#include <FlexbbRotamerSets.hh>

Inheritance diagram for protocols::flexpack::rotamer_set::FlexbbRotamerSets:

Collaboration diagram for protocols::flexpack::rotamer_set::FlexbbRotamerSets:

Public Types
typedef core::Size	Size

typedef core::PackerEnergy	PackerEnergy

typedef core::pose::Pose	Pose

typedef core::scoring::ScoreFunction	ScoreFunction

typedef core::scoring::methods::LongRangeTwoBodyEnergy	LongRangeTwoBodyEnergy

typedef core::pack::task::PackerTaskCOP	PackerTaskCOP

Public Member Functions
	FlexbbRotamerSets (PackerTaskCOP task)

virtual	~FlexbbRotamerSets ()

void	set_frames (Pose const &pose, utility::vector1< core::fragment::FrameCOP > const &frames)
	function to set up the internal mapping data structures More...

core::graph::GraphOP	flexpack_neighbor_graph (Pose const &pose, ScoreFunction const &sfxn, PackerTaskCOP task) const
	function to figure out the flexpack neighbor graph, see core::pack::create_packer_graph for fixbb version More...

core::Distance	determine_res_cb_deviation (Pose const &pose, Size resid) const
	function to determine the maximum deviation in the position of Cbs for the bbconfs of one residue This should use the "neighbor atom" instead of CB... CB exist for neither GLY nor non-protein residues. More...

void	build_rotamers (Pose const &pose, ScoreFunction const &sfxn, core::graph::Graph const &flexpack_neighbor_graph)

void	dump_pdbs (core::pose::Pose const &pose, std::string const &filename_base) const
	function to dump all the rotamer sets out to pdb files, more or less only used for debugging More...

void	precompute_energies (Pose const &pose, ScoreFunction const &sfxn, core::graph::GraphCOP flexpack_neighbor_graph, interaction_graph::FlexbbInteractionGraph &flexbb_ig) const

void	precompute_all_energies (Pose const &pose, ScoreFunction const &sfxn, core::graph::GraphCOP flexpack_neighbor_graph, interaction_graph::PrecomputedFlexbbInteractionGraph &flexbb_ig) const

void	compute_one_body_energies_for_otf_ig (Pose const &pose, ScoreFunction const &sfxn, core::graph::GraphCOP flexpack_neighbor_graph, interaction_graph::OTFFlexbbInteractionGraph &flexbb_ig) const

virtual core::uint	nrotamers () const
	Virtual functions from base class. More...

virtual core::uint	nrotamers_for_moltenres (core::uint) const

virtual core::uint	nmoltenres () const

virtual core::uint	total_residue () const

virtual core::uint	moltenres_2_resid (core::uint) const

virtual core::uint	resid_2_moltenres (core::uint) const

virtual core::uint	moltenres_for_rotamer (core::uint) const

virtual core::uint	res_for_rotamer (core::uint) const

virtual core::conformation::ResidueCOP	rotamer (core::uint) const

virtual core::conformation::ResidueCOP	rotamer_for_moltenres (core::uint moltenres_id, core::uint rotamerid) const

virtual core::uint	nrotamer_offset_for_moltenres (core::uint) const

virtual core::uint	rotid_on_moltenresidue (core::uint rotid) const
	convert rotid in full rotamer enumeration into rotamer id on its source residue More...

virtual core::uint	moltenres_rotid_2_rotid (core::uint moltenres, core::uint moltenresrotid) const
	convert moltenres rotid to id in full rotamer enumeration More...

Size	nmolten_res () const

Size	nrotamers_for_res (Size resid) const
	The total number of rotamers across all residues and all backbone conformations. More...

Size	nbbconfs_for_moltenres (core::Size moltenres) const

Size	nbbconfs_for_flexseg (core::Size flex_segment_id) const

Size	nbackbone_conformations () const
	the "total" number of backbone conformations, counting the input conformation for all flexible segments (but not counting the input conformation for residues with only a single backbone conformation) More...

Size	nbbconfs_for_res (core::Size resid) const

utility::vector1< Size > const &	num_states_per_backbone_for_moltenres (Size moltenres) const

Size	nrotamers_for_moltenres_in_bbconf (Size moltenres, Size bbconf) const

Size	nrotamers_for_resid_in_bbconf (Size resid, Size bbconf) const

Size	global_rotid_start_for_moltenres_in_bbconf (Size moltenres, Size bbconf) const

Size	local_rotid_start_for_moltenres_in_bbconf (Size moltenres, Size bbconf) const

Size	local_rotid_for_rotamer_on_moltenres (Size moltenres, Size rotamer_id) const
	Input: rotid in global enumeration, Output rotid in local enumeration. More...

Size	local_rotid_for_rotamer (Size rotamer_id) const

Size	nflexible_segments () const

Size	flexsegment_start_moltenresid (Size flex_segment_id) const

Size	flexsegment_stop_moltenresid (Size flex_segment_id) const

Size	flexsegment_size (Size flex_segment_id) const

Size	flexsegment_start_resid (Size flex_segment_id) const

Size	flexsegment_stop_resid (Size flex_segment_id) const

Size	flexsegid_for_moltenres (Size molten_resid) const

Size	flexsegid_for_res (Size resid) const

bool	moltenres_part_of_flexsegment (Size molten_resid) const

bool	res_part_of_flexsegment (Size resid) const

FlexbbRotamerSetCOP	rotset_for_moltenres (Size molten_resid, Size bbconf=1) const

FlexbbRotamerSetCOP	rotset_for_residue (Size resid, Size bbconf=1) const

core::conformation::ResidueCOP	rotamer_for_residue (Size resid, Size rotindex_on_residue) const
	Rotamer indexed locally. More...

core::conformation::Residue const &	backbone_for_resid_bbconf (Size resid, Size bbconf) const
	Rotamer indexed locally. More...

core::conformation::Residue const &	backbone_for_moltenres_bbconf (Size moltenres, Size bbconf) const

Size	bbconf_for_rotamer (Size rotamer_id) const
	rotamer_id in the global enumeration of rotamers. More...

Size	bbconf_for_rotamer_on_moltenres (Size moltenres, Size rotamer_id) const

bool	rotamers_on_same_bbconf (Size moltenres, Size rot1, Size rot2) const
	Do two rotamers originate from the same backbone conformation? Local enumeration for both rot1 and rot2; rot1 and rot2 must be rotamers of the same molten residue. More...

Public Member Functions inherited from core::pack::rotamer_set::RotamerSetsBase
	RotamerSetsBase ()

virtual	~RotamerSetsBase ()

Protected Member Functions
void	build_residue_vector_from_fragment (Pose &pose, core::fragment::FrameCOP frame, Size frag_num, utility::vector1< core::conformation::ResidueOP > &fragment_res)

Private Member Functions
void	update_offset_data ()

void	compute_sr_one_body_energies_for_flexsets (Size lowermoltenres, Size uppermoltenres, utility::vector1< utility::vector1< Size > > const &regular_representatives, utility::vector1< utility::vector1< Size > > const &proline_representatives, utility::vector1< utility::vector1< Size > > const &glycine_representatives, Pose const &pose, ScoreFunction const &sfxn, interaction_graph::OTFFlexbbInteractionGraph &flexbb_ig) const

void	compute_onebody_interactions_with_background (Size moltenres, Pose const &pose, ScoreFunction const &sfxn, core::graph::GraphCOP flexpack_neighbor_graph, interaction_graph::FlexbbInteractionGraph &flexbb_ig) const

Private Attributes
Size	nmoltenres_

Size	total_residue_

Size	nbbconfs_

PackerTaskCOP	task_

utility::vector1 < utility::vector1 < rotamer_set::FlexbbRotamerSetOP > >	rotamers_

Size	nrotamers_

utility::vector1< Size >	nrotamers_for_moltenres_

utility::vector1< Size >	moltenres_2_resid_

utility::vector1< Size >	resid_2_moltenres_

utility::vector1< Size >	moltenres_for_rotamer_

utility::vector1 < utility::vector1< Size > >	bbconf_for_rotamer_of_moltenres_

utility::vector1 < utility::vector1 < core::conformation::ResidueCOP > >	conformations_for_flexible_segments_

utility::vector1< std::pair < Size, Size > >	flexsegment_span_

utility::vector1< Size >	nbbconfs_for_flexseg_

utility::vector1< Size >	moltenres_2_flexseg_

utility::vector1< Size >	nrotoffset_for_moltenres_

utility::vector1 < utility::vector1< Size > >	nrots_for_moltenres_bbconf_

utility::vector1 < utility::vector1< Size > >	nrotoffset_for_moltenres_bbconf_

Detailed Description

Definition at line 52 of file FlexbbRotamerSets.hh.

Member Typedef Documentation

typedef core::scoring::methods::LongRangeTwoBodyEnergy protocols::flexpack::rotamer_set::FlexbbRotamerSets::LongRangeTwoBodyEnergy

Definition at line 59 of file FlexbbRotamerSets.hh.

typedef core::PackerEnergy protocols::flexpack::rotamer_set::FlexbbRotamerSets::PackerEnergy

Definition at line 56 of file FlexbbRotamerSets.hh.

typedef core::pack::task::PackerTaskCOP protocols::flexpack::rotamer_set::FlexbbRotamerSets::PackerTaskCOP

Definition at line 60 of file FlexbbRotamerSets.hh.

typedef core::pose::Pose protocols::flexpack::rotamer_set::FlexbbRotamerSets::Pose

Definition at line 57 of file FlexbbRotamerSets.hh.

typedef core::scoring::ScoreFunction protocols::flexpack::rotamer_set::FlexbbRotamerSets::ScoreFunction

Definition at line 58 of file FlexbbRotamerSets.hh.

typedef core::Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::Size

Definition at line 55 of file FlexbbRotamerSets.hh.

Constructor & Destructor Documentation

protocols::flexpack::rotamer_set::FlexbbRotamerSets::FlexbbRotamerSets ( PackerTaskCOP task)

Definition at line 68 of file FlexbbRotamerSets.cc.

protocols::flexpack::rotamer_set::FlexbbRotamerSets::~FlexbbRotamerSets ( )

virtual

Definition at line 73 of file FlexbbRotamerSets.cc.

Member Function Documentation

core::conformation::Residue const& protocols::flexpack::rotamer_set::FlexbbRotamerSets::backbone_for_moltenres_bbconf	(	Size	moltenres,
		Size	bbconf
	)		const

inline

Definition at line 321 of file FlexbbRotamerSets.hh.

References conformations_for_flexible_segments_.

core::conformation::Residue const& protocols::flexpack::rotamer_set::FlexbbRotamerSets::backbone_for_resid_bbconf	(	Size	resid,
		Size	bbconf
	)		const

inline

Rotamer indexed locally.

Rotamer indexed globally.

Definition at line 317 of file FlexbbRotamerSets.hh.

References conformations_for_flexible_segments_, and resid_2_moltenres_.

Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::bbconf_for_rotamer ( Size rotamer_id) const

inline

rotamer_id in the global enumeration of rotamers.

Definition at line 332 of file FlexbbRotamerSets.hh.

References bbconf_for_rotamer_of_moltenres_, local_rotid_for_rotamer_on_moltenres(), and moltenres_for_rotamer_.

Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::bbconf_for_rotamer_on_moltenres	(	Size	moltenres,
		Size	rotamer_id
	)		const

inline

Definition at line 338 of file FlexbbRotamerSets.hh.

References bbconf_for_rotamer_of_moltenres_.

void protocols::flexpack::rotamer_set::FlexbbRotamerSets::build_residue_vector_from_fragment	(	Pose &	pose,
		core::fragment::FrameCOP	frame,
		core::Size	frag_num,
		utility::vector1< core::conformation::ResidueOP > &	fragment_res
	)

protected

Definition at line 474 of file FlexbbRotamerSets.cc.

References core::pose::Pose::residue().

Referenced by set_frames().

void protocols::flexpack::rotamer_set::FlexbbRotamerSets::build_rotamers	(	Pose const &	pose,
		ScoreFunction const &	sfxn,
		core::graph::Graph const &	flexpack_neighbor_graph
	)

Definition at line 240 of file FlexbbRotamerSets.cc.

References conformations_for_flexible_segments_, dump_pdbs(), moltenres_2_resid_, nmoltenres_, rotamers_, task_, and update_offset_data().

void protocols::flexpack::rotamer_set::FlexbbRotamerSets::compute_one_body_energies_for_otf_ig	(	Pose const &	pose,
		ScoreFunction const &	sfxn,
		core::graph::GraphCOP	flexpack_neighbor_graph,
		interaction_graph::OTFFlexbbInteractionGraph &	flexbb_ig
	)		const

Definition at line 622 of file FlexbbRotamerSets.cc.

References core::chemical::aa_gly, core::chemical::aa_pro, core::pack::interaction_graph::InteractionGraphBase::add_edge(), compute_onebody_interactions_with_background(), compute_sr_one_body_energies_for_flexsets(), core::sequence::end, core::pose::Pose::energies(), core::pack::interaction_graph::InteractionGraphBase::get_edge_exists(), core::scoring::Energies::long_range_container(), core::scoring::ScoreFunction::long_range_energies_begin(), core::scoring::ScoreFunction::long_range_energies_end(), moltenres_2_resid_, nbbconfs_for_moltenres(), nmoltenres_, protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::note_long_range_interactions_exist_for_edge(), resid_2_moltenres_, and rotamers_.

Referenced by precompute_energies().

void protocols::flexpack::rotamer_set::FlexbbRotamerSets::compute_onebody_interactions_with_background	(	Size	moltenres,
		Pose const &	pose,
		ScoreFunction const &	sfxn,
		core::graph::GraphCOP	flexpack_neighbor_graph,
		interaction_graph::FlexbbInteractionGraph &	flexbb_ig
	)		const

private

Definition at line 951 of file FlexbbRotamerSets.cc.

References core::pack::interaction_graph::InteractionGraphBase::add_to_nodes_one_body_energy(), core::scoring::methods::n_energy_methods, nbbconfs_for_moltenres(), nrotamers_for_moltenres(), nrotoffset_for_moltenres_, nrotoffset_for_moltenres_bbconf_, core::scoring::ScoreFunction::prepare_rotamers_for_packing(), rotamers_, and task_.

Referenced by compute_one_body_energies_for_otf_ig().

void protocols::flexpack::rotamer_set::FlexbbRotamerSets::compute_sr_one_body_energies_for_flexsets	(	Size	lowermoltenres,
		Size	uppermoltenres,
		utility::vector1< utility::vector1< Size > > const &	regular_representatives,
		utility::vector1< utility::vector1< Size > > const &	proline_representatives,
		utility::vector1< utility::vector1< Size > > const &	glycine_representatives,
		Pose const &	pose,
		ScoreFunction const &	sfxn,
		interaction_graph::OTFFlexbbInteractionGraph &	flexbb_ig
	)		const

private

Computes the backbone/backbone and backbone/sidechain energies for a pair of molten residues. The interactions are separated into three kinds of backbone types: regular backbones, proline backbones and glycine backbones. The different solvation for proline's backbone nitrogen makes the proline correction necessary; the new carbon-hbond term makes the glycine correction necessary.

Definition at line 747 of file FlexbbRotamerSets.cc.

References core::conformation::Residue::aa(), core::chemical::aa_gly, core::chemical::aa_pro, core::pack::interaction_graph::InteractionGraphBase::add_edge(), bbconf_for_rotamer_of_moltenres_, flexsegid_for_moltenres(), core::pack::rotamer_set::RotamerSets::get_bb_bbE(), core::pack::rotamer_set::RotamerSets::get_sc_bbE(), nbbconfs_for_moltenres(), core::conformation::Residue::nheavyatoms(), nrotamers_for_moltenres_, rotamer_for_moltenres(), rotamers_, protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::set_GlyCorrection_values_for_edge(), protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::set_ProCorrection_values_for_edge(), and core::conformation::Residue::xyz().

Referenced by compute_one_body_energies_for_otf_ig().

core::Distance protocols::flexpack::rotamer_set::FlexbbRotamerSets::determine_res_cb_deviation	(	Pose const &	pose,
		Size	resid
	)		const

function to determine the maximum deviation in the position of Cbs for the bbconfs of one residue This should use the "neighbor atom" instead of CB... CB exist for neither GLY nor non-protein residues.

Definition at line 212 of file FlexbbRotamerSets.cc.

References conformations_for_flexible_segments_, moltenres_2_resid_, core::conformation::Residue::nbr_atom(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by flexpack_neighbor_graph().

void protocols::flexpack::rotamer_set::FlexbbRotamerSets::dump_pdbs	(	core::pose::Pose const &	pose,
		std::string const &	filename_base
	)		const

function to dump all the rotamer sets out to pdb files, more or less only used for debugging

currently modelled after the core/pack/rotamer_set/RotamerSets dump_pdb function

Definition at line 288 of file FlexbbRotamerSets.cc.

References core::io::pdb::dump_pdb_residue(), nmoltenres_, core::pose::Pose::residue(), rotamers_, core::io::serialization::size(), task_, and core::pose::Pose::total_residue().

Referenced by build_rotamers().

core::graph::GraphOP protocols::flexpack::rotamer_set::FlexbbRotamerSets::flexpack_neighbor_graph	(	Pose const &	pose,
		ScoreFunction const &	sfxn,
		PackerTaskCOP	task
	)		const

function to figure out the flexpack neighbor graph, see core::pack::create_packer_graph for fixbb version

problem: Ca/Cb not fixed, so we need to add a certain distance to the interaction energies. this distance will depend on the average deviation of the CBs in the flexible segments for each residue

Definition at line 191 of file FlexbbRotamerSets.cc.

References core::pack::create_packer_graph(), determine_res_cb_deviation(), core::pack::find_residue_max_radii(), resid_2_moltenres_, and total_residue_.

Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::flexsegid_for_moltenres ( Size molten_resid) const

inline

Definition at line 283 of file FlexbbRotamerSets.hh.

References moltenres_2_flexseg_.

Referenced by compute_sr_one_body_energies_for_flexsets(), and protocols::flexpack::interaction_graph::FlexbbInteractionGraph::initialize().

Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::flexsegid_for_res ( Size resid) const

inline

Definition at line 287 of file FlexbbRotamerSets.hh.

References moltenres_2_flexseg_, and resid_2_moltenres_.

Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::flexsegment_size ( Size flex_segment_id) const

inline

Definition at line 271 of file FlexbbRotamerSets.hh.

References flexsegment_span_.

Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::flexsegment_start_moltenresid ( Size flex_segment_id) const

inline

Definition at line 263 of file FlexbbRotamerSets.hh.

References flexsegment_span_, and resid_2_moltenres_.

Referenced by protocols::flexpack::interaction_graph::FlexbbInteractionGraph::initialize().

Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::flexsegment_start_resid ( Size flex_segment_id) const

inline

Definition at line 275 of file FlexbbRotamerSets.hh.

References flexsegment_span_.

Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::flexsegment_stop_moltenresid ( Size flex_segment_id) const

inline

Definition at line 267 of file FlexbbRotamerSets.hh.

References flexsegment_span_, and resid_2_moltenres_.

Referenced by protocols::flexpack::interaction_graph::FlexbbInteractionGraph::initialize().

Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::flexsegment_stop_resid ( Size flex_segment_id) const

inline

Definition at line 279 of file FlexbbRotamerSets.hh.

References flexsegment_span_.

Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::global_rotid_start_for_moltenres_in_bbconf	(	Size	moltenres,
		Size	bbconf
	)		const

inline

Definition at line 235 of file FlexbbRotamerSets.hh.

References nrotoffset_for_moltenres_bbconf_.

Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::local_rotid_for_rotamer ( Size rotamer_id) const

inline

Definition at line 255 of file FlexbbRotamerSets.hh.

References moltenres_for_rotamer_, and nrotoffset_for_moltenres_.

Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::local_rotid_for_rotamer_on_moltenres	(	Size	moltenres,
		Size	rotamer_id
	)		const

inline

Input: rotid in global enumeration, Output rotid in local enumeration.

Definition at line 250 of file FlexbbRotamerSets.hh.

References nrotoffset_for_moltenres_.

Referenced by bbconf_for_rotamer().

Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::local_rotid_start_for_moltenres_in_bbconf	(	Size	moltenres,
		Size	bbconf
	)		const

inline

Definition at line 239 of file FlexbbRotamerSets.hh.

References nrotoffset_for_moltenres_, and nrotoffset_for_moltenres_bbconf_.

Referenced by protocols::flexpack::interaction_graph::FlexbbInteractionGraph::initialize().

core::uint protocols::flexpack::rotamer_set::FlexbbRotamerSets::moltenres_2_resid ( core::uint moltres) const

virtual

Implements core::pack::rotamer_set::RotamerSetsBase.

Definition at line 402 of file FlexbbRotamerSets.cc.

References moltenres_2_resid_.

core::uint protocols::flexpack::rotamer_set::FlexbbRotamerSets::moltenres_for_rotamer ( core::uint rotid) const

virtual

Implements core::pack::rotamer_set::RotamerSetsBase.

Definition at line 416 of file FlexbbRotamerSets.cc.

References moltenres_for_rotamer_.

bool protocols::flexpack::rotamer_set::FlexbbRotamerSets::moltenres_part_of_flexsegment ( Size molten_resid) const

inline

Definition at line 291 of file FlexbbRotamerSets.hh.

References moltenres_2_flexseg_.

core::uint protocols::flexpack::rotamer_set::FlexbbRotamerSets::moltenres_rotid_2_rotid	(	core::uint	moltenres,
		core::uint	moltenresrotid
	)		const

virtual

convert moltenres rotid to id in full rotamer enumeration

Implements core::pack::rotamer_set::RotamerSetsBase.

Definition at line 467 of file FlexbbRotamerSets.cc.

FlexbbRotamerSets::Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::nbackbone_conformations ( ) const

the "total" number of backbone conformations, counting the input conformation for all flexible segments (but not counting the input conformation for residues with only a single backbone conformation)

Definition at line 180 of file FlexbbRotamerSets.cc.

References nbbconfs_.

Referenced by protocols::flexpack::interaction_graph::FlexbbInteractionGraph::initialize().

Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::nbbconfs_for_flexseg ( core::Size flex_segment_id) const

inline

Definition at line 209 of file FlexbbRotamerSets.hh.

References nbbconfs_for_flexseg_.

core::Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::nbbconfs_for_moltenres ( core::Size moltenres) const

Definition at line 493 of file FlexbbRotamerSets.cc.

References moltenres_2_flexseg_, and nbbconfs_for_flexseg_.

Referenced by compute_one_body_energies_for_otf_ig(), compute_onebody_interactions_with_background(), compute_sr_one_body_energies_for_flexsets(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::initialize(), and nbbconfs_for_res().

core::Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::nbbconfs_for_res ( core::Size resid) const

Definition at line 501 of file FlexbbRotamerSets.cc.

References nbbconfs_for_moltenres(), and resid_2_moltenres_.

Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::nflexible_segments ( ) const

inline

Definition at line 259 of file FlexbbRotamerSets.hh.

References flexsegment_span_.

Referenced by protocols::flexpack::interaction_graph::FlexbbInteractionGraph::initialize().

Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::nmolten_res ( ) const

inline

Definition at line 180 of file FlexbbRotamerSets.hh.

References nmoltenres_.

core::uint protocols::flexpack::rotamer_set::FlexbbRotamerSets::nmoltenres ( ) const

virtual

Implements core::pack::rotamer_set::RotamerSetsBase.

Definition at line 391 of file FlexbbRotamerSets.cc.

References nmoltenres_.

Referenced by protocols::flexpack::interaction_graph::FlexbbIGFactory::create_flexbb_interaction_graph(), and protocols::flexpack::interaction_graph::FlexbbInteractionGraph::initialize().

core::uint protocols::flexpack::rotamer_set::FlexbbRotamerSets::nrotamer_offset_for_moltenres ( core::uint moltres) const

virtual

Implements core::pack::rotamer_set::RotamerSetsBase.

Definition at line 450 of file FlexbbRotamerSets.cc.

References nrotoffset_for_moltenres_.

core::uint protocols::flexpack::rotamer_set::FlexbbRotamerSets::nrotamers ( ) const

virtual

Virtual functions from base class.

Implements core::pack::rotamer_set::RotamerSetsBase.

Definition at line 385 of file FlexbbRotamerSets.cc.

References nrotamers_.

core::uint protocols::flexpack::rotamer_set::FlexbbRotamerSets::nrotamers_for_moltenres ( core::uint moltres) const

virtual

Implements core::pack::rotamer_set::RotamerSetsBase.

Definition at line 386 of file FlexbbRotamerSets.cc.

References nrotamers_for_moltenres_.

Referenced by compute_onebody_interactions_with_background(), and protocols::flexpack::interaction_graph::FlexbbInteractionGraph::initialize().

Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::nrotamers_for_moltenres_in_bbconf	(	Size	moltenres,
		Size	bbconf
	)		const

inline

Definition at line 227 of file FlexbbRotamerSets.hh.

References nrots_for_moltenres_bbconf_.

Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::nrotamers_for_res ( Size resid) const

inline

The total number of rotamers across all residues and all backbone conformations.

Definition at line 202 of file FlexbbRotamerSets.hh.

References nrotamers_for_moltenres_, and resid_2_moltenres_.

Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::nrotamers_for_resid_in_bbconf	(	Size	resid,
		Size	bbconf
	)		const

inline

Definition at line 231 of file FlexbbRotamerSets.hh.

References nrots_for_moltenres_bbconf_, and resid_2_moltenres_.

utility::vector1< Size > const& protocols::flexpack::rotamer_set::FlexbbRotamerSets::num_states_per_backbone_for_moltenres ( Size moltenres) const

inline

Definition at line 222 of file FlexbbRotamerSets.hh.

References nrots_for_moltenres_bbconf_.

Referenced by protocols::flexpack::interaction_graph::FlexbbInteractionGraph::initialize().

void protocols::flexpack::rotamer_set::FlexbbRotamerSets::precompute_all_energies	(	Pose const &	pose,
		ScoreFunction const &	sfxn,
		core::graph::GraphCOP	flexpack_neighbor_graph,
		interaction_graph::PrecomputedFlexbbInteractionGraph &	flexbb_ig
	)		const

Definition at line 609 of file FlexbbRotamerSets.cc.

Referenced by precompute_energies().

void protocols::flexpack::rotamer_set::FlexbbRotamerSets::precompute_energies	(	Pose const &	pose,
		ScoreFunction const &	sfxn,
		core::graph::GraphCOP	flexpack_neighbor_graph,
		interaction_graph::FlexbbInteractionGraph &	flexbb_ig
	)		const

Definition at line 584 of file FlexbbRotamerSets.cc.

References compute_one_body_energies_for_otf_ig(), and precompute_all_energies().

core::uint protocols::flexpack::rotamer_set::FlexbbRotamerSets::res_for_rotamer ( core::uint rotid) const

virtual

Implements core::pack::rotamer_set::RotamerSetsBase.

Definition at line 423 of file FlexbbRotamerSets.cc.

References moltenres_2_resid_, and moltenres_for_rotamer_.

bool protocols::flexpack::rotamer_set::FlexbbRotamerSets::res_part_of_flexsegment ( Size resid) const

inline

Definition at line 295 of file FlexbbRotamerSets.hh.

References moltenres_2_flexseg_, and resid_2_moltenres_.

core::uint protocols::flexpack::rotamer_set::FlexbbRotamerSets::resid_2_moltenres ( core::uint resid) const

virtual

Implements core::pack::rotamer_set::RotamerSetsBase.

Definition at line 409 of file FlexbbRotamerSets.cc.

References resid_2_moltenres_.

core::conformation::ResidueCOP protocols::flexpack::rotamer_set::FlexbbRotamerSets::rotamer ( core::uint rotid) const

virtual

Implements core::pack::rotamer_set::RotamerSetsBase.

Definition at line 430 of file FlexbbRotamerSets.cc.

References bbconf_for_rotamer_of_moltenres_, moltenres_for_rotamer_, nrotoffset_for_moltenres_, nrotoffset_for_moltenres_bbconf_, and rotamers_.

core::conformation::ResidueCOP protocols::flexpack::rotamer_set::FlexbbRotamerSets::rotamer_for_moltenres	(	core::uint	moltenres_id,
		core::uint	rotamerid
	)		const

virtual

Implements core::pack::rotamer_set::RotamerSetsBase.

Definition at line 441 of file FlexbbRotamerSets.cc.

References bbconf_for_rotamer_of_moltenres_, nrotoffset_for_moltenres_, nrotoffset_for_moltenres_bbconf_, and rotamers_.

Referenced by compute_sr_one_body_energies_for_flexsets(), and rotamer_for_residue().

core::conformation::ResidueCOP protocols::flexpack::rotamer_set::FlexbbRotamerSets::rotamer_for_residue	(	Size	resid,
		Size	rotindex_on_residue
	)		const

Rotamer indexed locally.

Definition at line 85 of file FlexbbRotamerSets.cc.

References resid_2_moltenres_, and rotamer_for_moltenres().

bool protocols::flexpack::rotamer_set::FlexbbRotamerSets::rotamers_on_same_bbconf	(	Size	moltenres,
		Size	rot1,
		Size	rot2
	)		const

inline

Do two rotamers originate from the same backbone conformation? Local enumeration for both rot1 and rot2; rot1 and rot2 must be rotamers of the same molten residue.

Definition at line 346 of file FlexbbRotamerSets.hh.

References bbconf_for_rotamer_of_moltenres_, protocols::jumping::rot1, and protocols::jumping::rot2.

core::uint protocols::flexpack::rotamer_set::FlexbbRotamerSets::rotid_on_moltenresidue ( core::uint rotid) const

virtual

convert rotid in full rotamer enumeration into rotamer id on its source residue

– unimplemented!

Implements core::pack::rotamer_set::RotamerSetsBase.

Definition at line 458 of file FlexbbRotamerSets.cc.

FlexbbRotamerSetCOP protocols::flexpack::rotamer_set::FlexbbRotamerSets::rotset_for_moltenres	(	Size	molten_resid,
		Size	bbconf = `1`
	)		const

Definition at line 77 of file FlexbbRotamerSets.cc.

References rotamers_.

Referenced by protocols::flexpack::interaction_graph::FlexbbInteractionGraph::initialize().

FlexbbRotamerSetCOP protocols::flexpack::rotamer_set::FlexbbRotamerSets::rotset_for_residue	(	Size	resid,
		Size	bbconf = `1`
	)		const

Definition at line 81 of file FlexbbRotamerSets.cc.

References resid_2_moltenres_, and rotamers_.

void protocols::flexpack::rotamer_set::FlexbbRotamerSets::set_frames	(	Pose const &	pose,
		utility::vector1< core::fragment::FrameCOP > const &	frames
	)

function to set up the internal mapping data structures

Definition at line 91 of file FlexbbRotamerSets.cc.

References bbconf_for_rotamer_of_moltenres_, build_residue_vector_from_fragment(), conformations_for_flexible_segments_, core::sequence::end, flexsegment_span_, moltenres_2_flexseg_, moltenres_2_resid_, nbbconfs_, nbbconfs_for_flexseg_, nmoltenres_, nrotamers_for_moltenres_, nrotoffset_for_moltenres_, nrotoffset_for_moltenres_bbconf_, nrots_for_moltenres_bbconf_, resid_2_moltenres_, core::pose::Pose::residue(), rotamers_, core::io::serialization::size(), protocols::loops::start, task_, core::pose::Pose::total_residue(), and total_residue_.

core::uint protocols::flexpack::rotamer_set::FlexbbRotamerSets::total_residue ( ) const

virtual

Implements core::pack::rotamer_set::RotamerSetsBase.

Definition at line 396 of file FlexbbRotamerSets.cc.

References total_residue_.

void protocols::flexpack::rotamer_set::FlexbbRotamerSets::update_offset_data ( )

private

Definition at line 524 of file FlexbbRotamerSets.cc.

References bbconf_for_rotamer_of_moltenres_, conformations_for_flexible_segments_, moltenres_for_rotamer_, nmoltenres_, nrotamers_, nrotamers_for_moltenres_, nrotoffset_for_moltenres_, nrotoffset_for_moltenres_bbconf_, nrots_for_moltenres_bbconf_, rot(), rotamers_, and core::io::serialization::size().

Referenced by build_rotamers().

Member Data Documentation

utility::vector1< utility::vector1< Size > > protocols::flexpack::rotamer_set::FlexbbRotamerSets::bbconf_for_rotamer_of_moltenres_

private

Definition at line 403 of file FlexbbRotamerSets.hh.

Referenced by bbconf_for_rotamer(), bbconf_for_rotamer_on_moltenres(), compute_sr_one_body_energies_for_flexsets(), rotamer(), rotamer_for_moltenres(), rotamers_on_same_bbconf(), set_frames(), and update_offset_data().

utility::vector1< utility::vector1< core::conformation::ResidueCOP > > protocols::flexpack::rotamer_set::FlexbbRotamerSets::conformations_for_flexible_segments_

private

Definition at line 406 of file FlexbbRotamerSets.hh.

Referenced by backbone_for_moltenres_bbconf(), backbone_for_resid_bbconf(), build_rotamers(), determine_res_cb_deviation(), set_frames(), and update_offset_data().