Rosetta 3.4
Public Types | Public Member Functions | Protected Member Functions
protocols::flexpack::rotamer_set::FlexbbRotamerSets Class Reference

#include <FlexbbRotamerSets.hh>

Inheritance diagram for protocols::flexpack::rotamer_set::FlexbbRotamerSets:
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List of all members.

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
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
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.
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
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.
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
virtual core::uint moltenres_rotid_2_rotid (core::uint moltenres, core::uint moltenresrotid) const
 convert moltenres rotid to id in full rotamer enumeration
Size nmolten_res () const
Size nrotamers_for_res (Size resid) const
 The total number of rotamers across all residues and all backbone conformations.
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)
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.
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.
core::conformation::Residue const & backbone_for_resid_bbconf (Size resid, Size bbconf) const
 Rotamer indexed locally.
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.
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.

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)

Member Typedef Documentation


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]
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.

Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::bbconf_for_rotamer ( Size  rotamer_id) const [inline]

rotamer_id in the global enumeration of rotamers.

References local_rotid_for_rotamer_on_moltenres().

Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::bbconf_for_rotamer_on_moltenres ( Size  moltenres,
Size  rotamer_id 
) const [inline]
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().

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 
)
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
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 make_table_of_pilot_apps::begin, 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(), core::pose::Pose::residue(), 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(), and core::pack::find_residue_max_radii().

Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::flexsegid_for_moltenres ( Size  molten_resid) const [inline]
Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::flexsegid_for_res ( Size  resid) const [inline]
Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::flexsegment_size ( Size  flex_segment_id) const [inline]
Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::flexsegment_start_moltenresid ( Size  flex_segment_id) const [inline]
Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::flexsegment_start_resid ( Size  flex_segment_id) const [inline]
Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::flexsegment_stop_moltenresid ( Size  flex_segment_id) const [inline]
Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::flexsegment_stop_resid ( Size  flex_segment_id) const [inline]
Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::global_rotid_start_for_moltenres_in_bbconf ( Size  moltenres,
Size  bbconf 
) const [inline]
Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::local_rotid_for_rotamer ( Size  rotamer_id) const [inline]
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.

Referenced by bbconf_for_rotamer().

Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::local_rotid_start_for_moltenres_in_bbconf ( Size  moltenres,
Size  bbconf 
) const [inline]
core::uint protocols::flexpack::rotamer_set::FlexbbRotamerSets::moltenres_2_resid ( core::uint  moltres) const [virtual]
core::uint protocols::flexpack::rotamer_set::FlexbbRotamerSets::moltenres_for_rotamer ( core::uint  rotid) const [virtual]
bool protocols::flexpack::rotamer_set::FlexbbRotamerSets::moltenres_part_of_flexsegment ( Size  molten_resid) const [inline]
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.

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)

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

Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::nbbconfs_for_flexseg ( core::Size  flex_segment_id) const [inline]
core::Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::nbbconfs_for_moltenres ( core::Size  moltenres) const
core::Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::nbbconfs_for_res ( core::Size  resid) const
Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::nflexible_segments ( ) const [inline]
Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::nmolten_res ( ) const [inline]
core::uint protocols::flexpack::rotamer_set::FlexbbRotamerSets::nmoltenres ( ) const [virtual]
core::uint protocols::flexpack::rotamer_set::FlexbbRotamerSets::nrotamer_offset_for_moltenres ( core::uint  moltres) const [virtual]
core::uint protocols::flexpack::rotamer_set::FlexbbRotamerSets::nrotamers ( ) const [virtual]

Virtual functions from base class.

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

core::uint protocols::flexpack::rotamer_set::FlexbbRotamerSets::nrotamers_for_moltenres ( core::uint  moltres) const [virtual]
Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::nrotamers_for_moltenres_in_bbconf ( Size  moltenres,
Size  bbconf 
) const [inline]
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.

Size protocols::flexpack::rotamer_set::FlexbbRotamerSets::nrotamers_for_resid_in_bbconf ( Size  resid,
Size  bbconf 
) const [inline]
utility::vector1< Size > const& protocols::flexpack::rotamer_set::FlexbbRotamerSets::num_states_per_backbone_for_moltenres ( Size  moltenres) const [inline]
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
core::uint protocols::flexpack::rotamer_set::FlexbbRotamerSets::res_for_rotamer ( core::uint  rotid) const [virtual]
bool protocols::flexpack::rotamer_set::FlexbbRotamerSets::res_part_of_flexsegment ( Size  resid) const [inline]
core::uint protocols::flexpack::rotamer_set::FlexbbRotamerSets::resid_2_moltenres ( core::uint  resid) const [virtual]
core::conformation::ResidueCOP protocols::flexpack::rotamer_set::FlexbbRotamerSets::rotamer ( core::uint  rotid) const [virtual]
core::conformation::ResidueCOP protocols::flexpack::rotamer_set::FlexbbRotamerSets::rotamer_for_moltenres ( core::uint  moltenres_id,
core::uint  rotamerid 
) const [virtual]
core::conformation::ResidueCOP protocols::flexpack::rotamer_set::FlexbbRotamerSets::rotamer_for_residue ( Size  resid,
Size  rotindex_on_residue 
) const

Rotamer indexed locally.

References 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 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.

FlexbbRotamerSetCOP protocols::flexpack::rotamer_set::FlexbbRotamerSets::rotset_for_moltenres ( Size  molten_resid,
Size  bbconf = 1 
) const
FlexbbRotamerSetCOP protocols::flexpack::rotamer_set::FlexbbRotamerSets::rotset_for_residue ( Size  resid,
Size  bbconf = 1 
) const
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 build_residue_vector_from_fragment(), core::sequence::end, core::pose::Pose::residue(), and core::pose::Pose::total_residue().

core::uint protocols::flexpack::rotamer_set::FlexbbRotamerSets::total_residue ( ) const [virtual]

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