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Static Public Member Functions | Private Types | Static Private Member Functions | Static Private Attributes | List of all members
protocols::constel::SingResCnlCrea Class Reference

#include <SingResCnlCrea.hh>

Static Public Member Functions

static bool stripped ()
 
static void init (bool stripped)
 initializes the static members of this class More...
 
static utility::vector1< char > list_allowable_mutations (char const starting_aa)
 Lists the amino acid types that a given amino acid type can be reduced to. More...
 
static void zero_occ_for_deleted_atoms (core::pose::Pose &pose, core::Size seqpos, char const target_aa)
 sets occupancy to zero for a residue's non-constellation atoms. More...
 
static void strip_atoms (core::pose::Pose &pose, core::Size seqpos, char const target_aa)
 sets occupancy to zero for constellation atoms that are not to be printed on output. More...
 

Private Types

typedef std::pair< char, char > MutTyp
 mutation-specific lists of constellation atoms whose occupancy must be zeroed when the constellation is output to file More...
 

Static Private Member Functions

static void zero_occ_bb_h (core::pose::Pose &ps, core::Size seqpos)
 sets occupancy to 0 for a residue's backbone atoms and hydrogen atoms. Sets occupancy to 1 for the residue's remaining atoms. More...
 

Static Private Attributes

static bool stripped_
 True if constellations must be output to file in stripped form. More...
 
static std::map< MutTyp,
std::string > 
zeroed_occ_
 mutation-specific lists of constellation atoms whose occupancy must be zeroed when the constellation is output to file. More...
 

Member Typedef Documentation

typedef std::pair<char, char> protocols::constel::SingResCnlCrea::MutTyp
private

mutation-specific lists of constellation atoms whose occupancy must be zeroed when the constellation is output to file

Member Function Documentation

void protocols::constel::SingResCnlCrea::init ( bool  stripped)
static

initializes the static members of this class

Parameters
[in]strippedtrue if one wants to output stripped constellations; false if one wants to output full constellations.

References stripped_, and zeroed_occ_.

utility::vector1< char > protocols::constel::SingResCnlCrea::list_allowable_mutations ( char const  starting_aa)
static

Lists the amino acid types that a given amino acid type can be reduced to.

Returns the list of amino acid types that a given amino acid type can be reduced to.

Parameters
[in]starting_aathe given amino acid type.

Referenced by protocols::constel::pair_constel_set_idx2(), and protocols::constel::triple_constel_set_idx3().

void protocols::constel::SingResCnlCrea::strip_atoms ( core::pose::Pose pose,
core::Size  seqpos,
char const  target_aa 
)
static

sets occupancy to zero for constellation atoms that are not to be printed on output.

Parameters
[out]posepose to which the residue belongs.
[in]seqposindex of the residue in the pose.
[in]target_aaamino acid type that the residue has to be mutated into.

: it is assumed that function zero_occ_for_deleted_atoms(pose, seqpos, target_aa) was previously called.

References core::pose::Pose::aa(), protocols::motifs::mt(), core::chemical::oneletter_code_from_aa(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), protocols::constel::TR(), and zeroed_occ_.

Referenced by protocols::constel::out_pair_constel(), and protocols::constel::out_triple_constel().

static bool protocols::constel::SingResCnlCrea::stripped ( )
inlinestatic
void protocols::constel::SingResCnlCrea::zero_occ_bb_h ( core::pose::Pose ps,
core::Size  seqpos 
)
staticprivate

sets occupancy to 0 for a residue's backbone atoms and hydrogen atoms. Sets occupancy to 1 for the residue's remaining atoms.

Parameters
[in]pspose to which the residue belongs.
[in]seqposindex of the residue in the pose.

References core::pose::Pose::pdb_info(), and core::pose::Pose::residue().

Referenced by zero_occ_for_deleted_atoms().

void protocols::constel::SingResCnlCrea::zero_occ_for_deleted_atoms ( core::pose::Pose pose,
core::Size  seqpos,
char const  target_aa 
)
static

sets occupancy to zero for a residue's non-constellation atoms.

Sets occupancy to zero for a residue's non-constellation atoms.

Given a residue to be reduced to a smaller amino acid type, sets occupancy to zero for all atoms that are not to be printed (those forming the new residue too) and sets occupancy to 1 for all atoms that are to be printed (those forming the constellation).

Parameters
[out]posepose to which the residue belongs.
[in]seqposindex of the residue in the pose.
[in]target_aaamino acid type that the residue has to be mutated into.

References core::pose::Pose::aa(), core::chemical::oneletter_code_from_aa(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), protocols::constel::TR(), and zero_occ_bb_h().

Referenced by protocols::constel::pair_constel_set(), protocols::constel::pair_constel_set_idx2(), protocols::constel::target_constel(), and protocols::constel::triple_constel_set_idx3().

Member Data Documentation

bool protocols::constel::SingResCnlCrea::stripped_
staticprivate

True if constellations must be output to file in stripped form.

Referenced by init(), and stripped().

std::map< SingResCnlCrea::MutTyp, std::string > protocols::constel::SingResCnlCrea::zeroed_occ_
staticprivate

mutation-specific lists of constellation atoms whose occupancy must be zeroed when the constellation is output to file.

Referenced by init(), and strip_atoms().


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