core::pack::rotamer_set::ContinuousRotamerSet Class Reference

#include <ContinuousRotamerSet.hh>

Inheritance diagram for core::pack::rotamer_set::ContinuousRotamerSet:

Public Member Functions
	ContinuousRotamerSet ()
virtual	~ContinuousRotamerSet ()
void	build_rotamers (pose::Pose const &pose, Size resid, task::PackerTask const &task)
Size	get_n_residue_types () const
Size	get_n_sampling_rotamers_for_rotblock (Size which_restype) const
Size	get_n_baserotamers_for_rotblock (Size which_restype) const
Size	get_rotblock_index_for_sampling_rotamer (Size which_rotamer) const
	Rotamers i to i+j of all the same residue type are grouped together. This function returns the index of the residue type in a contiguous block of rotamers. E.g. rotamers 100 to 120 might all be lysine rotamers, and might be the 8th residue type, with the first 7 residue types spanning rotamers 1 to 99. If new lysine rotamers are appended to the end of the rotamer set, they are considered to be in a separate residue type block. Lysine rotamers 200 to 210 might be block 15 while lysine rotamers 100 to 120 are still block 7. More...
Size	num_base_rotamers_total () const
Size	num_sampling_rotamers_total () const
Size	sampling_id_for_current_rotamer () const
utility::vector1< Vector > const &	current_rotamer_coords () const
Size	resid () const
chemical::ResidueTypeCOP	restype_for_rotblock (Size rotblock) const
dunbrack::DunbrackRotamerSampleData const &	baserotamer_data (Size aa_ind, Size rotid_for_aa) const
Size	pick_baserotamer_from_rotblock (Size aa_ind, Real rand_btw_0_and_1) const

Private Types
typedef utility::pointer::ReferenceCount	parent
typedef utility::vector1 < dunbrack::DunbrackRotamerSampleData >	RotamersForAA

Private Member Functions
void	determine_rotcounts_for_restype (Size)

Private Attributes
Size	resid_
Size	input_rotamer_samplingrot_index_
Size	input_rotamer_rotblock_
utility::vector1< Vector >	input_rotamer_coords_
Size	n_restypes_
utility::vector1< chemical::AA >	aa_for_rotblock_
utility::vector1 < chemical::ResidueTypeCOP >	restype_for_rotblock_
Size	n_baserots_total_
utility::vector1< Size >	n_baserotamers_for_rotblock_
utility::vector1< Size >	baserots_offsets_
utility::vector1< Size >	aa_block_for_baserotamer_
Size	n_samplingrots_total_
utility::vector1< Size >	n_samplingrots_for_rotblock_
utility::vector1< Size >	samplingrot_offsets_
utility::vector1< Size >	aa_block_for_samplingrotamer_
utility::vector1< RotamersForAA >	samples_

Member Typedef Documentation

typedef utility::pointer::ReferenceCount core::pack::rotamer_set::ContinuousRotamerSet::parent

private

typedef utility::vector1< dunbrack::DunbrackRotamerSampleData > core::pack::rotamer_set::ContinuousRotamerSet::RotamersForAA

private

Constructor & Destructor Documentation

core::pack::rotamer_set::ContinuousRotamerSet::ContinuousRotamerSet

(

)

core::pack::rotamer_set::ContinuousRotamerSet::~ContinuousRotamerSet ( )

virtual

Member Function Documentation

dunbrack::DunbrackRotamerSampleData const & core::pack::rotamer_set::ContinuousRotamerSet::baserotamer_data	(	Size	aa_ind,
		Size	rotid_for_aa
	)		const

References samples_.

Referenced by core::pack::assign_random_continuous_rotamer().

void core::pack::rotamer_set::ContinuousRotamerSet::build_rotamers	(	pose::Pose const &	pose,
		Size	resid,
		task::PackerTask const &	task
	)

References aa_block_for_baserotamer_, aa_block_for_samplingrotamer_, aa_for_rotblock_, core::pack::task::ResidueLevelTask::allowed_residue_types_begin(), core::pack::task::ResidueLevelTask::allowed_residue_types_end(), baserots_offsets_, determine_rotcounts_for_restype(), core::pack::task::ResidueLevelTask::include_current(), input_rotamer_coords_, input_rotamer_rotblock_, input_rotamer_samplingrot_index_, core::chemical::ResidueType::is_beta_aa(), n_baserotamers_for_rotblock_, n_baserots_total_, n_restypes_, n_samplingrots_for_rotblock_, n_samplingrots_total_, core::conformation::Residue::natoms(), core::pose::Pose::phi(), core::pose::Pose::psi(), resid(), resid_, core::pose::Pose::residue(), core::pack::task::PackerTask::residue_task(), core::pose::Pose::residue_type(), restype_for_rotblock_, samples_, samplingrot_offsets_, core::pose::Pose::theta(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

utility::vector1< Vector > const & core::pack::rotamer_set::ContinuousRotamerSet::current_rotamer_coords

(

)

const

References input_rotamer_coords_.

Referenced by core::pack::assign_random_continuous_rotamer().

void core::pack::rotamer_set::ContinuousRotamerSet::determine_rotcounts_for_restype ( Size  restype_ind )

private

References input_rotamer_rotblock_, n_baserotamers_for_rotblock_, n_samplingrots_for_rotblock_, restype_for_rotblock_, and samples_.

Referenced by build_rotamers().

Size core::pack::rotamer_set::ContinuousRotamerSet::get_n_baserotamers_for_rotblock

(

Size

which_restype

)

const

References samples_.

Referenced by core::pack::assign_random_continuous_rotamer().

Size core::pack::rotamer_set::ContinuousRotamerSet::get_n_residue_types

(

)

const

Note, its entirely possible for two residue types to be the "same amino acid", e.g. HIS and HIS_D.

References n_restypes_.

Size core::pack::rotamer_set::ContinuousRotamerSet::get_n_sampling_rotamers_for_rotblock

(

Size

which_restype

)

const

References n_samplingrots_for_rotblock_.

Size core::pack::rotamer_set::ContinuousRotamerSet::get_rotblock_index_for_sampling_rotamer

(

Size

which_rotamer

)

const

Rotamers i to i+j of all the same residue type are grouped together. This function returns the index of the residue type in a contiguous block of rotamers. E.g. rotamers 100 to 120 might all be lysine rotamers, and might be the 8th residue type, with the first 7 residue types spanning rotamers 1 to 99. If new lysine rotamers are appended to the end of the rotamer set, they are considered to be in a separate residue type block. Lysine rotamers 200 to 210 might be block 15 while lysine rotamers 100 to 120 are still block 7.

References aa_block_for_samplingrotamer_.

Referenced by core::pack::assign_random_continuous_rotamer().

Size core::pack::rotamer_set::ContinuousRotamerSet::num_base_rotamers_total

(

)

const

References n_baserots_total_.

Size core::pack::rotamer_set::ContinuousRotamerSet::num_sampling_rotamers_total

(

)

const

References n_baserots_total_.

Size core::pack::rotamer_set::ContinuousRotamerSet::pick_baserotamer_from_rotblock	(	Size	aa_ind,
		Real	rand_btw_0_and_1
	)		const

References samples_.

Referenced by core::pack::assign_random_continuous_rotamer().

Size core::pack::rotamer_set::ContinuousRotamerSet::resid

(

)

const

References resid_.

Referenced by build_rotamers().

chemical::ResidueTypeCOP core::pack::rotamer_set::ContinuousRotamerSet::restype_for_rotblock

(

Size

rotblock

)

const

References restype_for_rotblock_.

Referenced by core::pack::assign_random_continuous_rotamer().

Size core::pack::rotamer_set::ContinuousRotamerSet::sampling_id_for_current_rotamer

(

)

const

References input_rotamer_samplingrot_index_.

Referenced by core::pack::assign_random_continuous_rotamer().

Member Data Documentation

utility::vector1< Size > core::pack::rotamer_set::ContinuousRotamerSet::aa_block_for_baserotamer_

private

Referenced by build_rotamers().

utility::vector1< Size > core::pack::rotamer_set::ContinuousRotamerSet::aa_block_for_samplingrotamer_

private

Referenced by build_rotamers(), and get_rotblock_index_for_sampling_rotamer().

utility::vector1< chemical::AA > core::pack::rotamer_set::ContinuousRotamerSet::aa_for_rotblock_

private

Referenced by build_rotamers().

utility::vector1< Size > core::pack::rotamer_set::ContinuousRotamerSet::baserots_offsets_

private

Referenced by build_rotamers().

utility::vector1< Vector > core::pack::rotamer_set::ContinuousRotamerSet::input_rotamer_coords_

private

Referenced by build_rotamers(), and current_rotamer_coords().

Size core::pack::rotamer_set::ContinuousRotamerSet::input_rotamer_rotblock_

private

Referenced by build_rotamers(), and determine_rotcounts_for_restype().

Size core::pack::rotamer_set::ContinuousRotamerSet::input_rotamer_samplingrot_index_

private

Referenced by build_rotamers(), and sampling_id_for_current_rotamer().

utility::vector1< Size > core::pack::rotamer_set::ContinuousRotamerSet::n_baserotamers_for_rotblock_

private

Referenced by build_rotamers(), and determine_rotcounts_for_restype().

Size core::pack::rotamer_set::ContinuousRotamerSet::n_baserots_total_

private

Referenced by build_rotamers(), num_base_rotamers_total(), and num_sampling_rotamers_total().

Size core::pack::rotamer_set::ContinuousRotamerSet::n_restypes_

private

Referenced by build_rotamers(), and get_n_residue_types().

utility::vector1< Size > core::pack::rotamer_set::ContinuousRotamerSet::n_samplingrots_for_rotblock_

private

Referenced by build_rotamers(), determine_rotcounts_for_restype(), and get_n_sampling_rotamers_for_rotblock().

Size core::pack::rotamer_set::ContinuousRotamerSet::n_samplingrots_total_

private

Referenced by build_rotamers().

Size core::pack::rotamer_set::ContinuousRotamerSet::resid_

private

Referenced by build_rotamers(), and resid().

utility::vector1< chemical::ResidueTypeCOP > core::pack::rotamer_set::ContinuousRotamerSet::restype_for_rotblock_

private

Referenced by build_rotamers(), determine_rotcounts_for_restype(), and restype_for_rotblock().

utility::vector1< RotamersForAA > core::pack::rotamer_set::ContinuousRotamerSet::samples_

private

Referenced by baserotamer_data(), build_rotamers(), determine_rotcounts_for_restype(), get_n_baserotamers_for_rotblock(), and pick_baserotamer_from_rotblock().

utility::vector1< Size > core::pack::rotamer_set::ContinuousRotamerSet::samplingrot_offsets_

private

Referenced by build_rotamers().

---

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

• src/core/pack/rotamer_set/ContinuousRotamerSet.hh
• src/core/pack/rotamer_set/ContinuousRotamerSet.cc