protocols::flexpack::rotamer_set::FlexbbRotamerSets Class Reference

#include <FlexbbRotamerSets.hh>

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...

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_

Member Typedef Documentation

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

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

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

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

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

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

Constructor & Destructor Documentation

protocols::flexpack::rotamer_set::FlexbbRotamerSets::FlexbbRotamerSets

(

PackerTaskCOP

task

)

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

virtual

Member Function Documentation

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

inline

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.

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.

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

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

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

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
	)

References begin, conformations_for_flexible_segments_, dump_pdbs(), basic::options::OptionKeys::packing::dump_rotamer_sets, moltenres_2_resid_, nmoltenres_, basic::options::option, rotamers_, task_, update_offset_data(), and user.

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

References aa_gly, aa_pro, begin, compute_onebody_interactions_with_background(), compute_sr_one_body_energies_for_flexsets(), end, core::pose::Pose::energies(), core::scoring::Energies::long_range_container(), 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

References core::scoring::methods::n_energy_methods, nbbconfs_for_moltenres(), nrotamers_for_moltenres(), nrotoffset_for_moltenres_, nrotoffset_for_moltenres_bbconf_, 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.

References core::conformation::Residue::aa(), core::chemical::aa_gly, core::chemical::aa_pro, 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.

References begin, conformations_for_flexible_segments_, numeric::xyzVector< class >::distance_squared(), 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

References core::io::pdb::dump_pdb_residue(), I, nmoltenres_, core::pose::Pose::residue(), rotamers_, size(), task_, utility::to_string(), 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

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

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

References moltenres_2_flexseg_, and resid_2_moltenres_.

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

inline

References flexsegment_span_.

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

inline

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

References flexsegment_span_.

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

inline

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

References flexsegment_span_.

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

inline

References nrotoffset_for_moltenres_bbconf_.

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

inline

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.

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

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

References moltenres_2_resid_.

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

virtual

References moltenres_for_rotamer_.

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

inline

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

References utility_exit_with_message.

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)

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

References nbbconfs_for_flexseg_.

core::Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::nbbconfs_for_moltenres

(

core::Size

moltenres

)

const

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

References nbbconfs_for_moltenres(), and resid_2_moltenres_.

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

inline

References flexsegment_span_.

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

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

inline

References nmoltenres_.

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

virtual

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

References nrotoffset_for_moltenres_.

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

virtual

Virtual functions from base class.

References nrotamers_.

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

virtual

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

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.

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

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

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

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

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

References moltenres_2_resid_, and moltenres_for_rotamer_.

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

inline

References moltenres_2_flexseg_, and resid_2_moltenres_.

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

virtual

References resid_2_moltenres_.

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

virtual

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

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.

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.

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!

References utility_exit_with_message.

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

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

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

References bbconf_for_rotamer_of_moltenres_, build_residue_vector_from_fragment(), conformations_for_flexible_segments_, 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_, size(), protocols::loops::start, task_, core::pose::Pose::total_residue(), and total_residue_.

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

virtual

References total_residue_.

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

private

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 size().

Referenced by build_rotamers().

Member Data Documentation

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

private

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

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

utility::vector1< std::pair< Size, Size > > protocols::flexpack::rotamer_set::FlexbbRotamerSets::flexsegment_span_

private

Referenced by flexsegment_size(), flexsegment_start_moltenresid(), flexsegment_start_resid(), flexsegment_stop_moltenresid(), flexsegment_stop_resid(), nflexible_segments(), and set_frames().

utility::vector1< Size > protocols::flexpack::rotamer_set::FlexbbRotamerSets::moltenres_2_flexseg_

private

Referenced by flexsegid_for_moltenres(), flexsegid_for_res(), moltenres_part_of_flexsegment(), nbbconfs_for_moltenres(), res_part_of_flexsegment(), and set_frames().

utility::vector1< Size > protocols::flexpack::rotamer_set::FlexbbRotamerSets::moltenres_2_resid_

private

Referenced by build_rotamers(), compute_one_body_energies_for_otf_ig(), determine_res_cb_deviation(), moltenres_2_resid(), res_for_rotamer(), and set_frames().

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

private

Referenced by bbconf_for_rotamer(), local_rotid_for_rotamer(), moltenres_for_rotamer(), res_for_rotamer(), rotamer(), and update_offset_data().

Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::nbbconfs_

private

Referenced by nbackbone_conformations(), and set_frames().

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

private

Referenced by nbbconfs_for_flexseg(), nbbconfs_for_moltenres(), and set_frames().

Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::nmoltenres_

private

Referenced by build_rotamers(), compute_one_body_energies_for_otf_ig(), dump_pdbs(), nmolten_res(), nmoltenres(), set_frames(), and update_offset_data().

Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::nrotamers_

private

Referenced by nrotamers(), and update_offset_data().

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

private

Referenced by compute_sr_one_body_energies_for_flexsets(), nrotamers_for_moltenres(), nrotamers_for_res(), set_frames(), and update_offset_data().

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

private

Referenced by compute_onebody_interactions_with_background(), local_rotid_for_rotamer(), local_rotid_for_rotamer_on_moltenres(), local_rotid_start_for_moltenres_in_bbconf(), nrotamer_offset_for_moltenres(), rotamer(), rotamer_for_moltenres(), set_frames(), and update_offset_data().

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

private

Referenced by compute_onebody_interactions_with_background(), global_rotid_start_for_moltenres_in_bbconf(), local_rotid_start_for_moltenres_in_bbconf(), rotamer(), rotamer_for_moltenres(), set_frames(), and update_offset_data().

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

private

Referenced by nrotamers_for_moltenres_in_bbconf(), nrotamers_for_resid_in_bbconf(), num_states_per_backbone_for_moltenres(), set_frames(), and update_offset_data().

utility::vector1< Size > protocols::flexpack::rotamer_set::FlexbbRotamerSets::resid_2_moltenres_

private

Referenced by backbone_for_resid_bbconf(), compute_one_body_energies_for_otf_ig(), flexpack_neighbor_graph(), flexsegid_for_res(), flexsegment_start_moltenresid(), flexsegment_stop_moltenresid(), nbbconfs_for_res(), nrotamers_for_res(), nrotamers_for_resid_in_bbconf(), res_part_of_flexsegment(), resid_2_moltenres(), rotamer_for_residue(), rotset_for_residue(), and set_frames().

utility::vector1< utility::vector1< rotamer_set::FlexbbRotamerSetOP > > protocols::flexpack::rotamer_set::FlexbbRotamerSets::rotamers_

private

Referenced by build_rotamers(), compute_one_body_energies_for_otf_ig(), compute_onebody_interactions_with_background(), compute_sr_one_body_energies_for_flexsets(), dump_pdbs(), rotamer(), rotamer_for_moltenres(), rotset_for_moltenres(), rotset_for_residue(), set_frames(), and update_offset_data().

PackerTaskCOP protocols::flexpack::rotamer_set::FlexbbRotamerSets::task_

private

Referenced by build_rotamers(), compute_onebody_interactions_with_background(), dump_pdbs(), and set_frames().

Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::total_residue_

private

Referenced by flexpack_neighbor_graph(), set_frames(), and total_residue().

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

• src/protocols/flexpack/rotamer_set/FlexbbRotamerSets.hh
• src/protocols/flexpack/rotamer_set/FlexbbRotamerSets.cc