh
• src/protocols/hybridization/HybridizeSetup.cc