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...
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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...
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class | PoseMatchOutputWriter |
| helper class for the MatcherMover that will put a match into a supplied pose More...
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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...
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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...
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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...
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class | UpstreamDownstreamCollisionFilter |
| This class is used to detect collisions between upstream residues and downstream poses. More...
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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...
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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="") |