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

#include <ContinuousRotamerSet.hh>

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

Collaboration 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_

Detailed Description

Definition at line 45 of file ContinuousRotamerSet.hh.

Member Typedef Documentation

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

private

Definition at line 48 of file ContinuousRotamerSet.hh.

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

private

Definition at line 49 of file ContinuousRotamerSet.hh.

Constructor & Destructor Documentation

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

(

)

Definition at line 42 of file ContinuousRotamerSet.cc.

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

virtual

Definition at line 51 of file ContinuousRotamerSet.cc.

Member Function Documentation

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

Definition at line 223 of file ContinuousRotamerSet.cc.

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
	)

Definition at line 53 of file ContinuousRotamerSet.cc.

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::dunbrack::RotamerLibrary::get_instance(), core::pack::dunbrack::RotamerLibrary::get_rsd_library(), core::pack::task::ResidueLevelTask::include_current(), input_rotamer_coords_, input_rotamer_rotblock_, input_rotamer_samplingrot_index_, 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_, and core::conformation::Residue::xyz().

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

(

)

const

Definition at line 206 of file ContinuousRotamerSet.cc.

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

Definition at line 243 of file ContinuousRotamerSet.cc.

References input_rotamer_rotblock_, n_baserotamers_for_rotblock_, n_samplingrots_for_rotblock_, restype_for_rotblock_, samples_, and core::io::serialization::size().

Referenced by build_rotamers().

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

(

Size

which_restype)

const

Definition at line 182 of file ContinuousRotamerSet.cc.

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.

Definition at line 163 of file ContinuousRotamerSet.cc.

References n_restypes_.

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

(

Size

which_restype)

const

Definition at line 176 of file ContinuousRotamerSet.cc.

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.

Definition at line 188 of file ContinuousRotamerSet.cc.

References aa_block_for_samplingrotamer_.

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

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

(

)

const

Definition at line 194 of file ContinuousRotamerSet.cc.

References n_baserots_total_.

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

(

)

const

Definition at line 197 of file ContinuousRotamerSet.cc.

References n_baserots_total_.

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

Definition at line 229 of file ContinuousRotamerSet.cc.

References samples_.

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

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

(

)

const

Definition at line 212 of file ContinuousRotamerSet.cc.

References resid_.

Referenced by build_rotamers().

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

(

Size

rotblock)

const

Definition at line 215 of file ContinuousRotamerSet.cc.

References restype_for_rotblock_.

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

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

(

)

const

Definition at line 200 of file ContinuousRotamerSet.cc.

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

Definition at line 124 of file ContinuousRotamerSet.hh.

Referenced by build_rotamers().

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

private

Definition at line 129 of file ContinuousRotamerSet.hh.

Referenced by build_rotamers(), and get_rotblock_index_for_sampling_rotamer().

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

private

Definition at line 118 of file ContinuousRotamerSet.hh.

Referenced by build_rotamers().

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

private

Definition at line 123 of file ContinuousRotamerSet.hh.

Referenced by build_rotamers().

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

private

Definition at line 115 of file ContinuousRotamerSet.hh.

Referenced by build_rotamers(), and current_rotamer_coords().

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

private

Definition at line 114 of file ContinuousRotamerSet.hh.

Referenced by build_rotamers(), and determine_rotcounts_for_restype().

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

private

Definition at line 113 of file ContinuousRotamerSet.hh.

Referenced by build_rotamers(), and sampling_id_for_current_rotamer().

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

private

Definition at line 122 of file ContinuousRotamerSet.hh.

Referenced by build_rotamers(), and determine_rotcounts_for_restype().

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

private

Definition at line 121 of file ContinuousRotamerSet.hh.

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

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

private

Definition at line 117 of file ContinuousRotamerSet.hh.

Referenced by build_rotamers(), and get_n_residue_types().

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

private

Definition at line 127 of file ContinuousRotamerSet.hh.

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

Definition at line 126 of file ContinuousRotamerSet.hh.

Referenced by build_rotamers().

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

private

Definition at line 111 of file ContinuousRotamerSet.hh.

Referenced by build_rotamers(), and resid().

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

private

Definition at line 119 of file ContinuousRotamerSet.hh.

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

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

private

Definition at line 131 of file ContinuousRotamerSet.hh.

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

Definition at line 128 of file ContinuousRotamerSet.hh.

Referenced by build_rotamers().

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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