Rosetta 3.4
Namespaces | Classes | Typedefs | Functions
protocols::topology_broker Namespace Reference

Namespaces

namespace  weights

Classes

class  AsymFoldandDockClaimer
class  ClaimerMessage
class  SuggestValueMessage
class  ConstraintClaimer
class  CoordConstraintClaimer
class  CutBiasClaimer
class  DensityScoringClaimer
class  DisulfJumpClaimer
 Claimer that works with the old system of BaseJumpSetup it supports only JumpFrames of type [ BBTorsion ] UpJump DownJump [ BBTorsion ] the class JumpSample is still used to transport the information jumps and jump_atoms, but cuts are ignored all functionality of JumpSample is not used anymore. More...
class  DofClaim
class  SequenceClaim
class  BBClaim
class  JumpClaim
class  CutClaim
class  RootClaim
class  EXCN_TopologyBroker
class  EXCN_Input
class  EXCN_Unknown
class  EXCN_FailedBroking
class  EXCN_FilterFailed
class  FibrilModelingClaimer
class  FoldandDockClaimer
class  FragmentClaimer
class  JumpClaimer
 Claimer that works with the old system of BaseJumpSetup it supports only JumpFrames of type [ BBTorsion ] UpJump DownJump [ BBTorsion ] the class JumpSample is still used to transport the information jumps and jump_atoms, but cuts are ignored all functionality of JumpSample is not used anymore. More...
class  LoopFragmentClaimer
class  MembraneTopologyClaimer
class  MetalloClaimer
class  PcsEnergyController
class  PseudocontactShiftEnergyController
class  RigidChunkClaimer
 defines a rigid part of structure... imagine a loop-relax application core structure is fixed via jumps and loops can move the rigid chunk takes a definition of rigid regions in form of an instance of Loops (just taken as bunch of start-end residue numbers --- here defining the rigid residues and not the loops). the rigid chunk to keep its integrity will need jumps, the claimer will reuse jumps if somebody else claims them, or submit in finalize_claims his own jumps, if not enough jumps are present. in "bExclusive_ mode" the RigidChunk will reclaim any jump claim that is useful and wihin the rigid region. (i.e., foreign claim is dissallowed but own claim with same residues is issued --- in this way the claimer uses e.g., beta-sheet jumps, where they are suggested the input pose is used to initialize the rigid region ( via copying of internal coordinates ) e.g., a hole in the structure shouldn't pose a problem, since we basically copy the atom-tree. More...
class  SequenceClaimer
class  StartStructClaimer
class  TemplateFragmentClaimer
 hacky wrapper to keep the old Template code alive a bit longer this claimer deals with the Jumpy part of the Templates. More...
class  TemplateJumpClaimer
 hacky wrapper to keep the old Template code alive a bit longer this claimer deals with the Jumpy part of the Templates. More...
class  TopologyBroker
class  TopologyClaimer
  More...
class  TopologyClaimerFactory
 A non-copyable factory for instantiating TopologyClaimers by name. Commonly used TopologyClaimers are registered in the constructor. Additional claimers can be registered after the fact using the add_type() method. More...
struct  CmdLineData

Typedefs

typedef
utility::pointer::owning_ptr
< AsymFoldandDockClaimer
AsymFoldandDockClaimerOP
typedef
utility::pointer::owning_ptr
< AsymFoldandDockClaimer const > 
AsymFoldandDockClaimerCOP
typedef
utility::pointer::access_ptr
< AsymFoldandDockClaimer
AsymFoldandDockClaimerAP
typedef
utility::pointer::access_ptr
< AsymFoldandDockClaimer const > 
AsymFoldandDockClaimerCAP
typedef
utility::pointer::owning_ptr
< ClaimerMessage
ClaimerMessageOP
typedef
utility::pointer::owning_ptr
< ClaimerMessage const > 
ClaimerMessageCOP
typedef
utility::pointer::access_ptr
< ClaimerMessage
ClaimerMessageAP
typedef
utility::pointer::access_ptr
< ClaimerMessage const > 
ClaimerMessageCAP
typedef
utility::pointer::owning_ptr
< ConstraintClaimer
ConstraintClaimerOP
typedef
utility::pointer::owning_ptr
< ConstraintClaimer const > 
ConstraintClaimerCOP
typedef
utility::pointer::access_ptr
< ConstraintClaimer
ConstraintClaimerAP
typedef
utility::pointer::access_ptr
< ConstraintClaimer const > 
ConstraintClaimerCAP
typedef
utility::pointer::owning_ptr
< CutBiasClaimer
CutBiasClaimerOP
typedef
utility::pointer::owning_ptr
< CutBiasClaimer const > 
CutBiasClaimerCOP
typedef
utility::pointer::access_ptr
< CutBiasClaimer
CutBiasClaimerAP
typedef
utility::pointer::access_ptr
< CutBiasClaimer const > 
CutBiasClaimerCAP
typedef
utility::pointer::owning_ptr
< DensityScoringClaimer
DensityScoringClaimerOP
typedef
utility::pointer::owning_ptr
< DensityScoringClaimer const > 
DensityScoringClaimerCOP
typedef
utility::pointer::access_ptr
< DensityScoringClaimer
DensityScoringClaimerAP
typedef
utility::pointer::access_ptr
< DensityScoringClaimer const > 
DensityScoringClaimerCAP
typedef
utility::pointer::owning_ptr
< DisulfJumpClaimer
DisulfJumpClaimerOP
typedef
utility::pointer::owning_ptr
< DisulfJumpClaimer const > 
DisulfJumpClaimerCOP
typedef
utility::pointer::access_ptr
< DisulfJumpClaimer
DisulfJumpClaimerAP
typedef
utility::pointer::access_ptr
< DisulfJumpClaimer const > 
DisulfJumpClaimerCAP
typedef
utility::pointer::owning_ptr
< DofClaim
DofClaimOP
typedef
utility::pointer::owning_ptr
< DofClaim const > 
DofClaimCOP
typedef
utility::pointer::access_ptr
< DofClaim
DofClaimAP
typedef
utility::pointer::access_ptr
< DofClaim const > 
DofClaimCAP
typedef utility::vector1
< DofClaimOP
DofClaims
typedef
utility::pointer::owning_ptr
< SequenceClaim
SequenceClaimOP
typedef
utility::pointer::owning_ptr
< SequenceClaim const > 
SequenceClaimCOP
typedef
utility::pointer::access_ptr
< SequenceClaim
SequenceClaimAP
typedef
utility::pointer::access_ptr
< SequenceClaim const > 
SequenceClaimCAP
typedef utility::vector1
< SequenceClaimOP
SequenceClaims
typedef
utility::pointer::owning_ptr
< JumpClaim
JumpClaimOP
typedef
utility::pointer::owning_ptr
< JumpClaim const > 
JumpClaimCOP
typedef
utility::pointer::access_ptr
< JumpClaim
JumpClaimAP
typedef
utility::pointer::access_ptr
< JumpClaim const > 
JumpClaimCAP
typedef
utility::pointer::owning_ptr
< BBClaim
BBClaimOP
typedef
utility::pointer::owning_ptr
< BBClaim const > 
BBClaimCOP
typedef
utility::pointer::access_ptr
< BBClaim
BBClaimAP
typedef
utility::pointer::access_ptr
< BBClaim const > 
BBClaimCAP
typedef
utility::pointer::owning_ptr
< FibrilModelingClaimer
FibrilModelingClaimerOP
typedef
utility::pointer::owning_ptr
< FibrilModelingClaimer const > 
FibrilModelingClaimerCOP
typedef
utility::pointer::access_ptr
< FibrilModelingClaimer
FibrilModelingClaimerAP
typedef
utility::pointer::access_ptr
< FibrilModelingClaimer const > 
FibrilModelingClaimerCAP
typedef
utility::pointer::owning_ptr
< FoldandDockClaimer
FoldandDockClaimerOP
typedef
utility::pointer::owning_ptr
< FoldandDockClaimer const > 
FoldandDockClaimerCOP
typedef
utility::pointer::access_ptr
< FoldandDockClaimer
FoldandDockClaimerAP
typedef
utility::pointer::access_ptr
< FoldandDockClaimer const > 
FoldandDockClaimerCAP
typedef
utility::pointer::owning_ptr
< FragmentClaimer
FragmentClaimerOP
typedef
utility::pointer::owning_ptr
< FragmentClaimer const > 
FragmentClaimerCOP
typedef
utility::pointer::access_ptr
< FragmentClaimer
FragmentClaimerAP
typedef
utility::pointer::access_ptr
< FragmentClaimer const > 
FragmentClaimerCAP
typedef
utility::pointer::owning_ptr
< JumpClaimer
JumpClaimerOP
typedef
utility::pointer::owning_ptr
< JumpClaimer const > 
JumpClaimerCOP
typedef
utility::pointer::access_ptr
< JumpClaimer
JumpClaimerAP
typedef
utility::pointer::access_ptr
< JumpClaimer const > 
JumpClaimerCAP
typedef
utility::pointer::owning_ptr
< LoopFragmentClaimer
LoopFragmentClaimerOP
typedef
utility::pointer::owning_ptr
< LoopFragmentClaimer const > 
LoopFragmentClaimerCOP
typedef
utility::pointer::access_ptr
< LoopFragmentClaimer
LoopFragmentClaimerAP
typedef
utility::pointer::access_ptr
< LoopFragmentClaimer const > 
LoopFragmentClaimerCAP
typedef
utility::pointer::owning_ptr
< MetalloClaimer
MetalloClaimerOP
typedef
utility::pointer::owning_ptr
< MetalloClaimer const > 
MetalloClaimerCOP
typedef
utility::pointer::access_ptr
< MetalloClaimer
MetalloClaimerAP
typedef
utility::pointer::access_ptr
< MetalloClaimer const > 
MetalloClaimerCAP
typedef
utility::pointer::owning_ptr
< PcsEnergyController
PcsEnergyControllerOP
typedef
utility::pointer::owning_ptr
< PcsEnergyController const > 
PcsEnergyControllerCOP
typedef
utility::pointer::access_ptr
< PcsEnergyController
PcsEnergyControllerAP
typedef
utility::pointer::access_ptr
< PcsEnergyController const > 
PcsEnergyControllerCAP
typedef
utility::pointer::owning_ptr
< PseudocontactShiftEnergyController
PseudocontactShiftEnergyControllerOP
typedef
utility::pointer::owning_ptr
< PseudocontactShiftEnergyController
const > 
PseudocontactShiftEnergyControllerCOP
typedef
utility::pointer::access_ptr
< PseudocontactShiftEnergyController
PseudocontactShiftEnergyControllerAP
typedef
utility::pointer::access_ptr
< PseudocontactShiftEnergyController
const > 
PseudocontactShiftEnergyControllerCAP
typedef
utility::pointer::owning_ptr
< RigidChunkClaimer
RigidChunkClaimerOP
typedef
utility::pointer::owning_ptr
< RigidChunkClaimer const > 
RigidChunkClaimerCOP
typedef
utility::pointer::access_ptr
< RigidChunkClaimer
RigidChunkClaimerAP
typedef
utility::pointer::access_ptr
< RigidChunkClaimer const > 
RigidChunkClaimerCAP
typedef
utility::pointer::owning_ptr
< SequenceClaimer
SequenceClaimerOP
typedef
utility::pointer::owning_ptr
< SequenceClaimer const > 
SequenceClaimerCOP
typedef
utility::pointer::access_ptr
< SequenceClaimer
SequenceClaimerAP
typedef
utility::pointer::access_ptr
< SequenceClaimer const > 
SequenceClaimerCAP
typedef
utility::pointer::owning_ptr
< StartStructClaimer
StartStructClaimerOP
typedef
utility::pointer::owning_ptr
< StartStructClaimer const > 
StartStructClaimerCOP
typedef
utility::pointer::access_ptr
< StartStructClaimer
StartStructClaimerAP
typedef
utility::pointer::access_ptr
< StartStructClaimer const > 
StartStructClaimerCAP
typedef
utility::pointer::owning_ptr
< TemplateFragmentClaimer
TemplateFragmentClaimerOP
typedef
utility::pointer::owning_ptr
< TemplateFragmentClaimer
const > 
TemplateFragmentClaimerCOP
typedef
utility::pointer::access_ptr
< TemplateFragmentClaimer
TemplateFragmentClaimerAP
typedef
utility::pointer::access_ptr
< TemplateFragmentClaimer
const > 
TemplateFragmentClaimerCAP
typedef
utility::pointer::owning_ptr
< TemplateJumpClaimer
TemplateJumpClaimerOP
typedef
utility::pointer::owning_ptr
< TemplateJumpClaimer const > 
TemplateJumpClaimerCOP
typedef
utility::pointer::access_ptr
< TemplateJumpClaimer
TemplateJumpClaimerAP
typedef
utility::pointer::access_ptr
< TemplateJumpClaimer const > 
TemplateJumpClaimerCAP
typedef
utility::pointer::owning_ptr
< TopologyBroker
TopologyBrokerOP
typedef
utility::pointer::owning_ptr
< TopologyBroker const > 
TopologyBrokerCOP
typedef
utility::pointer::access_ptr
< TopologyBroker
TopologyBrokerAP
typedef
utility::pointer::access_ptr
< TopologyBroker const > 
TopologyBrokerCAP
typedef
utility::pointer::owning_ptr
< TopologyClaimer
TopologyClaimerOP
typedef
utility::pointer::owning_ptr
< TopologyClaimer const > 
TopologyClaimerCOP
typedef
utility::pointer::access_ptr
< TopologyClaimer
TopologyClaimerAP
typedef
utility::pointer::access_ptr
< TopologyClaimer const > 
TopologyClaimerCAP

Functions

std::ostream & operator<< (std::ostream &os, ClaimerMessage const &cm)
std::ostream & operator<< (std::ostream &os, DofClaim const &dof)
std::ostream & operator<< (std::ostream &os, DofClaims const &dofs)
protocols::loops::Loops generate_rigid_from_alignment (pose::Pose query_pose, core::sequence::SequenceAlignment const &align, Size min_loop_size)
void fix_internal_coords_of_siblings (pose::Pose &pose, pose::Pose const &ref_pose, id::AtomID atom, id::AtomID ref_atom)
void fix_mainchain_connect (pose::Pose &pose, pose::Pose const &ref_pose, core::Size upper_residue)
void copy_internal_coords (pose::Pose &pose, pose::Pose const &ref_pose, loops::Loops core)
bool is_not_neighbor_to_rigid (loops::Loops const &rigid, Size pos1, Size pos2)
bool connects_rigid_regions (loops::Loops const &rigid, Size pos1, Size pos2)
std::istream & operator>> (std::istream &is, TopologyClaimer &tc)
core::fragment::FragSetOP read_frags (std::istream &is, core::fragment::FragmentIO &io)
void add_claims_from_stream (TopologyBroker &broker, std::istream &is, CmdLineData &cmdline_data)
void add_claims_from_file (TopologyBroker &broker, std::string const &file, CmdLineData &cmdline_data)
void add_cmdline_claims (TopologyBroker &, bool do_I_need_frags=true)
 read broker::setup flag and add all claims to Broker

Typedef Documentation


Function Documentation

void protocols::topology_broker::add_claims_from_file ( TopologyBroker &  broker,
std::string const &  file,
CmdLineData &  cmdline_data 
)

References add_claims_from_stream().

Referenced by add_cmdline_claims().

void protocols::topology_broker::add_claims_from_stream ( TopologyBroker &  broker,
std::istream &  is,
CmdLineData &  cmdline_data 
)
void protocols::topology_broker::add_cmdline_claims ( TopologyBroker &  broker,
bool const  do_I_need_frags 
)
bool protocols::topology_broker::connects_rigid_regions ( loops::Loops const &  rigid,
Size  pos1,
Size  pos2 
)
void protocols::topology_broker::copy_internal_coords ( pose::Pose pose,
pose::Pose const &  ref_pose,
loops::Loops  core 
)
void protocols::topology_broker::fix_internal_coords_of_siblings ( pose::Pose pose,
pose::Pose const &  ref_pose,
id::AtomID  atom,
id::AtomID  ref_atom 
)
void protocols::topology_broker::fix_mainchain_connect ( pose::Pose pose,
pose::Pose const &  ref_pose,
core::Size  upper_residue 
)
protocols::loops::Loops protocols::topology_broker::generate_rigid_from_alignment ( pose::Pose  query_pose,
core::sequence::SequenceAlignment const &  align,
Size  min_loop_size 
)
bool protocols::topology_broker::is_not_neighbor_to_rigid ( loops::Loops const &  rigid,
Size  pos1,
Size  pos2 
)
std::ostream & protocols::topology_broker::operator<< ( std::ostream &  os,
DofClaim const &  dof 
)
std::ostream& protocols::topology_broker::operator<< ( std::ostream &  os,
ClaimerMessage const &  cm 
)
std::ostream & protocols::topology_broker::operator<< ( std::ostream &  os,
DofClaims const &  dofs 
)
std::istream& protocols::topology_broker::operator>> ( std::istream &  is,
TopologyClaimer &  tc 
) [inline]
core::fragment::FragSetOP protocols::topology_broker::read_frags ( std::istream &  is,
core::fragment::FragmentIO io 
)
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