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protocols::frags Namespace Reference

Classes

class  FragLib
 
class  RMSVallData
 
class  SingleResidueTorsionFragmentLibrary
 a class for collection of fragments for a single residue position More...
 
class  TorsionFragment
 a class for single piece of torsion fragment More...
 
class  TorsionFragmentLibrary
 a class for classic Rosetta fragment library More...
 
class  TorsionFragmentMover
 
class  VallData
 

Typedefs

using Sizes = utility::vector1< core::Size >
 
typedef
utility::pointer::shared_ptr
< TorsionFragment
TorsionFragmentOP
 
typedef
utility::pointer::shared_ptr
< SingleResidueTorsionFragmentLibrary
SingleResidueTorsionFragmentLibraryOP
 
typedef
utility::pointer::shared_ptr
< TorsionFragmentLibrary
TorsionFragmentLibraryOP
 
typedef
utility::pointer::shared_ptr
< TorsionFragmentLibrary const > 
TorsionFragmentLibraryCOP
 
typedef
utility::pointer::shared_ptr
< FragLib
FragLibOP
 
typedef
utility::pointer::shared_ptr
< FragLib const > 
FragLibCOP
 
typedef
utility::pointer::shared_ptr
< TorsionFragmentMover
TorsionFragmentMoverOP
 

Functions

void heap_init (FArray1A_int heap, FArray1A_float coheap, int max_items)
 sets up an empty heap and stores the dimensioned size More...
 
void heap_extract (FArray1A_int heap, FArray1A_float coheap, int &val, float &coval, bool &err)
 modifes heap and last_val return val and err. More...
 
void heap_insert (FArray1A_int heap, FArray1A_float coheap, int val, float coval, bool &err)
 modifes heap and last_dummy, inserts val, returns err requires heap_max to be previously set via heap_init More...
 
void heap_replace (FArray1A_int heap, FArray1A_float coheap, int val, float coval)
 
void heap_down (FArray1A_int heap, FArray1A_float coheap, int index_in)
 
void heap_up (FArray1A_int heap, FArray1A_float coheap, int &index_in)
 
void heap_init (ObjexxFCL::FArray1A_int heap, ObjexxFCL::FArray1A_float coheap, int max_items)
 
void heap_extract (ObjexxFCL::FArray1A_int heap, ObjexxFCL::FArray1A_float coheap, int &val, float &coval, bool &err)
 
void heap_insert (ObjexxFCL::FArray1A_int heap, ObjexxFCL::FArray1A_float coheap, int val, float coval, bool &err)
 
void heap_replace (ObjexxFCL::FArray1A_int heap, ObjexxFCL::FArray1A_float coheap, int val, float coval)
 
void heap_down (ObjexxFCL::FArray1A_int heap, ObjexxFCL::FArray1A_float coheap, int index_in)
 
void heap_up (ObjexxFCL::FArray1A_int heap, ObjexxFCL::FArray1A_float coheap, int &index_in)
 
static basic::Tracer TR ("protocols.frags.TorsionFragment")
 
template<class T >
bool has_element (utility::vector1< T > const &v, T const &t)
 these will go into a helper file soon More...
 
template<class T >
bool has_element (T const &t, utility::vector1< T > const &v)
 never can remember the order... More...
 
bool ss_length_check (core::Size const min_len_helix, core::Size const min_len_strand, core::pose::Pose const &pose)
 
void add_vall_fragments (utility::vector1< core::Size > const &frag_sizes, core::Size const nfrags, pose::Pose const &pose, core::kinematics::MoveMap const &mm, std::string const &secstruct, Real const seq_weight, Real const ss_weight, FragLib &frag_lib, utility::vector1< core::Size > const &homs_to_exclude, Real const bb_weight, std::string const &bigbins, std::string const &inputseq)
 
void add_vall_fragments (utility::vector1< core::Size > const &frag_sizes, core::Size const nfrags, pose::Pose const &pose, core::kinematics::MoveMap const &mm, utility::vector1< std::map< char, core::Real > > const &target_ss, Real const seq_weight, Real const ss_weight, FragLib &frag_lib, utility::vector1< core::Size > const &homs_to_exclude, Real const bb_weight, std::string const &bigbins, std::string const &inputseq)
 
FragLibOP setup_vall_fragments (utility::vector1< core::Size > const &frag_sizes, core::Size const nfrags, pose::Pose const &pose, core::kinematics::MoveMap const &mm, std::string const &secstruct, Real const seq_weight, Real const ss_weight, utility::vector1< core::Size > const &homs_to_exclude)
 
void add_vall_cheating_fragments (utility::vector1< core::Size > const &frag_sizes, core::Size const nfrags, pose::Pose const &pose, core::kinematics::MoveMap const &mm, std::string const &secstruct, Real const seq_weight, Real const ss_weight, Real const torsion_weight, Real const min_torsion_dev, Real const max_torsion_dev, FragLib &frag_lib, utility::vector1< core::Size > const &homs_to_exclude)
 
FragLibOP setup_vall_cheating_fragments (utility::vector1< core::Size > const &frag_sizes, core::Size const nfrags, pose::Pose const &pose, core::kinematics::MoveMap const &mm, std::string const &secstruct, Real const seq_weight, Real const ss_weight, Real const torsion_weight, Real const min_torsion_dev, Real const max_torsion_dev, utility::vector1< core::Size > const &homs_to_exclude)
 
void fill_in_gaps (core::Size const nfrags, pose::Pose const &pose, std::string const &secstruct, Real const seq_weight, Real const ss_weight, FragLib &frag_lib, utility::vector1< core::Size > const &homs_to_exclude, bool const allow_uninitialized_secstruct)
 
void insert_fragment (core::Size const begin, core::Size const end, pose::Pose &pose, TorsionFragmentLibrary const &lib, core::Size const desired_insert_pos)
 
std::ostream & operator<< (std::ostream &out, TorsionFragment const &f)
 
std::istream & operator>> (std::istream &data, TorsionFragment &f)
 
std::ostream & operator<< (std::ostream &out, SingleResidueTorsionFragmentLibrary const &lib)
 
std::istream & operator>> (std::istream &data, SingleResidueTorsionFragmentLibrary &lib)
 
std::ostream & operator<< (std::ostream &out, TorsionFragmentLibrary const &lib)
 
std::istream & operator>> (std::istream &data, TorsionFragmentLibrary &lib)
 
std::ostream & operator<< (std::ostream &out, FragLib const &lib)
 
std::istream & operator>> (std::istream &data, FragLib &lib)
 
void get_min_and_max_contigs (Sizes const &seg_in, core::Size &min_seg, core::Size &max_seg)
 
void insert_random_fragments_in_flexible_protein_regions (Sizes const &flex_protein, FragLib const &frag_lib, pose::Pose &pose)
 
void insert_random_fragments_in_flexible_protein_regions (utility::vector1< core::Size > const &flex_protein, FragLib const &frag_lib, core::pose::Pose &pose)
 
Real torsion_dev_score (Real const frag_angle, Real const target_angle, Real const min_dev, Real const max_dev)
 
void get_frags (core::Size const nfrags, std::string const &target_seq, std::string const &target_ss, core::Real const seq_weight, core::Real const ss_weight, bool const exclude_gly, bool const exclude_pro, bool const exclude_cis_peptides, utility::vector1< core::Size > const &homs_to_exclude, SingleResidueTorsionFragmentLibrary &library, core::Real const bb_weight=0.0, std::string const &target_bb=std::string())
 handles loading the vall if necessary More...
 
void get_frags (core::Size const nfrags, std::string const &target_seq, utility::vector1< std::map< char, core::Real > > const &target_ss,core::Real const seq_weight, core::Real const ss_weight, bool const exclude_gly, bool const exclude_pro, bool const exclude_cis_peptides, utility::vector1< core::Size > const &homs_to_exclude, SingleResidueTorsionFragmentLibrary &library, core::Real const bb_weight=0.0, std::string const &target_bb=std::string())
 handles loading the vall if necessary More...
 
void get_cheating_frags (core::Size const nfrags, std::string const &target_seq, std::string const &target_ss, utility::vector1< Real > const &target_phi, utility::vector1< Real > const &target_psi, utility::vector1< Real > const &target_omega, Real const seq_weight, Real const ss_weight, Real const torsion_weight, Real const min_torsion_dev, Real const max_torsion_dev, utility::vector1< core::Size > const &homs_to_exclude, SingleResidueTorsionFragmentLibrary &library)
 
void dump_vall_fasta (std::string const &fasta_filename)
 
char torsion2big_bin (core::Real const phi, core::Real const psi, core::Real const omega)
 
void get_cheating_frags (core::Size const nfrags, std::string const &target_seq, std::string const &target_ss, utility::vector1< core::Real > const &target_phi, utility::vector1< core::Real > const &target_psi, utility::vector1< core::Real > const &target_omega, core::Real const seq_weight, core::Real const ss_weight, core::Real const torsion_weight, core::Real const min_torsion_dev, core::Real const max_torsion_dev, utility::vector1< core::Size > const &homs_to_exclude, SingleResidueTorsionFragmentLibrary &library)
 

Variables

utility::vector1< core::Size >
const 
empty_size_list
 

Typedef Documentation

typedef utility::pointer::shared_ptr< FragLib const > protocols::frags::FragLibCOP
typedef utility::pointer::shared_ptr< FragLib > protocols::frags::FragLibOP
using protocols::frags::Sizes = typedef utility::vector1<core::Size>
typedef utility::pointer::shared_ptr< TorsionFragmentLibrary const > protocols::frags::TorsionFragmentLibraryCOP
typedef utility::pointer::shared_ptr< TorsionFragmentLibrary > protocols::frags::TorsionFragmentLibraryOP
typedef utility::pointer::shared_ptr< TorsionFragmentMover > protocols::frags::TorsionFragmentMoverOP
typedef utility::pointer::shared_ptr< TorsionFragment > protocols::frags::TorsionFragmentOP

Function Documentation

void protocols::frags::add_vall_cheating_fragments ( utility::vector1< core::Size > const &  frag_sizes,
core::Size const  nfrags,
pose::Pose const &  pose,
core::kinematics::MoveMap const &  mm,
std::string const &  secstruct,
Real const  seq_weight,
Real const  ss_weight,
Real const  torsion_weight,
Real const  min_torsion_dev,
Real const  max_torsion_dev,
FragLib &  frag_lib,
utility::vector1< core::Size > const &  homs_to_exclude 
)
void protocols::frags::add_vall_fragments ( utility::vector1< core::Size > const &  frag_sizes,
core::Size const  nfrags,
pose::Pose const &  pose,
core::kinematics::MoveMap const &  mm,
std::string const &  secstruct,
Real const  seq_weight,
Real const  ss_weight,
FragLib &  frag_lib,
utility::vector1< core::Size > const &  homs_to_exclude,
Real const  bb_weight,
std::string const &  bigbins,
std::string const &  inputseq 
)
void protocols::frags::add_vall_fragments ( utility::vector1< core::Size > const &  frag_sizes,
core::Size const  nfrags,
pose::Pose const &  pose,
core::kinematics::MoveMap const &  mm,
utility::vector1< std::map< char, core::Real > > const &  target_ss,
Real const  seq_weight,
Real const  ss_weight,
FragLib &  frag_lib,
utility::vector1< core::Size > const &  homs_to_exclude,
Real const  bb_weight,
std::string const &  bigbins,
std::string const &  inputseq 
)
void protocols::frags::dump_vall_fasta ( std::string const &  fasta_filename)
void protocols::frags::fill_in_gaps ( core::Size const  nfrags,
pose::Pose const &  pose,
std::string const &  secstruct,
Real const  seq_weight,
Real const  ss_weight,
FragLib &  frag_lib,
utility::vector1< core::Size > const &  homs_to_exclude,
bool const  allow_uninitialized_secstruct 
)

Fill in gaps in the FragLib with fragments chosen from the vall

Note
Does not change the size of any of the individual fragment libraries

References protocols::frags::FragLib::frag_sizes(), get_frags(), core::conformation::Residue::is_protein(), protocols::frags::FragLib::library(), core::pose::Pose::residue(), core::pose::Pose::sequence(), core::pose::Pose::size(), and TR().

void protocols::frags::get_cheating_frags ( core::Size const  nfrags,
std::string const &  target_seq,
std::string const &  target_ss,
utility::vector1< core::Real > const &  target_phi,
utility::vector1< core::Real > const &  target_psi,
utility::vector1< core::Real > const &  target_omega,
core::Real const  seq_weight,
core::Real const  ss_weight,
core::Real const  torsion_weight,
core::Real const  min_torsion_dev,
core::Real const  max_torsion_dev,
utility::vector1< core::Size > const &  homs_to_exclude,
SingleResidueTorsionFragmentLibrary &  library 
)
void protocols::frags::get_cheating_frags ( core::Size const  nfrags,
std::string const &  target_seq,
std::string const &  target_ss,
utility::vector1< Real > const &  target_phi,
utility::vector1< Real > const &  target_psi,
utility::vector1< Real > const &  target_omega,
Real const  seq_weight,
Real const  ss_weight,
Real const  torsion_weight,
Real const  min_torsion_dev,
Real const  max_torsion_dev,
utility::vector1< core::Size > const &  homs_to_exclude,
SingleResidueTorsionFragmentLibrary &  library 
)
void protocols::frags::get_frags ( core::Size const  nfrags,
std::string const &  target_seq,
std::string const &  target_ss,
Real const  seq_weight,
Real const  ss_weight,
bool const  exclude_gly,
bool const  exclude_pro,
bool const  exclude_cis_peptides,
utility::vector1< core::Size > const &  homs_to_exclude,
SingleResidueTorsionFragmentLibrary &  library,
Real const  bb_weight,
std::string const &  target_bb 
)

handles loading the vall if necessary

Handles loading default vall, then calls above routine

References protocols::frags::VallData::get_frags().

Referenced by add_vall_fragments(), and fill_in_gaps().

void protocols::frags::get_frags ( core::Size const  nfrags,
std::string const &  target_seq,
utility::vector1< std::map< char, core::Real > > const &  target_ss,
Real const  seq_weight,
Real const  ss_weight,
bool const  exclude_gly,
bool const  exclude_pro,
bool const  exclude_cis_peptides,
utility::vector1< core::Size > const &  homs_to_exclude,
SingleResidueTorsionFragmentLibrary &  library,
Real const  bb_weight,
std::string const &  target_bb 
)

handles loading the vall if necessary

Handles loading default vall, then calls above routine

References protocols::frags::VallData::get_frags().

void protocols::frags::get_min_and_max_contigs ( Sizes const &  seg_in,
core::Size min_seg,
core::Size max_seg 
)

Determine length of shortest and longest contiguous segments

Referenced by insert_random_fragments_in_flexible_protein_regions().

template<class T >
bool protocols::frags::has_element ( utility::vector1< T > const &  v,
T const &  t 
)

these will go into a helper file soon

References protocols::hybridization::t.

Referenced by insert_random_fragments_in_flexible_protein_regions().

template<class T >
bool protocols::frags::has_element ( T const &  t,
utility::vector1< T > const &  v 
)

never can remember the order...

References protocols::hybridization::t.

void protocols::frags::heap_down ( ObjexxFCL::FArray1A_int  heap,
ObjexxFCL::FArray1A_float  coheap,
int  index_in 
)
void protocols::frags::heap_down ( FArray1A_int  heap,
FArray1A_float  coheap,
int  index_in 
)
Parameters
heap- [in/out]? - convert to zero offset matrix
coheap- [in/out]? -
index_in- [in/out]? -
Global Read:
Global Write:
Remarks
References:
Author

Referenced by heap_extract(), and heap_replace().

void protocols::frags::heap_extract ( ObjexxFCL::FArray1A_int  heap,
ObjexxFCL::FArray1A_float  coheap,
int &  val,
float &  coval,
bool err 
)
void protocols::frags::heap_extract ( FArray1A_int  heap,
FArray1A_float  coheap,
int &  val,
float &  coval,
bool err 
)

modifes heap and last_val return val and err.

Parameters
heap- [in/out]? - convert to zero offset matrix
coheap- [in/out]? -
val- [in/out]? -
coval- [in/out]? -
err- [in/out]? -
Global Read:
Global Write:
Remarks
References:
Author

References heap_down().

Referenced by protocols::frags::VallData::get_cheating_frags(), protocols::frags::RMSVallData::get_frags(), and protocols::frags::VallData::get_frags().

void protocols::frags::heap_init ( ObjexxFCL::FArray1A_int  heap,
ObjexxFCL::FArray1A_float  coheap,
int  max_items 
)
void protocols::frags::heap_init ( FArray1A_int  heap,
FArray1A_float  coheap,
int  max_items 
)

sets up an empty heap and stores the dimensioned size

Parameters
heap- [in/out]? -
coheap- [in/out]? -
max_items- [in/out]? -
Global Read:
Global Write:
Remarks
References:
Author

Referenced by protocols::frags::VallData::get_cheating_frags(), protocols::frags::RMSVallData::get_frags(), and protocols::frags::VallData::get_frags().

void protocols::frags::heap_insert ( ObjexxFCL::FArray1A_int  heap,
ObjexxFCL::FArray1A_float  coheap,
int  val,
float  coval,
bool err 
)
void protocols::frags::heap_insert ( FArray1A_int  heap,
FArray1A_float  coheap,
int  val,
float  coval,
bool err 
)

modifes heap and last_dummy, inserts val, returns err requires heap_max to be previously set via heap_init

Parameters
heap- [in/out]? - convert to zero offset matrix
coheap- [in/out]? -
val- [in/out]? -
coval- [in/out]? -
err- [in/out]? -
Global Read:
Global Write:
Remarks
References:
Author

References heap_replace(), heap_up(), and protocols::hybridization::val.

Referenced by protocols::frags::VallData::get_cheating_frags(), protocols::frags::RMSVallData::get_frags(), and protocols::frags::VallData::get_frags().

void protocols::frags::heap_replace ( ObjexxFCL::FArray1A_int  heap,
ObjexxFCL::FArray1A_float  coheap,
int  val,
float  coval 
)
void protocols::frags::heap_replace ( FArray1A_int  heap,
FArray1A_float  coheap,
int  val,
float  coval 
)
Parameters
heap- [in/out]? - convert to zero offset matrix
coheap- [in/out]? -
val- [in/out]? -
coval- [in/out]? -
Global Read:
Global Write:
Remarks
References:
Author

References heap_down(), and protocols::hybridization::val.

Referenced by heap_insert().

void protocols::frags::heap_up ( ObjexxFCL::FArray1A_int  heap,
ObjexxFCL::FArray1A_float  coheap,
int &  index_in 
)
void protocols::frags::heap_up ( FArray1A_int  heap,
FArray1A_float  coheap,
int &  index_in 
)
Parameters
heap- [in/out]? - convert to zero offset matrix
coheap- [in/out]? -
index_in- [in/out]? -
Global Read:
Global Write:
Remarks
References:
Author

Referenced by heap_insert().

void protocols::frags::insert_fragment ( core::Size const  begin,
core::Size const  end,
pose::Pose pose,
TorsionFragmentLibrary const &  lib,
core::Size const  desired_insert_pos 
)

if desired_insert_pos is specified, the fragmnet will be inserted into that position. Otherwise, it will be randonly inserted into a region between "begin" and "end". The fragment insetion is done by changing according backbone torsions in the pose and "refolding" will be handled by the Pose before next time XYZ coordindates are being accessed. PBMOD: allow for cases where not all windows between begin and end have fragments by adding a while loop within which insert_pos is chosen and the frag depth is checked.

References protocols::frags::TorsionFragmentLibrary::size(), core::pose::Pose::size(), and TR().

Referenced by insert_random_fragments_in_flexible_protein_regions().

void protocols::frags::insert_random_fragments_in_flexible_protein_regions ( utility::vector1< core::Size > const &  flex_protein,
FragLib const &  frag_lib,
core::pose::Pose pose 
)
void protocols::frags::insert_random_fragments_in_flexible_protein_regions ( Sizes const &  flex_protein,
FragLib const &  frag_lib,
pose::Pose pose 
)
std::ostream & protocols::frags::operator<< ( std::ostream &  out,
TorsionFragment const &  f 
)
std::ostream & protocols::frags::operator<< ( std::ostream &  out,
SingleResidueTorsionFragmentLibrary const &  lib 
)
std::ostream & protocols::frags::operator<< ( std::ostream &  out,
TorsionFragmentLibrary const &  lib 
)
std::ostream & protocols::frags::operator<< ( std::ostream &  out,
FragLib const &  lib 
)
std::istream & protocols::frags::operator>> ( std::istream &  data,
TorsionFragment &  f 
)
std::istream & protocols::frags::operator>> ( std::istream &  data,
SingleResidueTorsionFragmentLibrary &  lib 
)
std::istream & protocols::frags::operator>> ( std::istream &  data,
TorsionFragmentLibrary &  lib 
)
std::istream & protocols::frags::operator>> ( std::istream &  data,
FragLib &  lib 
)
FragLibOP protocols::frags::setup_vall_cheating_fragments ( utility::vector1< core::Size > const &  frag_sizes,
core::Size const  nfrags,
pose::Pose const &  pose,
core::kinematics::MoveMap const &  mm,
std::string const &  secstruct,
Real const  seq_weight,
Real const  ss_weight,
Real const  torsion_weight,
Real const  min_torsion_dev,
Real const  max_torsion_dev,
utility::vector1< core::Size > const &  homs_to_exclude 
)
FragLibOP protocols::frags::setup_vall_fragments ( utility::vector1< core::Size > const &  frag_sizes,
core::Size const  nfrags,
pose::Pose const &  pose,
core::kinematics::MoveMap const &  mm,
std::string const &  secstruct,
Real const  seq_weight,
Real const  ss_weight,
utility::vector1< core::Size > const &  homs_to_exclude 
)

References add_vall_fragments().

bool protocols::frags::ss_length_check ( core::Size const  min_len_helix,
core::Size const  min_len_strand,
core::pose::Pose const &  pose 
)
char protocols::frags::torsion2big_bin ( core::Real const  phi,
core::Real const  psi,
core::Real const  omega 
)
inline
Real protocols::frags::torsion_dev_score ( Real const  frag_angle,
Real const  target_angle,
Real const  min_dev,
Real const  max_dev 
)
static basic::Tracer protocols::frags::TR ( "protocols.frags.TorsionFragment"  )
static

Variable Documentation

utility::vector1< core::Size > const protocols::frags::empty_size_list