Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Classes | Typedefs | Functions
protocols::match::output Namespace Reference

Classes

class  BestMatchesCollection
 
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  DownstreamCoordinateKinemageWriter
 
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  MatchCollisionFilter
 
class  MatchConsolidator
 
class  MatchEvaluator
 
class  MatchFilter
 
class  MatchGrouper
 
class  MatchOutputter
 
class  MatchProcessor
 
class  MatchScoreWriter
 
class  OutputWriter
 
class  PDBWriter
 
class  PoseInserter
 
class  PoseMatchOutputWriter
 helper class for the MatcherMover that will put a match into a supplied pose More...
 
class  ProcessorFactory
 
class  ResidueKinemageWriter
 
class  SameChiBinComboGrouper
 
class  SameRotamerComboGrouper
 
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  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  SingleDownstreamResidueWriter
 Class for writing conformations of the downstream partner in a kinemage description. More...
 
class  StateAccumulatingMatchFilter
 
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  WriteUpstreamCoordinateKinemage
 
class  WriteUpstreamHitKinemage
 

Typedefs

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

Functions

static basic::Tracer TR ("protocols.match.output.MatchProcessor")
 
std::ostream & operator<< (std::ostream &output, MatchScoreWriter const &object_to_output)
 
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 const &extras="")
 TWO FUNCTIONS STOLEN FROM IAN: and slightly modified. More...
 
void print_node (std::ostream &out, int residue_num, int atom_num, core::conformation::Residue const &res, std::string const &extras="")
 
void print_node (std::ostream &out, int residue_num, std::string atom_name, core::conformation::Residue const &res, std::string const &extras="")
 

Typedef Documentation

typedef utility::pointer::shared_ptr< BestMatchesCollection const > protocols::match::output::BestMatchesCollectionCOP
typedef utility::pointer::shared_ptr< CloudPDBWriter const > protocols::match::output::CloudPDBWriterCOP
typedef utility::pointer::shared_ptr< CloudPDBWriter > protocols::match::output::CloudPDBWriterOP
typedef utility::pointer::shared_ptr< DownstreamRMSEvaluator const > protocols::match::output::DownstreamRMSEvaluatorCOP
typedef utility::pointer::shared_ptr< MatchConsolidator const > protocols::match::output::MatchConsolidatorCOP
typedef utility::pointer::shared_ptr< MatchConsolidator > protocols::match::output::MatchConsolidatorOP
typedef utility::pointer::shared_ptr< MatchEvaluator const > protocols::match::output::MatchEvaluatorCOP
typedef utility::pointer::shared_ptr< MatchEvaluator > protocols::match::output::MatchEvaluatorOP
typedef utility::pointer::shared_ptr< MatchFilter const > protocols::match::output::MatchFilterCOP
typedef utility::pointer::shared_ptr< MatchFilter > protocols::match::output::MatchFilterOP
typedef utility::pointer::shared_ptr< MatchGrouper const > protocols::match::output::MatchGrouperCOP
typedef utility::pointer::shared_ptr< MatchGrouper > protocols::match::output::MatchGrouperOP
typedef utility::pointer::shared_ptr< MatchOutputter const > protocols::match::output::MatchOutputterCOP
typedef utility::pointer::shared_ptr< MatchOutputter > protocols::match::output::MatchOutputterOP
typedef utility::pointer::shared_ptr< MatchProcessor const > protocols::match::output::MatchProcessorCOP
typedef utility::pointer::shared_ptr< MatchProcessor > protocols::match::output::MatchProcessorOP
typedef utility::pointer::shared_ptr<MatchScoreWriter const> protocols::match::output::MatchScoreWriterCOP
typedef utility::pointer::shared_ptr<MatchScoreWriter> protocols::match::output::MatchScoreWriterOP
typedef utility::pointer::shared_ptr< OutputWriter const > protocols::match::output::OutputWriterCOP
typedef utility::pointer::shared_ptr< OutputWriter > protocols::match::output::OutputWriterOP
typedef utility::pointer::shared_ptr< PDBWriter const > protocols::match::output::PDBWriterCOP
typedef utility::pointer::shared_ptr< PDBWriter > protocols::match::output::PDBWriterOP
typedef utility::pointer::shared_ptr< PoseInserter const > protocols::match::output::PoseInserterCOP
typedef utility::pointer::shared_ptr< PoseInserter > protocols::match::output::PoseInserterOP
typedef utility::pointer::shared_ptr< PoseMatchOutputWriter const > protocols::match::output::PoseMatchOutputWriterCOP
typedef utility::pointer::shared_ptr< ProcessorFactory const > protocols::match::output::ProcessorFactoryCOP
typedef utility::pointer::shared_ptr< ProcessorFactory > protocols::match::output::ProcessorFactoryOP
typedef utility::pointer::shared_ptr< SameChiBinComboGrouper const > protocols::match::output::SameChiBinComboGrouperCOP
typedef utility::pointer::shared_ptr< SameSequenceGrouper const > protocols::match::output::SameSequenceGrouperCOP
typedef utility::pointer::shared_ptr< UpstreamHitCacher const > protocols::match::output::UpstreamHitCacherCOP
typedef utility::pointer::shared_ptr< UpstreamHitCacher > protocols::match::output::UpstreamHitCacherOP
typedef utility::pointer::shared_ptr< WriteKinemageOutputter const > protocols::match::output::WriteKinemageOutputterCOP

Function Documentation

std::ostream& protocols::match::output::operator<< ( std::ostream &  output,
MatchScoreWriter const &  object_to_output 
)
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 const &  extras = "" 
)
void protocols::match::output::print_node ( std::ostream &  out,
int  residue_num,
int  atom_num,
core::conformation::Residue const &  res,
std::string const &  extras = "" 
)
void protocols::match::output::print_node ( std::ostream &  out,
int  residue_num,
std::string  atom_name,
core::conformation::Residue const &  res,
std::string const &  extras = "" 
)
static basic::Tracer protocols::match::output::TR ( "protocols.match.output.MatchProcessor"  )
static
static basic::Tracer protocols::match::output::TR ( "protocols.match.output.PDBWriter"  )
static
static basic::Tracer protocols::match::output::TR ( "protocols.match.output.ProcessorFactory"  )
static