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

MutTyp

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

init()

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

static

initializes the static members of this class

Parameters

[in]

stripped

true if one wants to output stripped constellations; false if one wants to output full constellations.

References stripped(), stripped_, and zeroed_occ_.

list_allowable_mutations()

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_aa

the given amino acid type.

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

strip_atoms()

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]	pose	pose to which the residue belongs.
[in]	seqpos	index of the residue in the pose.
[in]	target_aa	amino 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(), core::conformation::Residue::atom_index(), 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().

stripped()

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

inlinestatic

References stripped_.

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

zero_occ_bb_h()

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]	ps	pose to which the residue belongs.
[in]	seqpos	index of the residue in the pose.

References core::conformation::Residue::atom_is_backbone(), core::conformation::Residue::atom_is_hydrogen(), core::conformation::Residue::natoms(), core::pose::Pose::pdb_info(), and core::pose::Pose::residue().

Referenced by zero_occ_for_deleted_atoms().

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]	pose	pose to which the residue belongs.
[in]	seqpos	index of the residue in the pose.
[in]	target_aa	amino acid type that the residue has to be mutated into.

References core::pose::Pose::aa(), core::conformation::Residue::atom_index(), core::conformation::Residue::natoms(), 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

stripped_

bool protocols::constel::SingResCnlCrea::stripped_

staticprivate

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

Referenced by init(), and stripped().

zeroed_occ_

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().

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

• src/protocols/constel/SingResCnlCrea.hh
• src/protocols/constel/SingResCnlCrea.cc