Rosetta 3.4
Classes | Typedefs | Functions
protocols::match::output Namespace Reference

Classes

class  DownstreamRMSEvaluator
 In the best of all possible worlds, this class would be sufficiently generic such that I could compare RMS for arbitrary subsets of atoms on the downstream partner, but in my first pass implementation, I'm writing while aiming at the RigidLigandBuilder -- 1 residue -- and I'll compare all heavy atoms. More...
class  LimitHitsPerRotamerFilter
class  MatchConsolidator
class  BestMatchesCollection
class  MatchEvaluator
class  MatchFilter
class  StateAccumulatingMatchFilter
class  MatchGrouper
class  MatchOutputter
class  MatchProcessor
class  OutputWriter
class  PDBWriter
class  CloudPDBWriter
 an output writer that uses a grouper to group matches and then writes out one pdb file per group, with the different hits from the group in different MODEL sections More...
class  PoseMatchOutputWriter
 helper class for the MatcherMover that will put a match into a supplied pose More...
class  PoseInserter
class  ProcessorFactory
class  SameChiBinComboGrouper
class  SameRotamerComboGrouper
class  SameSequenceGrouper
 Class to group matches that represent the same amino acids at the same launch points. E.g. Two matches that both put a cys at launch point #33, a ser a launch point #42 and another ser at launch point #80 would be grouped together -- even if they are different rotamers. More...
class  SameSequenceAndDSPositionGrouper
 class that groups based on same sequence and proximity of the downstream object (based on rms ) NOTE: right now only the downstream position according to the first geomcst id upstream residue is taken into account More...
class  MatchCollisionFilter
class  UpstreamCollisionFilter
 This class is used to detect collisions between the upstream residues and filter out matches that have too much collision. It can perform either hard-sphere collision detection, or score-function (Etable) driven collision detection. Four command-line flags are read by the MatcherTask to initialize this class: match::filter_colliding_upstream_residues match::upstream_residue_collision_tolerance match::upstream_residue_collision_score_cutoff match::upstream_residue_collision_Wfa_atr match::upstream_residue_collision_Wfa_rep match::upstream_residue_collision_Wfa_sol. More...
class  UpstreamDownstreamCollisionFilter
 This class is used to detect collisions between upstream residues and downstream poses. More...
class  UpstreamHitCacher
class  WriteKinemageOutputter
class  ResidueKinemageWriter
class  WriteUpstreamCoordinateKinemage
class  WriteUpstreamHitKinemage
class  DownstreamCoordinateKinemageWriter
class  SingleDownstreamResidueWriter
 Class for writing conformations of the downstream partner in a kinemage description. More...

Typedefs

typedef
utility::pointer::owning_ptr
< DownstreamRMSEvaluator
DownstreamRMSEvaluatorOP
typedef
utility::pointer::owning_ptr
< DownstreamRMSEvaluator const > 
DownstreamRMSEvaluatorCOP
typedef
utility::pointer::owning_ptr
< LimitHitsPerRotamerFilter
LimitHitsPerRotamerFilterOP
typedef
utility::pointer::owning_ptr
< LimitHitsPerRotamerFilter
const > 
LimitHitsPerRotamerFilterCOP
typedef
utility::pointer::owning_ptr
< MatchConsolidator
MatchConsolidatorOP
typedef
utility::pointer::owning_ptr
< MatchConsolidator const > 
MatchConsolidatorCOP
typedef
utility::pointer::owning_ptr
< BestMatchesCollection
BestMatchesCollectionOP
typedef
utility::pointer::owning_ptr
< BestMatchesCollection const > 
BestMatchesCollectionCOP
typedef
utility::pointer::owning_ptr
< MatchEvaluator
MatchEvaluatorOP
typedef
utility::pointer::owning_ptr
< MatchEvaluator const > 
MatchEvaluatorCOP
typedef
utility::pointer::owning_ptr
< MatchFilter
MatchFilterOP
typedef
utility::pointer::owning_ptr
< MatchFilter const > 
MatchFilterCOP
typedef
utility::pointer::owning_ptr
< StateAccumulatingMatchFilter
StateAccumulatingMatchFilterOP
typedef
utility::pointer::owning_ptr
< StateAccumulatingMatchFilter
const > 
StateAccumulatingMatchFilterCOP
typedef
utility::pointer::owning_ptr
< MatchGrouper
MatchGrouperOP
typedef
utility::pointer::owning_ptr
< MatchGrouper const > 
MatchGrouperCOP
typedef
utility::pointer::owning_ptr
< MatchOutputter
MatchOutputterOP
typedef
utility::pointer::owning_ptr
< MatchOutputter const > 
MatchOutputterCOP
typedef
utility::pointer::owning_ptr
< MatchProcessor
MatchProcessorOP
typedef
utility::pointer::owning_ptr
< MatchProcessor const > 
MatchProcessorCOP
typedef
utility::pointer::owning_ptr
< OutputWriter
OutputWriterOP
typedef
utility::pointer::owning_ptr
< OutputWriter const > 
OutputWriterCOP
typedef
utility::pointer::owning_ptr
< PDBWriter
PDBWriterOP
typedef
utility::pointer::owning_ptr
< PDBWriter const > 
PDBWriterCOP
typedef
utility::pointer::owning_ptr
< CloudPDBWriter
CloudPDBWriterOP
typedef
utility::pointer::owning_ptr
< CloudPDBWriter const > 
CloudPDBWriterCOP
typedef
utility::pointer::owning_ptr
< PoseMatchOutputWriter
PoseMatchOutputWriterOP
typedef
utility::pointer::owning_ptr
< PoseMatchOutputWriter const > 
PoseMatchOutputWriterCOP
typedef
utility::pointer::owning_ptr
< PoseInserter
PoseInserterOP
typedef
utility::pointer::owning_ptr
< PoseInserter const > 
PoseInserterCOP
typedef
utility::pointer::owning_ptr
< ProcessorFactory
ProcessorFactoryOP
typedef
utility::pointer::owning_ptr
< ProcessorFactory const > 
ProcessorFactoryCOP
typedef
utility::pointer::owning_ptr
< SameChiBinComboGrouper
SameChiBinComboGrouperOP
typedef
utility::pointer::owning_ptr
< SameChiBinComboGrouper const > 
SameChiBinComboGrouperCOP
typedef
utility::pointer::owning_ptr
< SameRotamerComboGrouper
SameRotamerComboGrouperOP
typedef
utility::pointer::owning_ptr
< SameRotamerComboGrouper
const > 
SameRotamerComboGrouperCOP
typedef
utility::pointer::owning_ptr
< SameSequenceGrouper
SameSequenceGrouperOP
typedef
utility::pointer::owning_ptr
< SameSequenceGrouper const > 
SameSequenceGrouperCOP
typedef
utility::pointer::owning_ptr
< SameSequenceAndDSPositionGrouper
SameSequenceAndDSPositionGrouperOP
typedef
utility::pointer::owning_ptr
< SameSequenceAndDSPositionGrouper
const > 
SameSequenceAndDSPositionGrouperCOP
typedef
utility::pointer::owning_ptr
< UpstreamCollisionFilter
UpstreamCollisionFilterOP
typedef
utility::pointer::owning_ptr
< UpstreamCollisionFilter
const > 
UpstreamCollisionFilterCOP
typedef
utility::pointer::owning_ptr
< UpstreamDownstreamCollisionFilter
UpstreamDownstreamCollisionFilterOP
typedef
utility::pointer::owning_ptr
< UpstreamDownstreamCollisionFilter
const > 
UpstreamDownstreamCollisionFilterCOP
typedef
utility::pointer::owning_ptr
< UpstreamHitCacher
UpstreamHitCacherOP
typedef
utility::pointer::owning_ptr
< UpstreamHitCacher const > 
UpstreamHitCacherCOP
typedef
utility::pointer::owning_ptr
< WriteKinemageOutputter
WriteKinemageOutputterOP
typedef
utility::pointer::owning_ptr
< WriteKinemageOutputter const > 
WriteKinemageOutputterCOP
typedef
utility::pointer::owning_ptr
< WriteUpstreamCoordinateKinemage
WriteUpstreamCoordinateKinemageOP
typedef
utility::pointer::owning_ptr
< WriteUpstreamCoordinateKinemage
const > 
WriteUpstreamCoordinateKinemageCOP
typedef
utility::pointer::owning_ptr
< WriteUpstreamHitKinemage
WriteUpstreamHitKinemageOP
typedef
utility::pointer::owning_ptr
< WriteUpstreamHitKinemage
const > 
WriteUpstreamHitKinemageCOP
typedef
utility::pointer::owning_ptr
< DownstreamCoordinateKinemageWriter
DownstreamCoordinateKinemageWriterOP
typedef
utility::pointer::owning_ptr
< DownstreamCoordinateKinemageWriter
const > 
DownstreamCoordinateKinemageWriterCOP
typedef
utility::pointer::owning_ptr
< SingleDownstreamResidueWriter
SingleDownstreamResidueWriterOP
typedef
utility::pointer::owning_ptr
< SingleDownstreamResidueWriter
const > 
SingleDownstreamResidueWriterCOP

Functions

static basic::Tracer TR ("protocols.match.output.MatchProcessor")
static basic::Tracer TR ("protocols.match.output.PDBWriter")
static basic::Tracer TR ("protocols.match.output.ProcessorFactory")
void print_node (std::ostream &out, int residue_num, int atom_num, core::Vector const &atom_xyz, core::chemical::ResidueType const &res, std::string extras="")
 TWO FUNCTIONS STOLEN FROM IAN: and slightly modified.
void print_node (std::ostream &out, int residue_num, int atom_num, core::conformation::Residue const &res, std::string extras="")
void print_node (std::ostream &out, int residue_num, std::string atom_name, core::conformation::Residue const &res, std::string extras="")

Typedef Documentation


Function Documentation

void protocols::match::output::print_node ( std::ostream &  out,
int  residue_num,
int  atom_num,
core::Vector const &  atom_xyz,
core::chemical::ResidueType const &  res,
std::string  extras = "" 
)
void protocols::match::output::print_node ( std::ostream &  out,
int  residue_num,
int  atom_num,
core::conformation::Residue const &  res,
std::string  extras = "" 
)
void protocols::match::output::print_node ( std::ostream &  out,
int  residue_num,
std::string  atom_name,
core::conformation::Residue const &  res,
std::string  extras = "" 
)
static basic::Tracer protocols::match::output::TR ( "protocols.match.output.PDBWriter"  ) [static]
static basic::Tracer protocols::match::output::TR ( "protocols.match.output.MatchProcessor"  ) [static]
static basic::Tracer protocols::match::output::TR ( "protocols.match.output.ProcessorFactory"  ) [static]
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