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Rosetta
2020.50
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tiny helper class that knows the relative fractions of secondary structure L,H,E so far these fractions can be computed from a FragSet other input strategies are conceivable but not implemented, yet: eg. psipred files, a bunch of poses, More...
#include <SecondaryStructure.hh>
Public Member Functions | |
~SecondaryStructure () override | |
Automatically generated virtual destructor for class deriving directly from VirtualBase. More... | |
SecondaryStructure () | |
SecondaryStructure (utility::vector1< SecondaryStructureOP > &, utility::vector1< Real > &) | |
c'ctor that creates a SecondaryStructure as an average of several SecondaryStructure objects More... | |
SecondaryStructure (core::fragment::FragSet const &frags, core::Size nres=0, bool bJustCenterResidue=false) | |
c'stor compute fractions from fragments More... | |
SecondaryStructure (core::pose::Pose const &) | |
c'stor compute fractions from pose ( well it won't be "fractions" ) More... | |
core::Real | loop_fraction (core::Size pos) const |
return loop fraction at position More... | |
core::Real | strand_fraction (core::Size pos) const |
return strand fraction at position More... | |
core::Real | sheet_fraction (core::Size pos) const |
alias for strand-fraction ... More... | |
core::Real | helix_fraction (core::Size pos) const |
helix fraction at position More... | |
core::Real | confidence (core::Size pos) const |
confidence at position More... | |
void | set_fractions (core::Size pos, core::Real helix_fraction, core::Real sheet_fraction, core::Real loop_fraction, core::Real confidence=0) |
sets secondary structure probabilities at a given position More... | |
ObjexxFCL::FArray1D_float const & | loop_fraction () const |
return loop fraction - FArray More... | |
ObjexxFCL::FArray1D_float const & | strand_fraction () const |
return strand fraction - FArray More... | |
core::Size | total_residue () const |
returns regions (in loop-class format) that belong to contiguous pieces of ss-structure More... | |
char | secstruct (core::Size pos) const |
returns the most probably secstruct at that position More... | |
void | extend (core::Size) |
extends with pure 'L' at end until requested size is reached. More... | |
void | read_from_file (std::string fn) |
read from file More... | |
void | show (std::ostream &) const |
write to stream ( opposite from read_from_file ) More... | |
void | write_psipred_ss2 (std::ostream &os, std::string const &sequence) const |
write psipred format More... | |
void | read_psipred_ss2 (std::istream &os) |
write psipred format More... | |
void | read_psipred_ss2 (std::string filename) |
write psipred format More... | |
void | read_talos_ss (std::istream &os) |
read talos+ format More... | |
void | read_talos_ss (std::string filename) |
read talos+ format More... | |
Private Member Functions | |
void | compute_fractions (core::fragment::FragSet const &, bool bJustCenterResidue) |
Private Attributes | |
ObjexxFCL::FArray1D_float | loop_fraction_ |
store loop/strand fractions More... | |
ObjexxFCL::FArray1D_float | strand_fraction_ |
ObjexxFCL::FArray1D_float | confidence_ |
store confidence values: used by talos, but not by psipred More... | |
core::Size | total_residue_ |
length of FArrays More... | |
tiny helper class that knows the relative fractions of secondary structure L,H,E so far these fractions can be computed from a FragSet other input strategies are conceivable but not implemented, yet: eg. psipred files, a bunch of poses,
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overridedefault |
Automatically generated virtual destructor for class deriving directly from VirtualBase.
Auto-generated virtual destructor
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core::fragment::SecondaryStructure::SecondaryStructure | ( | utility::vector1< SecondaryStructureOP > & | components, |
utility::vector1< Real > & | weights | ||
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c'ctor that creates a SecondaryStructure as an average of several SecondaryStructure objects
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inline |
c'stor compute fractions from fragments
References compute_fractions().
core::fragment::SecondaryStructure::SecondaryStructure | ( | core::pose::Pose const & | pose | ) |
c'stor compute fractions from pose ( well it won't be "fractions" )
References core::pose::Pose::secstruct(), and core::pose::Pose::size().
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void core::fragment::SecondaryStructure::extend | ( | core::Size | nres | ) |
extends with pure 'L' at end until requested size is reached.
Referenced by protocols::jumping::JumpSample::JumpSample().
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inline |
helix fraction at position
References loop_fraction_, protocols::mean_field::max(), strand_fraction_, and total_residue_.
Referenced by protocols::abinitio::decide_on_beta_jumping_from_frags(), and protocols::loops::define_scorable_core_from_secondary_structure().
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return loop fraction at position
References loop_fraction_, and total_residue_.
Referenced by protocols::loops::compute_ss_regions(), protocols::environment::claims::CutBiasClaim::CutBiasClaim(), protocols::topology_broker::CutBiasClaimer::CutBiasClaimer(), protocols::loops::define_scorable_core_from_secondary_structure(), and protocols::jumping::JumpSample::JumpSample().
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return loop fraction - FArray
References loop_fraction_.
void core::fragment::SecondaryStructure::read_from_file | ( | std::string | fn | ) |
void core::fragment::SecondaryStructure::read_psipred_ss2 | ( | std::istream & | os | ) |
write psipred format
References protocols::cluster::calibur::aa, protocols::analysis::total, and core::fragment::tr().
void core::fragment::SecondaryStructure::read_psipred_ss2 | ( | std::string | filename | ) |
write psipred format
References core::fragment::tr().
void core::fragment::SecondaryStructure::read_talos_ss | ( | std::istream & | os | ) |
read talos+ format
References protocols::cluster::calibur::aa, protocols::analysis::total, and core::fragment::tr().
void core::fragment::SecondaryStructure::read_talos_ss | ( | std::string | filename | ) |
read talos+ format
References core::fragment::tr().
char core::fragment::SecondaryStructure::secstruct | ( | core::Size | pos | ) | const |
returns the most probably secstruct at that position
returns regions (in loop-class format) that belong to contiguous pieces of ss-structure
References protocols::mean_field::max().
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sets secondary structure probabilities at a given position
References confidence(), confidence_, loop_fraction_, sheet_fraction(), strand_fraction_, and total_residue_.
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alias for strand-fraction ...
References strand_fraction().
Referenced by protocols::abinitio::IterativeBase::guess_pairings_from_secondary_structure(), and set_fractions().
void core::fragment::SecondaryStructure::show | ( | std::ostream & | os | ) | const |
write to stream ( opposite from read_from_file )
References protocols::comparative_modeling::features::A, core::chemical::element::F, and core::chemical::element::I.
Referenced by core::fragment::operator<<().
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return strand fraction at position
References strand_fraction_, and total_residue_.
Referenced by protocols::abinitio::decide_on_beta_jumping_from_frags(), and protocols::jumping::SameStrand::do_strand_sum().
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returns regions (in loop-class format) that belong to contiguous pieces of ss-structure
number of residues for which information is available
References total_residue_.
Referenced by protocols::loops::compute_ss_regions(), protocols::environment::claims::CutBiasClaim::CutBiasClaim(), protocols::topology_broker::CutBiasClaimer::CutBiasClaimer(), protocols::abinitio::decide_on_beta_jumping_from_frags(), protocols::loops::define_scorable_core_from_secondary_structure(), protocols::jumping::SameStrand::do_strand_sum(), protocols::abinitio::IterativeBase::guess_pairings_from_secondary_structure(), and protocols::jumping::JumpSample::JumpSample().
void core::fragment::SecondaryStructure::write_psipred_ss2 | ( | std::ostream & | os, |
std::string const & | sequence | ||
) | const |
write psipred format
References protocols::comparative_modeling::features::A, core::chemical::element::F, and core::chemical::element::I.
Referenced by protocols::abinitio::IterativeBase::guess_pairings_from_secondary_structure().
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store confidence values: used by talos, but not by psipred
Referenced by confidence(), and set_fractions().
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store loop/strand fractions
Referenced by helix_fraction(), loop_fraction(), and set_fractions().
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Referenced by helix_fraction(), set_fractions(), and strand_fraction().
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length of FArrays
Referenced by confidence(), helix_fraction(), loop_fraction(), set_fractions(), strand_fraction(), and total_residue().