Rosetta Protocols  2014.35
Public Member Functions | Private Attributes | List of all members
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< Loopsexpand_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::stringtemplate_file_names ()
 
utility::vector1
< core::pose::PoseOP
template_poses () const
 
utility::vector1< std::stringtemplate_cst_fn () const
 
utility::vector1< core::Realtemplate_wts () const
 
utility::vector1< core::Realdomain_assembly_weights () const
 
utility::vector1< std::stringsymmdef_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::Sizestarting_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::stringtemplate_fn_
 
utility::vector1< std::stringtemplate_cst_fn_
 
utility::vector1< std::stringsymmdef_files_
 
utility::vector1< core::Realtemplate_weights_
 
utility::vector1< core::Realdomain_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::Sizesheets_
 
utility::vector1< core::Sizerandom_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) 
)
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" 
)
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 
)
void protocols::hybridization::HybridizeSetup::check_and_create_fragments ( core::pose::Pose const &  pose)
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
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 
)
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
core::Real protocols::hybridization::HybridizeSetup::hetatm_self_cst_weight ( ) const
inline
void protocols::hybridization::HybridizeSetup::init ( void  )
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 ( )
void protocols::hybridization::HybridizeSetup::realign_templates ( core::pose::PoseCOP  ref_pose)
void protocols::hybridization::HybridizeSetup::run_domain_assembly ( )
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
void protocols::hybridization::HybridizeSetup::set_align_domains_to_template ( bool  v)
inline
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
void protocols::hybridization::HybridizeSetup::set_hetatm_self_cst_weight ( core::Real  v)
inline
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
bool protocols::hybridization::HybridizeSetup::align_domains_to_template_
private
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
utility::vector1< core::Real > protocols::hybridization::HybridizeSetup::domain_assembly_weights_
private
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
utility::vector1<core::fragment::FragSetOP> protocols::hybridization::HybridizeSetup::fragments_small_
private
core::Real protocols::hybridization::HybridizeSetup::hcut_
private
core::Real protocols::hybridization::HybridizeSetup::hetatm_prot_cst_weight_
private
core::Real protocols::hybridization::HybridizeSetup::hetatm_self_cst_weight_
private
core::Size protocols::hybridization::HybridizeSetup::initial_template_index_
private
core::Size protocols::hybridization::HybridizeSetup::length_
private
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
core::Size protocols::hybridization::HybridizeSetup::nres_tgt_
private
std::string protocols::hybridization::HybridizeSetup::pairings_file_
private
core::Real protocols::hybridization::HybridizeSetup::pcut_
private
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
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
utility::vector1< protocols::loops::Loops > protocols::hybridization::HybridizeSetup::template_contigs_
private
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
utility::vector1< core::Real > protocols::hybridization::HybridizeSetup::template_weights_
private
core::Real protocols::hybridization::HybridizeSetup::template_weights_sum_
private
utility::vector1< core::pose::PoseOP > protocols::hybridization::HybridizeSetup::templates_
private

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