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protocols::simple_filters::SheetFilter Class Reference

#include <SheetFilter.hh>

Inheritance diagram for protocols::simple_filters::SheetFilter:
Inheritance graph
[legend]

Public Member Functions

 SheetFilter ()
 c-tor and d-tor More...
 
 ~SheetFilter () override=default
 
filters::FilterOP clone () const override
 
filters::FilterOP fresh_instance () const override
 
bool apply (core::pose::Pose const &pose) const override
 Returns true if the given pose passes the filter, false otherwise. More...
 
std::string name () const override
 
- Public Member Functions inherited from protocols::simple_filters::AbinitioBaseFilter
 AbinitioBaseFilter ()
 c-tor and d-tor More...
 
 ~AbinitioBaseFilter () override=default
 
std::string get_protein_sstype (core::pose::Pose const &pose) const
 
- Public Member Functions inherited from protocols::filters::Filter
 Filter ()
 
 Filter (std::string const &)
 
 Filter (Filter const &)
 
 ~Filter () override
 
virtual void report (std::ostream &, core::pose::Pose const &) const
 
virtual core::Real report_sm (core::pose::Pose const &) const
 used to report filter internals through a score or silent file More...
 
virtual std::string get_type () const
 
std::string get_user_defined_name () const
 
void set_user_defined_name (std::string const &name)
 
virtual void clear ()
 used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual More...
 
virtual void parse_my_tag (utility::tag::TagCOP, basic::datacache::DataMap &, Filters_map const &, moves::Movers_map const &, core::pose::Pose const &)
 
virtual core::Real score (core::pose::Pose &pose)
 
virtual bool filter_provides_citation_info () const
 Does this filter provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 		provide_citation_info () const
 Provide the citation. More...
 
virtual bool filter_is_unpublished () const
 Does this filter indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 		provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Attributes

static int const max_nstr = 50
 

Private Member Functions

void ingo_diamers (int const &nres, ObjexxFCL::FArray1A_int strnm, int natm, ObjexxFCL::FArray2D_float const &atmps, ObjexxFCL::FArray1D_int &rnm, ObjexxFCL::FArray1D_int &indC, ObjexxFCL::FArray1D_int &indN, ObjexxFCL::FArray2A_float strdm, ObjexxFCL::FArray1A_int inddm) const
 Private: Methods ///. More...
 
void ingo_find_dir (int shnm, int hm, int &nstr, ObjexxFCL::FArray1A_int slct, ObjexxFCL::FArray1A_int order, ObjexxFCL::FArray1A_int strlbl, ObjexxFCL::FArray2A_float strdr, ObjexxFCL::FArray1A_int directions) const
 THIS PROGRAM FINDS THE DIRECTIONS OF THE STRANDS IN THE SHEETS. More...
 
void ingo_find_ord (int shnm, int hm, int &nstr, ObjexxFCL::FArray1A_int strlbl, ObjexxFCL::FArray2A_float dstrmin, float ngbhct, ObjexxFCL::FArray1A_int order, ObjexxFCL::FArray1A_int sequence, ObjexxFCL::FArray1A_int slct, int &rubbish) const
 THIS PROGRAM FINDS THE ORDER OF THE STRANDS IN THE SHEETS. More...
 
void ingo_hand (int const k, int const hm, ObjexxFCL::FArray1A_int stpppt, ObjexxFCL::FArray1A_int strtpt, int const str1, int const str2, ObjexxFCL::FArray1A_int order, ObjexxFCL::FArray2A_float strdr, int const nstr, int const nres, ObjexxFCL::FArray1A_int sequence, ObjexxFCL::FArray1A_int directions, ObjexxFCL::FArray1A_int scstr, ObjexxFCL::FArray2A_float lctn, bool const use_whole_helix, int &rubbish) const
 THIS PROGRAM CHECKS THE HANDEDNESS OF A SHEET. More...
 
void ingo_ident_sheets (int &nstr, ObjexxFCL::FArray2A_float dstrmin, float ngbhct, ObjexxFCL::FArray2A_int strprs, int &nsht, ObjexxFCL::FArray1A_int strsht, ObjexxFCL::FArray1A_int strlbl, int &rubbish) const
 THIS PROGRAM IDENTIFIES THE SHEETS. More...
 
void ingo_lnl (int hm, ObjexxFCL::FArray1A_int order, int &nloc, int &nnloc) const
 THIS PROGRAM DETERMINES THE NUMBER OF LOCALS AND NONLOCAL STRAND PAIRS. More...
 
void ingo_locations (int const &nres, int natm, ObjexxFCL::FArray1D_int &indCA, ObjexxFCL::FArray2D_float const &atmps, ObjexxFCL::FArray2A_float lctn) const
 THIS FUNCTION DETERMINES THE CA LOCATION OF EACH RESIDUE. More...
 
void ingo_number_of_strands (int const &nres, ObjexxFCL::FArray1A_int scstr, int &nstr) const
 THIS FUNCTION COUNTS THE NUBER OF STRANDS IN THE PROTEIN/DECOY. More...
 
void ingo_proper_sheets (int &nstr, int &nsht, float ngbhct, ObjexxFCL::FArray2A_float dstrmin, ObjexxFCL::FArray2A_float strdr, ObjexxFCL::FArray1A_int strsht, ObjexxFCL::FArray1A_int strlbl, int &rubbish, float &maxdist, float &mindotprodabs, ObjexxFCL::FArray1A_int strtpt, ObjexxFCL::FArray1A_int stpppt, ObjexxFCL::FArray2A_int locdsm, ObjexxFCL::FArray2A_float lctn, int const &nres) const
 THIS PROGRAM CHECKS THE CONFIGURATION OF THE STRANDS FROM THE SECONDARY STRUCTURE PREDICTION. More...
 
void ingo_sheet_stuff (int const &nres, ObjexxFCL::FArray1A_int scstr, int natm, ObjexxFCL::FArray2D_float const &atmps, ObjexxFCL::FArray1D_int &indN, ObjexxFCL::FArray1D_int &indCA, ObjexxFCL::FArray1D_int &indC, ObjexxFCL::FArray1D_int &rnm, float ngbhct, int &nstr, int &nsht, float &maxdt, float &mindp, int &nloc, int &nnloc, int &rubbish) const
 THIS FUNCTION SPITS OUT THE BETA SHEET INFORMATION. More...
 
void ingo_start_stop (int const &nres, ObjexxFCL::FArray1A_int scstr, int &nstr, ObjexxFCL::FArray1A_int strnm, ObjexxFCL::FArray1A_int strtpt, ObjexxFCL::FArray1A_int stpppt) const
 THIS FUNCTION IDENTIFIES THE START AND END POINTS OF THE STRANDS. More...
 
void ingo_strand_dirs (int const &nres, int &nstr, ObjexxFCL::FArray1A_int strtpt, ObjexxFCL::FArray1A_int stpppt, ObjexxFCL::FArray2A_float lctn, ObjexxFCL::FArray2A_float strdr) const
 THIS PROGRAM DETERMINES THE STRAND DIRECTIONS. More...
 
void ingo_strand_dists_min (int const &nres, int &nstr, ObjexxFCL::FArray1A_int inddm, ObjexxFCL::FArray1A_int strnm, ObjexxFCL::FArray2A_float strdm, ObjexxFCL::FArray2A_float dstrmin, ObjexxFCL::FArray2A_int locdsm) const
 THIS PROGRAM DETERMINES THE MINIMUM STRAND DISTANCES. More...
 
void ingo_clean_ss (int const &nres, ObjexxFCL::FArray1A_int scstr) const
 THIS PROGRAM CLEANS THE SECONDARY STRUCTURE OF DECOYS. More...
 

Private Attributes

float handedness_score_
 initialized_ is true if init() has been called, false otherwise. More...
 

Additional Inherited Members

- Protected Attributes inherited from protocols::simple_filters::AbinitioBaseFilter
int max_helix_length_
 
core::Real max_helix_fraction_
 
int beta_
 
float beta_ratio_
 
std::string sstype_
 
- Protected Attributes inherited from protocols::filters::Filter
std::string scorename_
 

Constructor & Destructor Documentation

protocols::simple_filters::SheetFilter::SheetFilter ( )
inline

c-tor and d-tor

protocols::simple_filters::SheetFilter::~SheetFilter ( )
overridedefault

Member Function Documentation

bool protocols::simple_filters::SheetFilter::apply ( core::pose::Pose const &  pose) const
overridevirtual

Returns true if the given pose passes the filter, false otherwise.

Implements protocols::simple_filters::AbinitioBaseFilter.

References core::conformation::Residue::atom(), core::pose::Pose::residue(), core::pose::Pose::secstruct(), core::pose::Pose::size(), core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().

filters::FilterOP protocols::simple_filters::SheetFilter::clone ( ) const
inlineoverridevirtual

Implements protocols::simple_filters::AbinitioBaseFilter.

filters::FilterOP protocols::simple_filters::SheetFilter::fresh_instance ( ) const
inlineoverridevirtual

Implements protocols::simple_filters::AbinitioBaseFilter.

void protocols::simple_filters::SheetFilter::ingo_clean_ss ( int const &  nres,
ObjexxFCL::FArray1A_int  scstr 
) const
private

THIS PROGRAM CLEANS THE SECONDARY STRUCTURE OF DECOYS.

car notes from ingo

$$$ If I understand my notes $$$correctly, the big trouble makers were mostly the single strand residue $$$that popped up quite frequently. So they are cleaned up. Also, if a strand $$$is interrupted by one non-strand residue, that gets turned into a strand $$$residue too, so two short strands get turned into one long strand. That $$$worked the best, according to my notes.

$$$The secstr cleanup doesn't contain one of the issues that David had $$$mentioned: if you have strands like that: $$$ $$$ xxxxxxxx xxxxxxxx $$$ xxxxxxxxxxxxxxxxxx $$$ $$$That is, there's a hole in one strand and it pops up as two strands, $$$paired up with another strand. A single residue missing gets cought by the $$$secstr cleaner, so I think most cases are taken care of in the beginning. $$$There should be something in there as well that catches two or three $$$residues missing. But that couldn't occur of course before you identified $$$sheets. I didn't see anything in the ident_sheets function (the most $$$obvious place where something like that could be).

Parameters
nres- [in/out]? -
scstr- [in/out]? -
Global Read:
Global Write:
Remarks
References:
Author
void protocols::simple_filters::SheetFilter::ingo_diamers ( int const &  nres,
ObjexxFCL::FArray1A_int  strnm,
int  natm,
ObjexxFCL::FArray2D_float const &  atmps,
ObjexxFCL::FArray1D_int &  rnm,
ObjexxFCL::FArray1D_int &  indC,
ObjexxFCL::FArray1D_int &  indN,
ObjexxFCL::FArray2A_float  strdm,
ObjexxFCL::FArray1A_int  inddm 
) const
private

Private: Methods ///.

THIS PROGRAM IDENTIFIES THE STRAND DIAMERS

Parameters
nres- [in/out]? -
strnm- [in/out]? -
natm- [in/out]? -
atmps- [in/out]? -
rnm- [in/out]? -
indC- [in/out]? -
indN- [in/out]? -
strdm- [in/out]? -
inddm- [in/out]? -
Global Read:
Global Write:
Remarks
References:
Author
void protocols::simple_filters::SheetFilter::ingo_find_dir ( int  shnm,
int  hm,
int &  nstr,
ObjexxFCL::FArray1A_int  slct,
ObjexxFCL::FArray1A_int  order,
ObjexxFCL::FArray1A_int  strlbl,
ObjexxFCL::FArray2A_float  strdr,
ObjexxFCL::FArray1A_int  directions 
) const
private

THIS PROGRAM FINDS THE DIRECTIONS OF THE STRANDS IN THE SHEETS.

Parameters
shnm- [in/out]? -
hm- [in/out]? -
nstr- [in/out]? -
slct- [in/out]? -
order- [in/out]? -
strlbl- [in/out]? -
strdr- [in/out]? -
proper- [in/out]? - Not used
directions- [in/out]? -
Global Read:
Global Write:
Remarks
References:
Author

References protocols::forge::methods::order().

void protocols::simple_filters::SheetFilter::ingo_find_ord ( int  shnm,
int  hm,
int &  nstr,
ObjexxFCL::FArray1A_int  strlbl,
ObjexxFCL::FArray2A_float  dstrmin,
float  ngbhct,
ObjexxFCL::FArray1A_int  order,
ObjexxFCL::FArray1A_int  sequence,
ObjexxFCL::FArray1A_int  slct,
int &  rubbish 
) const
private

THIS PROGRAM FINDS THE ORDER OF THE STRANDS IN THE SHEETS.

Parameters
shnm- [in/out]? -
hm- [in/out]? -
nstr- [in/out]? -
strlbl- [in/out]? -
dstrmin- [in/out]? -
ngbhct- [in/out]? -
order- [in/out]? -
sequence- [in/out]? -
slct- [in/out]? -
rubbish- [in/out]? -
Global Read:
Global Write:
Remarks
References:
Author

References protocols::forge::methods::order().

void protocols::simple_filters::SheetFilter::ingo_hand ( int const  k,
int const  hm,
ObjexxFCL::FArray1A_int  stpppt,
ObjexxFCL::FArray1A_int  strtpt,
int const  str1,
int const  str2,
ObjexxFCL::FArray1A_int  order,
ObjexxFCL::FArray2A_float  strdr,
int const  nstr,
int const  nres,
ObjexxFCL::FArray1A_int  sequence,
ObjexxFCL::FArray1A_int  directions,
ObjexxFCL::FArray1A_int  scstr,
ObjexxFCL::FArray2A_float  lctn,
bool const  use_whole_helix,
int &  rubbish 
) const
private

THIS PROGRAM CHECKS THE HANDEDNESS OF A SHEET.

Parameters
k- [in/out]? -
shnm- [in/out]? -
hm- [in/out]? -
stpppt- [in/out]? -
strtpt- [in/out]? -
str1- [in/out]? -
str2- [in/out]? -
order- [in/out]? -
strdr- [in/out]? -
nstr- [in/out]? -
nres- [in/out]? -
sequence- [in/out]? -
directions- [in/out]? -
scstr- [in/out]? -
lctn- [in/out]? -
rubbish- [in/out]? -
Global Read:
Global Write:
Remarks
References:
Author
void protocols::simple_filters::SheetFilter::ingo_ident_sheets ( int &  nstr,
ObjexxFCL::FArray2A_float  dstrmin,
float  ngbhct,
ObjexxFCL::FArray2A_int  strprs,
int &  nsht,
ObjexxFCL::FArray1A_int  strsht,
ObjexxFCL::FArray1A_int  strlbl,
int &  rubbish 
) const
private

THIS PROGRAM IDENTIFIES THE SHEETS.

Parameters
nres- [in/out]? -
nstr- [in/out]? -
dstrmin- [in/out]? -
ngbhct- [in/out]? -
strprs- [in/out]? -
nsht- [in/out]? -
strsht- [in/out]? -
strlbl- [in/out]? -
rubbish- [in/out]? -
Global Read:
Global Write:
Remarks
References:
Author

References protocols::mean_field::min().

void protocols::simple_filters::SheetFilter::ingo_lnl ( int  hm,
ObjexxFCL::FArray1A_int  order,
int &  nloc,
int &  nnloc 
) const
private

THIS PROGRAM DETERMINES THE NUMBER OF LOCALS AND NONLOCAL STRAND PAIRS.

Parameters
hm- [in/out]? -
order- [in/out]? -
nloc- [in/out]? -
nnloc- [in/out]? -
Global Read:
Global Write:
Remarks
References:
Author

References protocols::forge::methods::order().

void protocols::simple_filters::SheetFilter::ingo_locations ( int const &  nres,
int  natm,
ObjexxFCL::FArray1D_int &  indCA,
ObjexxFCL::FArray2D_float const &  atmps,
ObjexxFCL::FArray2A_float  lctn 
) const
private

THIS FUNCTION DETERMINES THE CA LOCATION OF EACH RESIDUE.

Parameters
nres- [in/out]? -
natm- [in/out]? -
indCA- [in/out]? -
atmps- [in/out]? -
lctn- [in/out]? -
Global Read:
Global Write:
Remarks
References:
Author
void protocols::simple_filters::SheetFilter::ingo_number_of_strands ( int const &  nres,
ObjexxFCL::FArray1A_int  scstr,
int &  nstr 
) const
private

THIS FUNCTION COUNTS THE NUBER OF STRANDS IN THE PROTEIN/DECOY.

Parameters
nres- [in/out]? -
scstr- [in/out]? -
nstr- [in/out]? -
Global Read:
Global Write:
Remarks
References:
Author
void protocols::simple_filters::SheetFilter::ingo_proper_sheets ( int &  nstr,
int &  nsht,
float  ngbhct,
ObjexxFCL::FArray2A_float  dstrmin,
ObjexxFCL::FArray2A_float  strdr,
ObjexxFCL::FArray1A_int  strsht,
ObjexxFCL::FArray1A_int  strlbl,
int &  rubbish,
float &  maxdist,
float &  mindotprodabs,
ObjexxFCL::FArray1A_int  strtpt,
ObjexxFCL::FArray1A_int  stpppt,
ObjexxFCL::FArray2A_int  locdsm,
ObjexxFCL::FArray2A_float  lctn,
int const &  nres 
) const
private

THIS PROGRAM CHECKS THE CONFIGURATION OF THE STRANDS FROM THE SECONDARY STRUCTURE PREDICTION.

Parameters
nstr- [in/out]? -
nsht- [in/out]? -
ngbhct- [in/out]? -
dotcut- [in/out]? -
dstrmin- [in/out]? -
strdr- [in/out]? -
strsht- [in/out]? -
strlbl- [in/out]? -
rubbish- [in/out]? -
maxdist- [in/out]? -
mindotprodabs- [in/out]? -
strtpt- [in/out]? -
stpppt- [in/out]? -
locdsm- [in/out]? -
lctn- [in/out]? -
nres- [in/out]? -
Global Read:
Global Write:
Remarks
References:
Author

References protocols::mean_field::max().

void protocols::simple_filters::SheetFilter::ingo_sheet_stuff ( int const &  nres,
ObjexxFCL::FArray1A_int  scstr,
int  natm,
ObjexxFCL::FArray2D_float const &  atmps,
ObjexxFCL::FArray1D_int &  indN,
ObjexxFCL::FArray1D_int &  indCA,
ObjexxFCL::FArray1D_int &  indC,
ObjexxFCL::FArray1D_int &  rnm,
float  ngbhct,
int &  nstr,
int &  nsht,
float &  maxdt,
float &  mindp,
int &  nloc,
int &  nnloc,
int &  rubbish 
) const
private

THIS FUNCTION SPITS OUT THE BETA SHEET INFORMATION.

Parameters
nres- [in/out]? -
scstr- [in/out]? -
natm- [in/out]? -
atmps- [in/out]? -
indN- [in/out]? -
indCA- [in/out]? -
indC- [in/out]? -
rnm- [in/out]? -
ngbhct- [in/out]? -
dotcut- [in/out]? -
nstr- [in/out]? -
nsht- [in/out]? -
maxdt- [in/out]? -
mindp- [in/out]? -
nloc- [in/out]? -
nnloc- [in/out]? -
rubbish- [in/out]? -
Global Read:
Global Write:
Remarks
References:
Author

References protocols::forge::methods::order().

void protocols::simple_filters::SheetFilter::ingo_start_stop ( int const &  nres,
ObjexxFCL::FArray1A_int  scstr,
int &  nstr,
ObjexxFCL::FArray1A_int  strnm,
ObjexxFCL::FArray1A_int  strtpt,
ObjexxFCL::FArray1A_int  stpppt 
) const
private

THIS FUNCTION IDENTIFIES THE START AND END POINTS OF THE STRANDS.

Parameters
nres- [in/out]? -
scstr- [in/out]? -
nstr- [in/out]? -
strnm- [in/out]? -
strtpt- [in/out]? -
stpppt- [in/out]? -
Global Read:
Global Write:
Remarks
References:
Author

References protocols::loops::start.

void protocols::simple_filters::SheetFilter::ingo_strand_dirs ( int const &  nres,
int &  nstr,
ObjexxFCL::FArray1A_int  strtpt,
ObjexxFCL::FArray1A_int  stpppt,
ObjexxFCL::FArray2A_float  lctn,
ObjexxFCL::FArray2A_float  strdr 
) const
private

THIS PROGRAM DETERMINES THE STRAND DIRECTIONS.

Parameters
nres- [in/out]? -
nstr- [in/out]? -
strtpt- [in/out]? -
stpppt- [in/out]? -
lctn- [in/out]? -
strdr- [in/out]? -
Global Read:
Global Write:
Remarks
References:
Author
void protocols::simple_filters::SheetFilter::ingo_strand_dists_min ( int const &  nres,
int &  nstr,
ObjexxFCL::FArray1A_int  inddm,
ObjexxFCL::FArray1A_int  strnm,
ObjexxFCL::FArray2A_float  strdm,
ObjexxFCL::FArray2A_float  dstrmin,
ObjexxFCL::FArray2A_int  locdsm 
) const
private

THIS PROGRAM DETERMINES THE MINIMUM STRAND DISTANCES.

Parameters
nres- [in/out]? -
nstr- [in/out]? -
inddm- [in/out]? -
strnm- [in/out]? -
strdm- [in/out]? -
dstrmin- [in/out]? -
locdsm- [in/out]? -
Global Read:
Global Write:
Remarks
References:
Author
std::string protocols::simple_filters::SheetFilter::name ( ) const
inlineoverridevirtual

Reimplemented from protocols::simple_filters::AbinitioBaseFilter.

Member Data Documentation

float protocols::simple_filters::SheetFilter::handedness_score_
mutableprivate

initialized_ is true if init() has been called, false otherwise.

int const protocols::simple_filters::SheetFilter::max_nstr = 50
static
The documentation for this class was generated from the following files:
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