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protocols::topology_broker Namespace Reference

Namespaces

 weights
 

Classes

class  AsymFoldandDockClaimer
 
class  ClaimerMessage
 
class  SuggestValueMessage
 
class  ConstraintClaimer
 
class  ConstraintEvaluatorWrapper
 
class  ConstraintEvaluatorWrapperCreator
 creator for the ConstraintsEvaluatorWrapperCreator class More...
 
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
 
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
< ConstraintEvaluatorWrapper
ConstraintEvaluatorWrapperOP
 
typedef
utility::pointer::owning_ptr
< ConstraintEvaluatorWrapper
const > 
ConstraintEvaluatorWrapperCOP
 
typedef
utility::pointer::access_ptr
< ConstraintEvaluatorWrapper
ConstraintEvaluatorWrapperAP
 
typedef
utility::pointer::access_ptr
< ConstraintEvaluatorWrapper
const > 
ConstraintEvaluatorWrapperCAP
 
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 More...
 

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,
ClaimerMessage const &  cm 
)
std::ostream & protocols::topology_broker::operator<< ( std::ostream &  os,
DofClaim const &  dof 
)
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 
)