output

Bindings for protocols::match::output namespace

class pyrosetta.rosetta.protocols.match.output.BestMatchesCollection

Bases: pybind11_builtins.pybind11_object

add_match(self: pyrosetta.rosetta.protocols.match.output.BestMatchesCollection, m: pyrosetta.rosetta.utility.vector1_protocols_match_Hit, score: float) None

C++: protocols::match::output::BestMatchesCollection::add_match(const class utility::vector1<class protocols::match::Hit, class std::allocator<class protocols::match::Hit> > &, double) –> void

add_match_dspos1(self: pyrosetta.rosetta.protocols.match.output.BestMatchesCollection, m: pyrosetta.rosetta.protocols.match.match_dspos1, score: float) None

C++: protocols::match::output::BestMatchesCollection::add_match_dspos1(const struct protocols::match::match_dspos1 &, double) –> void

dspos1_mode(self: pyrosetta.rosetta.protocols.match.output.BestMatchesCollection) bool

C++: protocols::match::output::BestMatchesCollection::dspos1_mode() const –> bool

kept_match(self: pyrosetta.rosetta.protocols.match.output.BestMatchesCollection, which_match: int) pyrosetta.rosetta.utility.vector1_protocols_match_Hit

C++: protocols::match::output::BestMatchesCollection::kept_match(unsigned long) const –> const class utility::vector1<class protocols::match::Hit, class std::allocator<class protocols::match::Hit> > &

kept_match_dspos1(self: pyrosetta.rosetta.protocols.match.output.BestMatchesCollection, which_match: int) pyrosetta.rosetta.protocols.match.match_dspos1

C++: protocols::match::output::BestMatchesCollection::kept_match_dspos1(unsigned long) const –> const struct protocols::match::match_dspos1 &

n_kept_matches(self: pyrosetta.rosetta.protocols.match.output.BestMatchesCollection) int

C++: protocols::match::output::BestMatchesCollection::n_kept_matches() const –> unsigned long

class pyrosetta.rosetta.protocols.match.output.CloudPDBWriter

Bases: pyrosetta.rosetta.protocols.match.output.PDBWriter

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

assemble_remark_lines(self: pyrosetta.rosetta.protocols.match.output.PDBWriter, outpose: pyrosetta.rosetta.core.pose.Pose, upstream_matchres: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, redundant_upstream_res: pyrosetta.rosetta.std.map_unsigned_long_unsigned_long, ex_geom_ids_for_upstream_res: pyrosetta.rosetta.utility.vector1_unsigned_long) None

C++: protocols::match::output::PDBWriter::assemble_remark_lines(class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, const class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

assign(self: pyrosetta.rosetta.protocols.match.output.CloudPDBWriter, : pyrosetta.rosetta.protocols.match.output.CloudPDBWriter) pyrosetta.rosetta.protocols.match.output.CloudPDBWriter

C++: protocols::match::output::CloudPDBWriter::operator=(const class protocols::match::output::CloudPDBWriter &) –> class protocols::match::output::CloudPDBWriter &

create_output_upstream_pose(self: pyrosetta.rosetta.protocols.match.output.PDBWriter, upstream_matchres: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, redundant_upstream_res: pyrosetta.rosetta.std.map_unsigned_long_unsigned_long, ex_geom_ids_for_upstream_res: pyrosetta.rosetta.utility.vector1_unsigned_long) pyrosetta.rosetta.core.pose.Pose

C++: protocols::match::output::PDBWriter::create_output_upstream_pose(const class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, const class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> class std::shared_ptr<const class core::pose::Pose>

cst_io(self: pyrosetta.rosetta.protocols.match.output.OutputWriter) pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO

C++: protocols::match::output::OutputWriter::cst_io() const –> class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::EnzConstraintIO>

cstfile_name(self: pyrosetta.rosetta.protocols.match.output.PDBWriter) str

C++: protocols::match::output::PDBWriter::cstfile_name() const –> std::string

determine_redundant_upstream_matchres(self: pyrosetta.rosetta.protocols.match.output.OutputWriter, m: pyrosetta.rosetta.protocols.match.match_dspos1, redundant_upstream_res: pyrosetta.rosetta.std.map_unsigned_long_unsigned_long) None
determine if any upstream res are at the same scaffold

position, i.e. if one of them is a backbone interaction the redundant_upstream_res map is a mapping from the redundant geometric constraint id of the redundant residue to the geomcst_id of the “nonredundant” res i.e. if cstres 1 happens to be a cys at position 10 and cstres 3 is a gly at position 10 (and it’s backbone is used in satisfying constraint 3), the mapping will contain the 3,1 pair.

C++: protocols::match::output::OutputWriter::determine_redundant_upstream_matchres(const struct protocols::match::match_dspos1 &, class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > > &) const –> void

ds_hitset_end_its(self: pyrosetta.rosetta.protocols.match.output.CloudPDBWriter) pyrosetta.rosetta.utility.vector1_std__Rb_tree_const_iterator_protocols_match_downstream_hit_t

C++: protocols::match::output::CloudPDBWriter::ds_hitset_end_its() const –> const class utility::vector1<struct std::_Rb_tree_const_iterator<class protocols::match::downstream_hit>, class std::allocator<struct std::_Rb_tree_const_iterator<class protocols::match::downstream_hit> > > &

ds_hitset_its(self: pyrosetta.rosetta.protocols.match.output.CloudPDBWriter) pyrosetta.rosetta.utility.vector1_std__Rb_tree_const_iterator_protocols_match_downstream_hit_t

C++: protocols::match::output::CloudPDBWriter::ds_hitset_its() const –> const class utility::vector1<struct std::_Rb_tree_const_iterator<class protocols::match::downstream_hit>, class std::allocator<struct std::_Rb_tree_const_iterator<class protocols::match::downstream_hit> > > &

end_output_writing(self: pyrosetta.rosetta.protocols.match.output.CloudPDBWriter) None

C++: protocols::match::output::CloudPDBWriter::end_output_writing() –> void

initialize_from_matcher_task(self: pyrosetta.rosetta.protocols.match.output.PDBWriter, mtask: pyrosetta.rosetta.protocols.match.MatcherTask) None

C++: protocols::match::output::PDBWriter::initialize_from_matcher_task(class std::shared_ptr<const class protocols::match::MatcherTask>) –> void

match_groups_dshits(self: pyrosetta.rosetta.protocols.match.output.CloudPDBWriter) pyrosetta.rosetta.utility.vector1_utility_vector1_std_set_protocols_match_downstream_hit_std_less_protocols_match_downstream_hit_std_allocator_protocols_match_downstream_hit_std_allocator_std_set_protocols_match_downstream_hit_std_less_protocols_match_downstream_hit_std_allocator_protocols_match_downstream_hit_t

C++: protocols::match::output::CloudPDBWriter::match_groups_dshits() const –> const class utility::vector1<class utility::vector1<class std::set<class protocols::match::downstream_hit, struct std::less<class protocols::match::downstream_hit>, class std::allocator<class protocols::match::downstream_hit> >, class std::allocator<class std::set<class protocols::match::downstream_hit, struct std::less<class protocols::match::downstream_hit>, class std::allocator<class protocols::match::downstream_hit> > > >, class std::allocator<class utility::vector1<class std::set<class protocols::match::downstream_hit, struct std::less<class protocols::match::downstream_hit>, class std::allocator<class protocols::match::downstream_hit> >, class std::allocator<class std::set<class protocols::match::downstream_hit, struct std::less<class protocols::match::downstream_hit>, class std::allocator<class protocols::match::downstream_hit> > > > > > &

match_groups_ushits(self: pyrosetta.rosetta.protocols.match.output.CloudPDBWriter) pyrosetta.rosetta.utility.vector1_utility_vector1_std_set_protocols_match_upstream_hit_std_less_protocols_match_upstream_hit_std_allocator_protocols_match_upstream_hit_std_allocator_std_set_protocols_match_upstream_hit_std_less_protocols_match_upstream_hit_std_allocator_protocols_match_upstream_hit_t

C++: protocols::match::output::CloudPDBWriter::match_groups_ushits() const –> const class utility::vector1<class utility::vector1<class std::set<class protocols::match::upstream_hit, struct std::less<class protocols::match::upstream_hit>, class std::allocator<class protocols::match::upstream_hit> >, class std::allocator<class std::set<class protocols::match::upstream_hit, struct std::less<class protocols::match::upstream_hit>, class std::allocator<class protocols::match::upstream_hit> > > >, class std::allocator<class utility::vector1<class std::set<class protocols::match::upstream_hit, struct std::less<class protocols::match::upstream_hit>, class std::allocator<class protocols::match::upstream_hit> >, class std::allocator<class std::set<class protocols::match::upstream_hit, struct std::less<class protocols::match::upstream_hit>, class std::allocator<class protocols::match::upstream_hit> > > > > > &

num_geom_cst(self: pyrosetta.rosetta.protocols.match.output.PDBWriter) int

C++: protocols::match::output::PDBWriter::num_geom_cst() const –> unsigned long

prefix(self: pyrosetta.rosetta.protocols.match.output.PDBWriter) str

C++: protocols::match::output::PDBWriter::prefix() const –> std::string

prepare_for_output_writing(self: pyrosetta.rosetta.protocols.match.output.CloudPDBWriter) None

C++: protocols::match::output::CloudPDBWriter::prepare_for_output_writing() –> void

record_match(*args, **kwargs)

Overloaded function.

  1. record_match(self: pyrosetta.rosetta.protocols.match.output.CloudPDBWriter, m: pyrosetta.rosetta.utility.vector1_protocols_match_Hit, evaluator: pyrosetta.rosetta.protocols.match.output.MatchEvaluator, match_score_writer: pyrosetta.rosetta.protocols.match.output.MatchScoreWriter) -> None

no writing in this function, only saving the hits according

to what group they belong to

C++: protocols::match::output::CloudPDBWriter::record_match(const class utility::vector1<class protocols::match::Hit, class std::allocator<class protocols::match::Hit> > &, class std::shared_ptr<class protocols::match::output::MatchEvaluator>, class std::shared_ptr<class protocols::match::output::MatchScoreWriter>) –> void

  1. record_match(self: pyrosetta.rosetta.protocols.match.output.CloudPDBWriter, m: pyrosetta.rosetta.protocols.match.match_dspos1) -> None

C++: protocols::match::output::CloudPDBWriter::record_match(const struct protocols::match::match_dspos1 &) –> void

representative_group_matches(self: pyrosetta.rosetta.protocols.match.output.CloudPDBWriter) pyrosetta.rosetta.utility.vector1_protocols_match_match_dspos1

C++: protocols::match::output::CloudPDBWriter::representative_group_matches() const –> const class utility::vector1<struct protocols::match::match_dspos1, class std::allocator<struct protocols::match::match_dspos1> > &

scaf_name(self: pyrosetta.rosetta.protocols.match.output.PDBWriter) str

C++: protocols::match::output::PDBWriter::scaf_name() const –> std::string

set_coordinate_cacher(self: pyrosetta.rosetta.protocols.match.output.PDBWriter, : protocols::match::output::UpstreamHitCacher) None

C++: protocols::match::output::PDBWriter::set_coordinate_cacher(class std::shared_ptr<class protocols::match::output::UpstreamHitCacher>) –> void

set_downstream_builder(self: pyrosetta.rosetta.protocols.match.output.PDBWriter, geomcst_id: int, dsbuilder: pyrosetta.rosetta.protocols.match.downstream.DownstreamBuilder) None

C++: protocols::match::output::PDBWriter::set_downstream_builder(unsigned long, class std::shared_ptr<const class protocols::match::downstream::DownstreamBuilder>) –> void

set_prefix(self: pyrosetta.rosetta.protocols.match.output.PDBWriter, prefix: str) None

C++: protocols::match::output::PDBWriter::set_prefix(const std::string &) –> void

signature_string(self: pyrosetta.rosetta.protocols.match.output.PDBWriter, upstream_matchres: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) str

C++: protocols::match::output::PDBWriter::signature_string(const class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &) const –> std::string

write_match_groups(self: pyrosetta.rosetta.protocols.match.output.CloudPDBWriter) None

this is where the actual writing happens

C++: protocols::match::output::CloudPDBWriter::write_match_groups() –> void

class pyrosetta.rosetta.protocols.match.output.DownstreamCoordinateKinemageWriter

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.match.output.DownstreamCoordinateKinemageWriter, : pyrosetta.rosetta.protocols.match.output.DownstreamCoordinateKinemageWriter) pyrosetta.rosetta.protocols.match.output.DownstreamCoordinateKinemageWriter

C++: protocols::match::output::DownstreamCoordinateKinemageWriter::operator=(const class protocols::match::output::DownstreamCoordinateKinemageWriter &) –> class protocols::match::output::DownstreamCoordinateKinemageWriter &

set_downstream_master(self: pyrosetta.rosetta.protocols.match.output.DownstreamCoordinateKinemageWriter, str: str) None

C++: protocols::match::output::DownstreamCoordinateKinemageWriter::set_downstream_master(const std::string &) –> void

write_downstream_coordinates(self: pyrosetta.rosetta.protocols.match.output.DownstreamCoordinateKinemageWriter, hit: pyrosetta.rosetta.protocols.match.Hit, ostr: pyrosetta.rosetta.std.ostream) None

C++: protocols::match::output::DownstreamCoordinateKinemageWriter::write_downstream_coordinates(const class protocols::match::Hit &, std::ostream &) const –> void

class pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator

Bases: pyrosetta.rosetta.protocols.match.output.MatchEvaluator

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.

assign(self: pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator, : pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator) pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator

C++: protocols::match::output::DownstreamRMSEvaluator::operator=(const class protocols::match::output::DownstreamRMSEvaluator &) –> class protocols::match::output::DownstreamRMSEvaluator &

score(*args, **kwargs)

Overloaded function.

  1. score(self: pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator, m: pyrosetta.rosetta.utility.vector1_protocols_match_Hit) -> float

C++: protocols::match::output::DownstreamRMSEvaluator::score(const class utility::vector1<class protocols::match::Hit, class std::allocator<class protocols::match::Hit> > &) const –> double

  1. score(self: pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator, m: pyrosetta.rosetta.protocols.match.match_dspos1) -> float

Causes a graceful exit. The DownstreamRMSEvaluator is incompatible with

the match_dspos1 match definition!

C++: protocols::match::output::DownstreamRMSEvaluator::score(const struct protocols::match::match_dspos1 &) const –> double

set_downstream_builder(self: pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator, which_geom_cst: int, ds_builder: pyrosetta.rosetta.protocols.match.downstream.DownstreamBuilder) None

C++: protocols::match::output::DownstreamRMSEvaluator::set_downstream_builder(unsigned long, class std::shared_ptr<const class protocols::match::downstream::DownstreamBuilder>) –> void

set_downstream_pose(self: pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator, dspose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::match::output::DownstreamRMSEvaluator::set_downstream_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_n_geometric_constraints(self: pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator, setting: int) None

C++: protocols::match::output::DownstreamRMSEvaluator::set_n_geometric_constraints(unsigned long) –> void

class pyrosetta.rosetta.protocols.match.output.LimitHitsPerRotamerFilter

Bases: pyrosetta.rosetta.protocols.match.output.StateAccumulatingMatchFilter

assign(self: pyrosetta.rosetta.protocols.match.output.LimitHitsPerRotamerFilter, : pyrosetta.rosetta.protocols.match.output.LimitHitsPerRotamerFilter) pyrosetta.rosetta.protocols.match.output.LimitHitsPerRotamerFilter

C++: protocols::match::output::LimitHitsPerRotamerFilter::operator=(const class protocols::match::output::LimitHitsPerRotamerFilter &) –> class protocols::match::output::LimitHitsPerRotamerFilter &

filter_name(self: pyrosetta.rosetta.protocols.match.output.MatchFilter) str

C++: protocols::match::output::MatchFilter::filter_name() const –> std::string

note_match_accepted(self: pyrosetta.rosetta.protocols.match.output.LimitHitsPerRotamerFilter, m: pyrosetta.rosetta.utility.vector1_protocols_match_Hit) None

Note that a particular match has passed all the filters and will be output.

C++: protocols::match::output::LimitHitsPerRotamerFilter::note_match_accepted(const class utility::vector1<class protocols::match::Hit, class std::allocator<class protocols::match::Hit> > &) –> void

passes_filter(self: pyrosetta.rosetta.protocols.match.output.LimitHitsPerRotamerFilter, m: pyrosetta.rosetta.utility.vector1_protocols_match_Hit) bool

Returns true if the given match passes this filter

C++: protocols::match::output::LimitHitsPerRotamerFilter::passes_filter(const class utility::vector1<class protocols::match::Hit, class std::allocator<class protocols::match::Hit> > &) const –> bool

reset(self: pyrosetta.rosetta.protocols.match.output.LimitHitsPerRotamerFilter) None

Erase all tracking data on which matches have already been output.

C++: protocols::match::output::LimitHitsPerRotamerFilter::reset() –> void

set_limit_for_rotamer_combo(self: pyrosetta.rosetta.protocols.match.output.LimitHitsPerRotamerFilter, limit: int) None

C++: protocols::match::output::LimitHitsPerRotamerFilter::set_limit_for_rotamer_combo(unsigned long) –> void

set_n_geometric_constraints(self: pyrosetta.rosetta.protocols.match.output.LimitHitsPerRotamerFilter, n_csts: int) None

C++: protocols::match::output::LimitHitsPerRotamerFilter::set_n_geometric_constraints(unsigned long) –> void

class pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter

Bases: pyrosetta.rosetta.protocols.match.output.MatchFilter

assign(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter, : pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter) pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter

C++: protocols::match::output::MatchCollisionFilter::operator=(const class protocols::match::output::MatchCollisionFilter &) –> class protocols::match::output::MatchCollisionFilter &

bump_grid(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter) pyrosetta.rosetta.protocols.match.BumpGrid

C++: protocols::match::output::MatchCollisionFilter::bump_grid() const –> class std::shared_ptr<const class protocols::match::BumpGrid>

empty_pose(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter) pyrosetta.rosetta.core.pose.Pose

C++: protocols::match::output::MatchCollisionFilter::empty_pose() const –> class std::shared_ptr<const class core::pose::Pose>

empty_sfxn(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter) pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::match::output::MatchCollisionFilter::empty_sfxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

etable_energy(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter) pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy

C++: protocols::match::output::MatchCollisionFilter::etable_energy() const –> class std::shared_ptr<const class core::scoring::methods::ShortRangeTwoBodyEnergy>

filter_by_lj(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter) bool

C++: protocols::match::output::MatchCollisionFilter::filter_by_lj() const –> bool

filter_name(self: pyrosetta.rosetta.protocols.match.output.MatchFilter) str

C++: protocols::match::output::MatchFilter::filter_name() const –> std::string

lj_cutoff(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter) float

C++: protocols::match::output::MatchCollisionFilter::lj_cutoff() const –> double

passes_filter(*args, **kwargs)

Overloaded function.

  1. passes_filter(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter, m: pyrosetta.rosetta.utility.vector1_protocols_match_Hit) -> bool

C++: protocols::match::output::MatchCollisionFilter::passes_filter(const class utility::vector1<class protocols::match::Hit, class std::allocator<class protocols::match::Hit> > &) const –> bool

  1. passes_filter(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter, m: pyrosetta.rosetta.protocols.match.match_dspos1) -> bool

C++: protocols::match::output::MatchCollisionFilter::passes_filter(const struct protocols::match::match_dspos1 &) const –> bool

set_filter_by_lj(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter, setting: bool) None

C++: protocols::match::output::MatchCollisionFilter::set_filter_by_lj(bool) –> void

set_lj_atr_weight(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter, setting: float) None

C++: protocols::match::output::MatchCollisionFilter::set_lj_atr_weight(double) –> void

set_lj_cutoff(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter, setting: float) None

C++: protocols::match::output::MatchCollisionFilter::set_lj_cutoff(double) –> void

set_lj_rep_weight(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter, setting: float) None

C++: protocols::match::output::MatchCollisionFilter::set_lj_rep_weight(double) –> void

set_lj_sol_weight(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter, setting: float) None

C++: protocols::match::output::MatchCollisionFilter::set_lj_sol_weight(double) –> void

set_tolerated_overlap(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter, setting: float) None

C++: protocols::match::output::MatchCollisionFilter::set_tolerated_overlap(double) –> void

tolerated_overlap(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter) float

C++: protocols::match::output::MatchCollisionFilter::tolerated_overlap() const –> double

wfa_atr(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter) float

C++: protocols::match::output::MatchCollisionFilter::wfa_atr() const –> double

wfa_rep(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter) float

C++: protocols::match::output::MatchCollisionFilter::wfa_rep() const –> double

wfa_sol(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter) float

C++: protocols::match::output::MatchCollisionFilter::wfa_sol() const –> double

class pyrosetta.rosetta.protocols.match.output.MatchConsolidator

Bases: pyrosetta.rosetta.protocols.match.output.MatchProcessor

add_filter(self: pyrosetta.rosetta.protocols.match.output.MatchProcessor, filter: pyrosetta.rosetta.protocols.match.output.MatchFilter) None

C++: protocols::match::output::MatchProcessor::add_filter(class std::shared_ptr<class protocols::match::output::MatchFilter>) –> void

assign(self: pyrosetta.rosetta.protocols.match.output.MatchConsolidator, : pyrosetta.rosetta.protocols.match.output.MatchConsolidator) pyrosetta.rosetta.protocols.match.output.MatchConsolidator

C++: protocols::match::output::MatchConsolidator::operator=(const class protocols::match::output::MatchConsolidator &) –> class protocols::match::output::MatchConsolidator &

begin_processing(self: pyrosetta.rosetta.protocols.match.output.MatchConsolidator) None

C++: protocols::match::output::MatchConsolidator::begin_processing() –> void

clear_filters(self: pyrosetta.rosetta.protocols.match.output.MatchProcessor) None

C++: protocols::match::output::MatchProcessor::clear_filters() –> void

end_processing(self: pyrosetta.rosetta.protocols.match.output.MatchConsolidator) None

C++: protocols::match::output::MatchConsolidator::end_processing() –> void

match_processing_successful(self: pyrosetta.rosetta.protocols.match.output.MatchProcessor) bool

C++: protocols::match::output::MatchProcessor::match_processing_successful() const –> bool

output_writer(self: pyrosetta.rosetta.protocols.match.output.MatchProcessor) protocols::match::output::OutputWriter
const access to the output writer, e.g.

for the MatcherMover when incorporating matches into the pose

C++: protocols::match::output::MatchProcessor::output_writer() –> class std::shared_ptr<class protocols::match::output::OutputWriter>

process_match(*args, **kwargs)

Overloaded function.

  1. process_match(self: pyrosetta.rosetta.protocols.match.output.MatchConsolidator, m: pyrosetta.rosetta.utility.vector1_protocols_match_Hit) -> None

C++: protocols::match::output::MatchConsolidator::process_match(const class utility::vector1<class protocols::match::Hit, class std::allocator<class protocols::match::Hit> > &) –> void

  1. process_match(self: pyrosetta.rosetta.protocols.match.output.MatchConsolidator, m: pyrosetta.rosetta.protocols.match.match_dspos1) -> None

C++: protocols::match::output::MatchConsolidator::process_match(const struct protocols::match::match_dspos1 &) –> void

reset_filters(self: pyrosetta.rosetta.protocols.match.output.MatchProcessor) None

C++: protocols::match::output::MatchProcessor::reset_filters() –> void

reset_grouper(self: pyrosetta.rosetta.protocols.match.output.MatchConsolidator) None

C++: protocols::match::output::MatchConsolidator::reset_grouper() –> void

set_evaluator(self: pyrosetta.rosetta.protocols.match.output.MatchProcessor, evaluator: pyrosetta.rosetta.protocols.match.output.MatchEvaluator) None

C++: protocols::match::output::MatchProcessor::set_evaluator(class std::shared_ptr<class protocols::match::output::MatchEvaluator>) –> void

set_grouper(self: pyrosetta.rosetta.protocols.match.output.MatchConsolidator, grouper: protocols::match::output::MatchGrouper) None

C++: protocols::match::output::MatchConsolidator::set_grouper(class std::shared_ptr<class protocols::match::output::MatchGrouper>) –> void

set_match_score_writer(self: pyrosetta.rosetta.protocols.match.output.MatchProcessor, scorewriter: protocols::match::output::MatchScoreWriter) None

C++: protocols::match::output::MatchProcessor::set_match_score_writer(class std::shared_ptr<class protocols::match::output::MatchScoreWriter>) –> void

set_n_to_output_per_group(self: pyrosetta.rosetta.protocols.match.output.MatchConsolidator, setting: int) None

C++: protocols::match::output::MatchConsolidator::set_n_to_output_per_group(unsigned long) –> void

set_output_writer(self: pyrosetta.rosetta.protocols.match.output.MatchProcessor, writer: protocols::match::output::OutputWriter) None

C++: protocols::match::output::MatchProcessor::set_output_writer(class std::shared_ptr<class protocols::match::output::OutputWriter>) –> void

up_coll_filt(self: pyrosetta.rosetta.protocols.match.output.MatchProcessor) protocols::match::output::UpstreamCollisionFilter

C++: protocols::match::output::MatchProcessor::up_coll_filt() const –> class std::shared_ptr<const class protocols::match::output::UpstreamCollisionFilter>

up_down_filt(self: pyrosetta.rosetta.protocols.match.output.MatchProcessor) protocols::match::output::UpstreamDownstreamCollisionFilter

C++: protocols::match::output::MatchProcessor::up_down_filt() const –> class std::shared_ptr<const class protocols::match::output::UpstreamDownstreamCollisionFilter>

class pyrosetta.rosetta.protocols.match.output.MatchEvaluator

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.match.output.MatchEvaluator, : pyrosetta.rosetta.protocols.match.output.MatchEvaluator) pyrosetta.rosetta.protocols.match.output.MatchEvaluator

C++: protocols::match::output::MatchEvaluator::operator=(const class protocols::match::output::MatchEvaluator &) –> class protocols::match::output::MatchEvaluator &

score(*args, **kwargs)

Overloaded function.

  1. score(self: pyrosetta.rosetta.protocols.match.output.MatchEvaluator, m: pyrosetta.rosetta.utility.vector1_protocols_match_Hit) -> float

C++: protocols::match::output::MatchEvaluator::score(const class utility::vector1<class protocols::match::Hit, class std::allocator<class protocols::match::Hit> > &) const –> double

  1. score(self: pyrosetta.rosetta.protocols.match.output.MatchEvaluator, m: pyrosetta.rosetta.protocols.match.match_dspos1) -> float

C++: protocols::match::output::MatchEvaluator::score(const struct protocols::match::match_dspos1 &) const –> double

class pyrosetta.rosetta.protocols.match.output.MatchFilter

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.match.output.MatchFilter, : pyrosetta.rosetta.protocols.match.output.MatchFilter) pyrosetta.rosetta.protocols.match.output.MatchFilter

C++: protocols::match::output::MatchFilter::operator=(const class protocols::match::output::MatchFilter &) –> class protocols::match::output::MatchFilter &

filter_name(self: pyrosetta.rosetta.protocols.match.output.MatchFilter) str

C++: protocols::match::output::MatchFilter::filter_name() const –> std::string

passes_filter(*args, **kwargs)

Overloaded function.

  1. passes_filter(self: pyrosetta.rosetta.protocols.match.output.MatchFilter, m: pyrosetta.rosetta.utility.vector1_protocols_match_Hit) -> bool

Returns true if the given match passes this filter

C++: protocols::match::output::MatchFilter::passes_filter(const class utility::vector1<class protocols::match::Hit, class std::allocator<class protocols::match::Hit> > &) const –> bool

  1. passes_filter(self: pyrosetta.rosetta.protocols.match.output.MatchFilter, m: pyrosetta.rosetta.protocols.match.match_dspos1) -> bool

C++: protocols::match::output::MatchFilter::passes_filter(const struct protocols::match::match_dspos1 &) const –> bool

class pyrosetta.rosetta.protocols.match.output.MatchGrouper

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.match.output.MatchGrouper, : pyrosetta.rosetta.protocols.match.output.MatchGrouper) pyrosetta.rosetta.protocols.match.output.MatchGrouper

C++: protocols::match::output::MatchGrouper::operator=(const class protocols::match::output::MatchGrouper &) –> class protocols::match::output::MatchGrouper &

assign_group_for_match(*args, **kwargs)

Overloaded function.

  1. assign_group_for_match(self: pyrosetta.rosetta.protocols.match.output.MatchGrouper, m: pyrosetta.rosetta.utility.vector1_protocols_match_Hit) -> int

C++: protocols::match::output::MatchGrouper::assign_group_for_match(const class utility::vector1<class protocols::match::Hit, class std::allocator<class protocols::match::Hit> > &) –> unsigned long

  1. assign_group_for_match(self: pyrosetta.rosetta.protocols.match.output.MatchGrouper, m: pyrosetta.rosetta.protocols.match.match_dspos1) -> int

C++: protocols::match::output::MatchGrouper::assign_group_for_match(const struct protocols::match::match_dspos1 &) –> unsigned long

reset(self: pyrosetta.rosetta.protocols.match.output.MatchGrouper) None

C++: protocols::match::output::MatchGrouper::reset() –> void

class pyrosetta.rosetta.protocols.match.output.MatchOutputter

Bases: pyrosetta.rosetta.protocols.match.output.MatchProcessor

add_filter(self: pyrosetta.rosetta.protocols.match.output.MatchProcessor, filter: pyrosetta.rosetta.protocols.match.output.MatchFilter) None

C++: protocols::match::output::MatchProcessor::add_filter(class std::shared_ptr<class protocols::match::output::MatchFilter>) –> void

assign(self: pyrosetta.rosetta.protocols.match.output.MatchOutputter, : pyrosetta.rosetta.protocols.match.output.MatchOutputter) pyrosetta.rosetta.protocols.match.output.MatchOutputter

C++: protocols::match::output::MatchOutputter::operator=(const class protocols::match::output::MatchOutputter &) –> class protocols::match::output::MatchOutputter &

begin_processing(self: pyrosetta.rosetta.protocols.match.output.MatchOutputter) None

C++: protocols::match::output::MatchOutputter::begin_processing() –> void

clear_filters(self: pyrosetta.rosetta.protocols.match.output.MatchProcessor) None

C++: protocols::match::output::MatchProcessor::clear_filters() –> void

end_processing(self: pyrosetta.rosetta.protocols.match.output.MatchOutputter) None

C++: protocols::match::output::MatchOutputter::end_processing() –> void

match_processing_successful(self: pyrosetta.rosetta.protocols.match.output.MatchProcessor) bool

C++: protocols::match::output::MatchProcessor::match_processing_successful() const –> bool

output_writer(self: pyrosetta.rosetta.protocols.match.output.MatchProcessor) protocols::match::output::OutputWriter
const access to the output writer, e.g.

for the MatcherMover when incorporating matches into the pose

C++: protocols::match::output::MatchProcessor::output_writer() –> class std::shared_ptr<class protocols::match::output::OutputWriter>

process_match(*args, **kwargs)

Overloaded function.

  1. process_match(self: pyrosetta.rosetta.protocols.match.output.MatchOutputter, m: pyrosetta.rosetta.utility.vector1_protocols_match_Hit) -> None

C++: protocols::match::output::MatchOutputter::process_match(const class utility::vector1<class protocols::match::Hit, class std::allocator<class protocols::match::Hit> > &) –> void

  1. process_match(self: pyrosetta.rosetta.protocols.match.output.MatchOutputter, m: pyrosetta.rosetta.protocols.match.match_dspos1) -> None

C++: protocols::match::output::MatchOutputter::process_match(const struct protocols::match::match_dspos1 &) –> void

reset_filters(self: pyrosetta.rosetta.protocols.match.output.MatchProcessor) None

C++: protocols::match::output::MatchProcessor::reset_filters() –> void

set_evaluator(self: pyrosetta.rosetta.protocols.match.output.MatchProcessor, evaluator: pyrosetta.rosetta.protocols.match.output.MatchEvaluator) None

C++: protocols::match::output::MatchProcessor::set_evaluator(class std::shared_ptr<class protocols::match::output::MatchEvaluator>) –> void

set_match_score_writer(self: pyrosetta.rosetta.protocols.match.output.MatchProcessor, scorewriter: protocols::match::output::MatchScoreWriter) None

C++: protocols::match::output::MatchProcessor::set_match_score_writer(class std::shared_ptr<class protocols::match::output::MatchScoreWriter>) –> void

set_output_writer(self: pyrosetta.rosetta.protocols.match.output.MatchProcessor, writer: protocols::match::output::OutputWriter) None

C++: protocols::match::output::MatchProcessor::set_output_writer(class std::shared_ptr<class protocols::match::output::OutputWriter>) –> void

up_coll_filt(self: pyrosetta.rosetta.protocols.match.output.MatchProcessor) protocols::match::output::UpstreamCollisionFilter

C++: protocols::match::output::MatchProcessor::up_coll_filt() const –> class std::shared_ptr<const class protocols::match::output::UpstreamCollisionFilter>

up_down_filt(self: pyrosetta.rosetta.protocols.match.output.MatchProcessor) protocols::match::output::UpstreamDownstreamCollisionFilter

C++: protocols::match::output::MatchProcessor::up_down_filt() const –> class std::shared_ptr<const class protocols::match::output::UpstreamDownstreamCollisionFilter>

class pyrosetta.rosetta.protocols.match.output.MatchProcessor

Bases: pybind11_builtins.pybind11_object

add_filter(self: pyrosetta.rosetta.protocols.match.output.MatchProcessor, filter: pyrosetta.rosetta.protocols.match.output.MatchFilter) None

C++: protocols::match::output::MatchProcessor::add_filter(class std::shared_ptr<class protocols::match::output::MatchFilter>) –> void

assign(self: pyrosetta.rosetta.protocols.match.output.MatchProcessor, : pyrosetta.rosetta.protocols.match.output.MatchProcessor) pyrosetta.rosetta.protocols.match.output.MatchProcessor

C++: protocols::match::output::MatchProcessor::operator=(const class protocols::match::output::MatchProcessor &) –> class protocols::match::output::MatchProcessor &

begin_processing(self: pyrosetta.rosetta.protocols.match.output.MatchProcessor) None
Invoked by the Matcher before it begins feeding matches to the processor.

Base-class has a no-op implementation.

C++: protocols::match::output::MatchProcessor::begin_processing() –> void

clear_filters(self: pyrosetta.rosetta.protocols.match.output.MatchProcessor) None

C++: protocols::match::output::MatchProcessor::clear_filters() –> void

end_processing(self: pyrosetta.rosetta.protocols.match.output.MatchProcessor) None
Invoked by the Matcher after it finishes feeding matches to the processor.

Base-class has a no-op implementation.

C++: protocols::match::output::MatchProcessor::end_processing() –> void

match_processing_successful(self: pyrosetta.rosetta.protocols.match.output.MatchProcessor) bool

C++: protocols::match::output::MatchProcessor::match_processing_successful() const –> bool

output_writer(self: pyrosetta.rosetta.protocols.match.output.MatchProcessor) protocols::match::output::OutputWriter
const access to the output writer, e.g.

for the MatcherMover when incorporating matches into the pose

C++: protocols::match::output::MatchProcessor::output_writer() –> class std::shared_ptr<class protocols::match::output::OutputWriter>

process_match(*args, **kwargs)

Overloaded function.

  1. process_match(self: pyrosetta.rosetta.protocols.match.output.MatchProcessor, m: pyrosetta.rosetta.utility.vector1_protocols_match_Hit) -> None

C++: protocols::match::output::MatchProcessor::process_match(const class utility::vector1<class protocols::match::Hit, class std::allocator<class protocols::match::Hit> > &) –> void

  1. process_match(self: pyrosetta.rosetta.protocols.match.output.MatchProcessor, m: pyrosetta.rosetta.protocols.match.match_dspos1) -> None

C++: protocols::match::output::MatchProcessor::process_match(const struct protocols::match::match_dspos1 &) –> void

reset_filters(self: pyrosetta.rosetta.protocols.match.output.MatchProcessor) None

C++: protocols::match::output::MatchProcessor::reset_filters() –> void

set_evaluator(self: pyrosetta.rosetta.protocols.match.output.MatchProcessor, evaluator: pyrosetta.rosetta.protocols.match.output.MatchEvaluator) None

C++: protocols::match::output::MatchProcessor::set_evaluator(class std::shared_ptr<class protocols::match::output::MatchEvaluator>) –> void

set_match_score_writer(self: pyrosetta.rosetta.protocols.match.output.MatchProcessor, scorewriter: protocols::match::output::MatchScoreWriter) None

C++: protocols::match::output::MatchProcessor::set_match_score_writer(class std::shared_ptr<class protocols::match::output::MatchScoreWriter>) –> void

set_output_writer(self: pyrosetta.rosetta.protocols.match.output.MatchProcessor, writer: protocols::match::output::OutputWriter) None

C++: protocols::match::output::MatchProcessor::set_output_writer(class std::shared_ptr<class protocols::match::output::OutputWriter>) –> void

up_coll_filt(self: pyrosetta.rosetta.protocols.match.output.MatchProcessor) protocols::match::output::UpstreamCollisionFilter

C++: protocols::match::output::MatchProcessor::up_coll_filt() const –> class std::shared_ptr<const class protocols::match::output::UpstreamCollisionFilter>

up_down_filt(self: pyrosetta.rosetta.protocols.match.output.MatchProcessor) protocols::match::output::UpstreamDownstreamCollisionFilter

C++: protocols::match::output::MatchProcessor::up_down_filt() const –> class std::shared_ptr<const class protocols::match::output::UpstreamDownstreamCollisionFilter>

class pyrosetta.rosetta.protocols.match.output.MatchScoreWriter

Bases: pybind11_builtins.pybind11_object

Writes out a score file based on the sum of RMS of geometric constrainst satisfaction with the desired ligan positioning

add_match(*args, **kwargs)

Overloaded function.

  1. add_match(self: pyrosetta.rosetta.protocols.match.output.MatchScoreWriter, match_name: str, score: float) -> None

Add a match name (along with score) to be outputed in score file

C++: protocols::match::output::MatchScoreWriter::add_match(std::string, double) –> void

  1. add_match(self: pyrosetta.rosetta.protocols.match.output.MatchScoreWriter, score: float) -> None

Add an unnamed match (along with score) to be outputed in score file

Each additional match will have an incremented name

C++: protocols::match::output::MatchScoreWriter::add_match(double) –> void

assign(self: pyrosetta.rosetta.protocols.match.output.MatchScoreWriter, object_to_copy: pyrosetta.rosetta.protocols.match.output.MatchScoreWriter) pyrosetta.rosetta.protocols.match.output.MatchScoreWriter

C++: protocols::match::output::MatchScoreWriter::operator=(const class protocols::match::output::MatchScoreWriter &) –> class protocols::match::output::MatchScoreWriter &

set_output(self: pyrosetta.rosetta.protocols.match.output.MatchScoreWriter, output_on: bool) None

Set whether or not to output

C++: protocols::match::output::MatchScoreWriter::set_output(bool) –> void

set_output_filename(self: pyrosetta.rosetta.protocols.match.output.MatchScoreWriter, output_filename: str) None

Set output filename, which also turns on output

C++: protocols::match::output::MatchScoreWriter::set_output_filename(std::string) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.match.output.MatchScoreWriter) -> None

  2. show(self: pyrosetta.rosetta.protocols.match.output.MatchScoreWriter, output: pyrosetta.rosetta.std.ostream) -> None

Generate string representation of MatchScoreWriter for debugging purposes.

C++: protocols::match::output::MatchScoreWriter::show(std::ostream &) const –> void

write_match_scores(self: pyrosetta.rosetta.protocols.match.output.MatchScoreWriter) None

Write out the match scores once all scores have been added

C++: protocols::match::output::MatchScoreWriter::write_match_scores() –> void

class pyrosetta.rosetta.protocols.match.output.OutputWriter

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.match.output.OutputWriter, : pyrosetta.rosetta.protocols.match.output.OutputWriter) pyrosetta.rosetta.protocols.match.output.OutputWriter

C++: protocols::match::output::OutputWriter::operator=(const class protocols::match::output::OutputWriter &) –> class protocols::match::output::OutputWriter &

cst_io(self: pyrosetta.rosetta.protocols.match.output.OutputWriter) pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO

C++: protocols::match::output::OutputWriter::cst_io() const –> class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::EnzConstraintIO>

determine_redundant_upstream_matchres(self: pyrosetta.rosetta.protocols.match.output.OutputWriter, m: pyrosetta.rosetta.protocols.match.match_dspos1, redundant_upstream_res: pyrosetta.rosetta.std.map_unsigned_long_unsigned_long) None
determine if any upstream res are at the same scaffold

position, i.e. if one of them is a backbone interaction the redundant_upstream_res map is a mapping from the redundant geometric constraint id of the redundant residue to the geomcst_id of the “nonredundant” res i.e. if cstres 1 happens to be a cys at position 10 and cstres 3 is a gly at position 10 (and it’s backbone is used in satisfying constraint 3), the mapping will contain the 3,1 pair.

C++: protocols::match::output::OutputWriter::determine_redundant_upstream_matchres(const struct protocols::match::match_dspos1 &, class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > > &) const –> void

end_output_writing(self: pyrosetta.rosetta.protocols.match.output.OutputWriter) None

C++: protocols::match::output::OutputWriter::end_output_writing() –> void

initialize_from_matcher_task(self: pyrosetta.rosetta.protocols.match.output.OutputWriter, mtask: pyrosetta.rosetta.protocols.match.MatcherTask) None

C++: protocols::match::output::OutputWriter::initialize_from_matcher_task(class std::shared_ptr<const class protocols::match::MatcherTask>) –> void

prepare_for_output_writing(self: pyrosetta.rosetta.protocols.match.output.OutputWriter) None

C++: protocols::match::output::OutputWriter::prepare_for_output_writing() –> void

record_match(*args, **kwargs)

Overloaded function.

  1. record_match(self: pyrosetta.rosetta.protocols.match.output.OutputWriter, m: pyrosetta.rosetta.utility.vector1_protocols_match_Hit, evaluator: pyrosetta.rosetta.protocols.match.output.MatchEvaluator, match_score_writer: pyrosetta.rosetta.protocols.match.output.MatchScoreWriter) -> None

C++: protocols::match::output::OutputWriter::record_match(const class utility::vector1<class protocols::match::Hit, class std::allocator<class protocols::match::Hit> > &, class std::shared_ptr<class protocols::match::output::MatchEvaluator>, class std::shared_ptr<class protocols::match::output::MatchScoreWriter>) –> void

  1. record_match(self: pyrosetta.rosetta.protocols.match.output.OutputWriter, m: pyrosetta.rosetta.protocols.match.match_dspos1) -> None

evaluator and score writer are not passed in because single-downstream-position match currently have no way of being evaluated

C++: protocols::match::output::OutputWriter::record_match(const struct protocols::match::match_dspos1 &) –> void

class pyrosetta.rosetta.protocols.match.output.PDBWriter

Bases: pyrosetta.rosetta.protocols.match.output.OutputWriter

assemble_remark_lines(self: pyrosetta.rosetta.protocols.match.output.PDBWriter, outpose: pyrosetta.rosetta.core.pose.Pose, upstream_matchres: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, redundant_upstream_res: pyrosetta.rosetta.std.map_unsigned_long_unsigned_long, ex_geom_ids_for_upstream_res: pyrosetta.rosetta.utility.vector1_unsigned_long) None

C++: protocols::match::output::PDBWriter::assemble_remark_lines(class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, const class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

assign(self: pyrosetta.rosetta.protocols.match.output.PDBWriter, : pyrosetta.rosetta.protocols.match.output.PDBWriter) pyrosetta.rosetta.protocols.match.output.PDBWriter

C++: protocols::match::output::PDBWriter::operator=(const class protocols::match::output::PDBWriter &) –> class protocols::match::output::PDBWriter &

create_output_upstream_pose(self: pyrosetta.rosetta.protocols.match.output.PDBWriter, upstream_matchres: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, redundant_upstream_res: pyrosetta.rosetta.std.map_unsigned_long_unsigned_long, ex_geom_ids_for_upstream_res: pyrosetta.rosetta.utility.vector1_unsigned_long) pyrosetta.rosetta.core.pose.Pose

C++: protocols::match::output::PDBWriter::create_output_upstream_pose(const class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, const class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> class std::shared_ptr<const class core::pose::Pose>

cst_io(self: pyrosetta.rosetta.protocols.match.output.OutputWriter) pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO

C++: protocols::match::output::OutputWriter::cst_io() const –> class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::EnzConstraintIO>

cstfile_name(self: pyrosetta.rosetta.protocols.match.output.PDBWriter) str

C++: protocols::match::output::PDBWriter::cstfile_name() const –> std::string

determine_redundant_upstream_matchres(self: pyrosetta.rosetta.protocols.match.output.OutputWriter, m: pyrosetta.rosetta.protocols.match.match_dspos1, redundant_upstream_res: pyrosetta.rosetta.std.map_unsigned_long_unsigned_long) None
determine if any upstream res are at the same scaffold

position, i.e. if one of them is a backbone interaction the redundant_upstream_res map is a mapping from the redundant geometric constraint id of the redundant residue to the geomcst_id of the “nonredundant” res i.e. if cstres 1 happens to be a cys at position 10 and cstres 3 is a gly at position 10 (and it’s backbone is used in satisfying constraint 3), the mapping will contain the 3,1 pair.

C++: protocols::match::output::OutputWriter::determine_redundant_upstream_matchres(const struct protocols::match::match_dspos1 &, class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > > &) const –> void

end_output_writing(self: pyrosetta.rosetta.protocols.match.output.OutputWriter) None

C++: protocols::match::output::OutputWriter::end_output_writing() –> void

initialize_from_matcher_task(self: pyrosetta.rosetta.protocols.match.output.PDBWriter, mtask: pyrosetta.rosetta.protocols.match.MatcherTask) None

C++: protocols::match::output::PDBWriter::initialize_from_matcher_task(class std::shared_ptr<const class protocols::match::MatcherTask>) –> void

num_geom_cst(self: pyrosetta.rosetta.protocols.match.output.PDBWriter) int

C++: protocols::match::output::PDBWriter::num_geom_cst() const –> unsigned long

prefix(self: pyrosetta.rosetta.protocols.match.output.PDBWriter) str

C++: protocols::match::output::PDBWriter::prefix() const –> std::string

prepare_for_output_writing(self: pyrosetta.rosetta.protocols.match.output.PDBWriter) None

C++: protocols::match::output::PDBWriter::prepare_for_output_writing() –> void

record_match(*args, **kwargs)

Overloaded function.

  1. record_match(self: pyrosetta.rosetta.protocols.match.output.PDBWriter, m: pyrosetta.rosetta.utility.vector1_protocols_match_Hit, evaluator: pyrosetta.rosetta.protocols.match.output.MatchEvaluator, match_score_writer: pyrosetta.rosetta.protocols.match.output.MatchScoreWriter) -> None

C++: protocols::match::output::PDBWriter::record_match(const class utility::vector1<class protocols::match::Hit, class std::allocator<class protocols::match::Hit> > &, class std::shared_ptr<class protocols::match::output::MatchEvaluator>, class std::shared_ptr<class protocols::match::output::MatchScoreWriter>) –> void

  1. record_match(self: pyrosetta.rosetta.protocols.match.output.PDBWriter, m: pyrosetta.rosetta.protocols.match.match_dspos1) -> None

evaluator and score writer are not passed in because single-downstream-position match currently have no way of being evaluated

C++: protocols::match::output::PDBWriter::record_match(const struct protocols::match::match_dspos1 &) –> void

scaf_name(self: pyrosetta.rosetta.protocols.match.output.PDBWriter) str

C++: protocols::match::output::PDBWriter::scaf_name() const –> std::string

set_coordinate_cacher(self: pyrosetta.rosetta.protocols.match.output.PDBWriter, : protocols::match::output::UpstreamHitCacher) None

C++: protocols::match::output::PDBWriter::set_coordinate_cacher(class std::shared_ptr<class protocols::match::output::UpstreamHitCacher>) –> void

set_downstream_builder(self: pyrosetta.rosetta.protocols.match.output.PDBWriter, geomcst_id: int, dsbuilder: pyrosetta.rosetta.protocols.match.downstream.DownstreamBuilder) None

C++: protocols::match::output::PDBWriter::set_downstream_builder(unsigned long, class std::shared_ptr<const class protocols::match::downstream::DownstreamBuilder>) –> void

set_prefix(self: pyrosetta.rosetta.protocols.match.output.PDBWriter, prefix: str) None

C++: protocols::match::output::PDBWriter::set_prefix(const std::string &) –> void

signature_string(self: pyrosetta.rosetta.protocols.match.output.PDBWriter, upstream_matchres: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) str

C++: protocols::match::output::PDBWriter::signature_string(const class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &) const –> std::string

class pyrosetta.rosetta.protocols.match.output.PoseInserter

Bases: pyrosetta.rosetta.protocols.match.upstream.UpstreamResidueProcessor

assign(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResidueProcessor, : pyrosetta.rosetta.protocols.match.upstream.UpstreamResidueProcessor) pyrosetta.rosetta.protocols.match.upstream.UpstreamResidueProcessor

C++: protocols::match::upstream::UpstreamResidueProcessor::operator=(const class protocols::match::upstream::UpstreamResidueProcessor &) –> class protocols::match::upstream::UpstreamResidueProcessor &

process_hit(self: pyrosetta.rosetta.protocols.match.output.PoseInserter, hit: pyrosetta.rosetta.protocols.match.Hit, upstream_conformation: pyrosetta.rosetta.core.conformation.Residue) None
Take a conformation::Residue from the upstream builder and

call Pose::replace_residue at a particular position.

C++: protocols::match::output::PoseInserter::process_hit(const class protocols::match::Hit &, const class core::conformation::Residue &) –> void

set_replacement_resid(self: pyrosetta.rosetta.protocols.match.output.PoseInserter, seqpos: int) None

C++: protocols::match::output::PoseInserter::set_replacement_resid(unsigned long) –> void

class pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter

Bases: pyrosetta.rosetta.protocols.match.output.CloudPDBWriter

helper class for the MatcherMover that will put a match into a supplied pose

assemble_remark_lines(self: pyrosetta.rosetta.protocols.match.output.PDBWriter, outpose: pyrosetta.rosetta.core.pose.Pose, upstream_matchres: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, redundant_upstream_res: pyrosetta.rosetta.std.map_unsigned_long_unsigned_long, ex_geom_ids_for_upstream_res: pyrosetta.rosetta.utility.vector1_unsigned_long) None

C++: protocols::match::output::PDBWriter::assemble_remark_lines(class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, const class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

assign(self: pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter, : pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter) pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter

C++: protocols::match::output::PoseMatchOutputWriter::operator=(const class protocols::match::output::PoseMatchOutputWriter &) –> class protocols::match::output::PoseMatchOutputWriter &

create_output_upstream_pose(self: pyrosetta.rosetta.protocols.match.output.PDBWriter, upstream_matchres: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, redundant_upstream_res: pyrosetta.rosetta.std.map_unsigned_long_unsigned_long, ex_geom_ids_for_upstream_res: pyrosetta.rosetta.utility.vector1_unsigned_long) pyrosetta.rosetta.core.pose.Pose

C++: protocols::match::output::PDBWriter::create_output_upstream_pose(const class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, const class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> class std::shared_ptr<const class core::pose::Pose>

cst_io(self: pyrosetta.rosetta.protocols.match.output.OutputWriter) pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO

C++: protocols::match::output::OutputWriter::cst_io() const –> class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::EnzConstraintIO>

cstfile_name(self: pyrosetta.rosetta.protocols.match.output.PDBWriter) str

C++: protocols::match::output::PDBWriter::cstfile_name() const –> std::string

determine_redundant_upstream_matchres(self: pyrosetta.rosetta.protocols.match.output.OutputWriter, m: pyrosetta.rosetta.protocols.match.match_dspos1, redundant_upstream_res: pyrosetta.rosetta.std.map_unsigned_long_unsigned_long) None
determine if any upstream res are at the same scaffold

position, i.e. if one of them is a backbone interaction the redundant_upstream_res map is a mapping from the redundant geometric constraint id of the redundant residue to the geomcst_id of the “nonredundant” res i.e. if cstres 1 happens to be a cys at position 10 and cstres 3 is a gly at position 10 (and it’s backbone is used in satisfying constraint 3), the mapping will contain the 3,1 pair.

C++: protocols::match::output::OutputWriter::determine_redundant_upstream_matchres(const struct protocols::match::match_dspos1 &, class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > > &) const –> void

ds_hitset_end_its(self: pyrosetta.rosetta.protocols.match.output.CloudPDBWriter) pyrosetta.rosetta.utility.vector1_std__Rb_tree_const_iterator_protocols_match_downstream_hit_t

C++: protocols::match::output::CloudPDBWriter::ds_hitset_end_its() const –> const class utility::vector1<struct std::_Rb_tree_const_iterator<class protocols::match::downstream_hit>, class std::allocator<struct std::_Rb_tree_const_iterator<class protocols::match::downstream_hit> > > &

ds_hitset_its(self: pyrosetta.rosetta.protocols.match.output.CloudPDBWriter) pyrosetta.rosetta.utility.vector1_std__Rb_tree_const_iterator_protocols_match_downstream_hit_t

C++: protocols::match::output::CloudPDBWriter::ds_hitset_its() const –> const class utility::vector1<struct std::_Rb_tree_const_iterator<class protocols::match::downstream_hit>, class std::allocator<struct std::_Rb_tree_const_iterator<class protocols::match::downstream_hit> > > &

end_output_writing(self: pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter) None

C++: protocols::match::output::PoseMatchOutputWriter::end_output_writing() –> void

initialize_from_matcher_task(self: pyrosetta.rosetta.protocols.match.output.PDBWriter, mtask: pyrosetta.rosetta.protocols.match.MatcherTask) None

C++: protocols::match::output::PDBWriter::initialize_from_matcher_task(class std::shared_ptr<const class protocols::match::MatcherTask>) –> void

insert_match_into_pose(*args, **kwargs)

Overloaded function.

  1. insert_match_into_pose(self: pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter, pose: pyrosetta.rosetta.core.pose.Pose, match_group: int) -> None

C++: protocols::match::output::PoseMatchOutputWriter::insert_match_into_pose(class core::pose::Pose &, unsigned long) –> void

  1. insert_match_into_pose(self: pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter, pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::match::output::PoseMatchOutputWriter::insert_match_into_pose(class core::pose::Pose &) –> void

match_groups_dshits(self: pyrosetta.rosetta.protocols.match.output.CloudPDBWriter) pyrosetta.rosetta.utility.vector1_utility_vector1_std_set_protocols_match_downstream_hit_std_less_protocols_match_downstream_hit_std_allocator_protocols_match_downstream_hit_std_allocator_std_set_protocols_match_downstream_hit_std_less_protocols_match_downstream_hit_std_allocator_protocols_match_downstream_hit_t

C++: protocols::match::output::CloudPDBWriter::match_groups_dshits() const –> const class utility::vector1<class utility::vector1<class std::set<class protocols::match::downstream_hit, struct std::less<class protocols::match::downstream_hit>, class std::allocator<class protocols::match::downstream_hit> >, class std::allocator<class std::set<class protocols::match::downstream_hit, struct std::less<class protocols::match::downstream_hit>, class std::allocator<class protocols::match::downstream_hit> > > >, class std::allocator<class utility::vector1<class std::set<class protocols::match::downstream_hit, struct std::less<class protocols::match::downstream_hit>, class std::allocator<class protocols::match::downstream_hit> >, class std::allocator<class std::set<class protocols::match::downstream_hit, struct std::less<class protocols::match::downstream_hit>, class std::allocator<class protocols::match::downstream_hit> > > > > > &

match_groups_ushits(self: pyrosetta.rosetta.protocols.match.output.CloudPDBWriter) pyrosetta.rosetta.utility.vector1_utility_vector1_std_set_protocols_match_upstream_hit_std_less_protocols_match_upstream_hit_std_allocator_protocols_match_upstream_hit_std_allocator_std_set_protocols_match_upstream_hit_std_less_protocols_match_upstream_hit_std_allocator_protocols_match_upstream_hit_t

C++: protocols::match::output::CloudPDBWriter::match_groups_ushits() const –> const class utility::vector1<class utility::vector1<class std::set<class protocols::match::upstream_hit, struct std::less<class protocols::match::upstream_hit>, class std::allocator<class protocols::match::upstream_hit> >, class std::allocator<class std::set<class protocols::match::upstream_hit, struct std::less<class protocols::match::upstream_hit>, class std::allocator<class protocols::match::upstream_hit> > > >, class std::allocator<class utility::vector1<class std::set<class protocols::match::upstream_hit, struct std::less<class protocols::match::upstream_hit>, class std::allocator<class protocols::match::upstream_hit> >, class std::allocator<class std::set<class protocols::match::upstream_hit, struct std::less<class protocols::match::upstream_hit>, class std::allocator<class protocols::match::upstream_hit> > > > > > &

num_geom_cst(self: pyrosetta.rosetta.protocols.match.output.PDBWriter) int

C++: protocols::match::output::PDBWriter::num_geom_cst() const –> unsigned long

prefix(self: pyrosetta.rosetta.protocols.match.output.PDBWriter) str

C++: protocols::match::output::PDBWriter::prefix() const –> std::string

prepare_for_output_writing(self: pyrosetta.rosetta.protocols.match.output.CloudPDBWriter) None

C++: protocols::match::output::CloudPDBWriter::prepare_for_output_writing() –> void

record_match(*args, **kwargs)

Overloaded function.

  1. record_match(self: pyrosetta.rosetta.protocols.match.output.CloudPDBWriter, m: pyrosetta.rosetta.utility.vector1_protocols_match_Hit, evaluator: pyrosetta.rosetta.protocols.match.output.MatchEvaluator, match_score_writer: pyrosetta.rosetta.protocols.match.output.MatchScoreWriter) -> None

no writing in this function, only saving the hits according

to what group they belong to

C++: protocols::match::output::CloudPDBWriter::record_match(const class utility::vector1<class protocols::match::Hit, class std::allocator<class protocols::match::Hit> > &, class std::shared_ptr<class protocols::match::output::MatchEvaluator>, class std::shared_ptr<class protocols::match::output::MatchScoreWriter>) –> void

  1. record_match(self: pyrosetta.rosetta.protocols.match.output.CloudPDBWriter, m: pyrosetta.rosetta.protocols.match.match_dspos1) -> None

C++: protocols::match::output::CloudPDBWriter::record_match(const struct protocols::match::match_dspos1 &) –> void

representative_group_matches(self: pyrosetta.rosetta.protocols.match.output.CloudPDBWriter) pyrosetta.rosetta.utility.vector1_protocols_match_match_dspos1

C++: protocols::match::output::CloudPDBWriter::representative_group_matches() const –> const class utility::vector1<struct protocols::match::match_dspos1, class std::allocator<struct protocols::match::match_dspos1> > &

scaf_name(self: pyrosetta.rosetta.protocols.match.output.PDBWriter) str

C++: protocols::match::output::PDBWriter::scaf_name() const –> std::string

set_coordinate_cacher(self: pyrosetta.rosetta.protocols.match.output.PDBWriter, : protocols::match::output::UpstreamHitCacher) None

C++: protocols::match::output::PDBWriter::set_coordinate_cacher(class std::shared_ptr<class protocols::match::output::UpstreamHitCacher>) –> void

set_downstream_builder(self: pyrosetta.rosetta.protocols.match.output.PDBWriter, geomcst_id: int, dsbuilder: pyrosetta.rosetta.protocols.match.downstream.DownstreamBuilder) None

C++: protocols::match::output::PDBWriter::set_downstream_builder(unsigned long, class std::shared_ptr<const class protocols::match::downstream::DownstreamBuilder>) –> void

set_prefix(self: pyrosetta.rosetta.protocols.match.output.PDBWriter, prefix: str) None

C++: protocols::match::output::PDBWriter::set_prefix(const std::string &) –> void

signature_string(self: pyrosetta.rosetta.protocols.match.output.PDBWriter, upstream_matchres: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) str

C++: protocols::match::output::PDBWriter::signature_string(const class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &) const –> std::string

write_match_groups(self: pyrosetta.rosetta.protocols.match.output.CloudPDBWriter) None

this is where the actual writing happens

C++: protocols::match::output::CloudPDBWriter::write_match_groups() –> void

class pyrosetta.rosetta.protocols.match.output.ProcessorFactory

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.match.output.ProcessorFactory, : pyrosetta.rosetta.protocols.match.output.ProcessorFactory) pyrosetta.rosetta.protocols.match.output.ProcessorFactory

C++: protocols::match::output::ProcessorFactory::operator=(const class protocols::match::output::ProcessorFactory &) –> class protocols::match::output::ProcessorFactory &

static create_processor(matcher: pyrosetta.rosetta.protocols.match.Matcher, task: pyrosetta.rosetta.protocols.match.MatcherTask) pyrosetta.rosetta.protocols.match.output.MatchProcessor

C++: protocols::match::output::ProcessorFactory::create_processor(class std::shared_ptr<const class protocols::match::Matcher>, class std::shared_ptr<const class protocols::match::MatcherTask>) –> class std::shared_ptr<class protocols::match::output::MatchProcessor>

class pyrosetta.rosetta.protocols.match.output.ResidueKinemageWriter

Bases: pybind11_builtins.pybind11_object

animate(self: pyrosetta.rosetta.protocols.match.output.ResidueKinemageWriter, setting: bool) None

C++: protocols::match::output::ResidueKinemageWriter::animate(bool) –> void

assign(self: pyrosetta.rosetta.protocols.match.output.ResidueKinemageWriter, : pyrosetta.rosetta.protocols.match.output.ResidueKinemageWriter) pyrosetta.rosetta.protocols.match.output.ResidueKinemageWriter

C++: protocols::match::output::ResidueKinemageWriter::operator=(const class protocols::match::output::ResidueKinemageWriter &) –> class protocols::match::output::ResidueKinemageWriter &

dominant(self: pyrosetta.rosetta.protocols.match.output.ResidueKinemageWriter, setting: bool) None

C++: protocols::match::output::ResidueKinemageWriter::dominant(bool) –> void

group(self: pyrosetta.rosetta.protocols.match.output.ResidueKinemageWriter, setting: bool) None

C++: protocols::match::output::ResidueKinemageWriter::group(bool) –> void

master(self: pyrosetta.rosetta.protocols.match.output.ResidueKinemageWriter, setting: str) None

C++: protocols::match::output::ResidueKinemageWriter::master(const std::string &) –> void

write_rsd_coords(*args, **kwargs)

Overloaded function.

  1. write_rsd_coords(self: pyrosetta.rosetta.protocols.match.output.ResidueKinemageWriter, ostr: pyrosetta.rosetta.std.ostream, scaffold_build_point_id: int, upstream_conf_id: int, rsd: pyrosetta.rosetta.core.conformation.Residue) -> None

  2. write_rsd_coords(self: pyrosetta.rosetta.protocols.match.output.ResidueKinemageWriter, ostr: pyrosetta.rosetta.std.ostream, scaffold_build_point_id: int, upstream_conf_id: int, rsd: pyrosetta.rosetta.core.conformation.Residue, is_instance: bool) -> None

Write out the coordinates for a particular residue; the kinemage tag

is assumed to have been writen already.

C++: protocols::match::output::ResidueKinemageWriter::write_rsd_coords(std::ostream &, const unsigned long, const unsigned long, const class core::conformation::Residue &, bool) const –> void

write_virtual_atoms(self: pyrosetta.rosetta.protocols.match.output.ResidueKinemageWriter, setting: bool) None

C++: protocols::match::output::ResidueKinemageWriter::write_virtual_atoms(bool) –> void

class pyrosetta.rosetta.protocols.match.output.SameChiBinComboGrouper

Bases: pyrosetta.rosetta.protocols.match.output.MatchGrouper

assign(self: pyrosetta.rosetta.protocols.match.output.SameChiBinComboGrouper, : pyrosetta.rosetta.protocols.match.output.SameChiBinComboGrouper) pyrosetta.rosetta.protocols.match.output.SameChiBinComboGrouper

C++: protocols::match::output::SameChiBinComboGrouper::operator=(const class protocols::match::output::SameChiBinComboGrouper &) –> class protocols::match::output::SameChiBinComboGrouper &

assign_group_for_match(*args, **kwargs)

Overloaded function.

  1. assign_group_for_match(self: pyrosetta.rosetta.protocols.match.output.SameChiBinComboGrouper, m: pyrosetta.rosetta.utility.vector1_protocols_match_Hit) -> int

C++: protocols::match::output::SameChiBinComboGrouper::assign_group_for_match(const class utility::vector1<class protocols::match::Hit, class std::allocator<class protocols::match::Hit> > &) –> unsigned long

  1. assign_group_for_match(self: pyrosetta.rosetta.protocols.match.output.SameChiBinComboGrouper, m: pyrosetta.rosetta.protocols.match.match_dspos1) -> int

C++: protocols::match::output::SameChiBinComboGrouper::assign_group_for_match(const struct protocols::match::match_dspos1 &) –> unsigned long

reset(self: pyrosetta.rosetta.protocols.match.output.SameChiBinComboGrouper) None

C++: protocols::match::output::SameChiBinComboGrouper::reset() –> void

set_hit_cacher(self: pyrosetta.rosetta.protocols.match.output.SameChiBinComboGrouper, cacher: protocols::match::output::UpstreamHitCacher) None

C++: protocols::match::output::SameChiBinComboGrouper::set_hit_cacher(class std::shared_ptr<class protocols::match::output::UpstreamHitCacher>) –> void

set_n_geometric_constraints(self: pyrosetta.rosetta.protocols.match.output.SameChiBinComboGrouper, n_csts: int) None

C++: protocols::match::output::SameChiBinComboGrouper::set_n_geometric_constraints(unsigned long) –> void

class pyrosetta.rosetta.protocols.match.output.SameRotamerComboGrouper

Bases: pyrosetta.rosetta.protocols.match.output.MatchGrouper

assign(self: pyrosetta.rosetta.protocols.match.output.SameRotamerComboGrouper, : pyrosetta.rosetta.protocols.match.output.SameRotamerComboGrouper) pyrosetta.rosetta.protocols.match.output.SameRotamerComboGrouper

C++: protocols::match::output::SameRotamerComboGrouper::operator=(const class protocols::match::output::SameRotamerComboGrouper &) –> class protocols::match::output::SameRotamerComboGrouper &

assign_group_for_match(*args, **kwargs)

Overloaded function.

  1. assign_group_for_match(self: pyrosetta.rosetta.protocols.match.output.SameRotamerComboGrouper, m: pyrosetta.rosetta.utility.vector1_protocols_match_Hit) -> int

C++: protocols::match::output::SameRotamerComboGrouper::assign_group_for_match(const class utility::vector1<class protocols::match::Hit, class std::allocator<class protocols::match::Hit> > &) –> unsigned long

  1. assign_group_for_match(self: pyrosetta.rosetta.protocols.match.output.SameRotamerComboGrouper, m: pyrosetta.rosetta.protocols.match.match_dspos1) -> int

C++: protocols::match::output::SameRotamerComboGrouper::assign_group_for_match(const struct protocols::match::match_dspos1 &) –> unsigned long

reset(self: pyrosetta.rosetta.protocols.match.output.SameRotamerComboGrouper) None

C++: protocols::match::output::SameRotamerComboGrouper::reset() –> void

set_n_geometric_constraints(self: pyrosetta.rosetta.protocols.match.output.SameRotamerComboGrouper, n_csts: int) None

C++: protocols::match::output::SameRotamerComboGrouper::set_n_geometric_constraints(unsigned long) –> void

class pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper

Bases: pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper

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

assign(self: pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper, : pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper) pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper

C++: protocols::match::output::SameSequenceAndDSPositionGrouper::operator=(const class protocols::match::output::SameSequenceAndDSPositionGrouper &) –> class protocols::match::output::SameSequenceAndDSPositionGrouper &

assign_group_for_match(self: pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper, m: pyrosetta.rosetta.protocols.match.match_dspos1) int

C++: protocols::match::output::SameSequenceAndDSPositionGrouper::assign_group_for_match(const struct protocols::match::match_dspos1 &) –> unsigned long

reset(self: pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper) None

C++: protocols::match::output::SameSequenceAndDSPositionGrouper::reset() –> void

set_downstream_builder(self: pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper, geomcst_id: int, dsbuilder: pyrosetta.rosetta.protocols.match.downstream.DownstreamBuilder) None

C++: protocols::match::output::SameSequenceAndDSPositionGrouper::set_downstream_builder(unsigned long, class std::shared_ptr<const class protocols::match::downstream::DownstreamBuilder>) –> void

set_hit_cacher(self: pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper, cacher: protocols::match::output::UpstreamHitCacher) None

C++: protocols::match::output::SameSequenceGrouper::set_hit_cacher(class std::shared_ptr<class protocols::match::output::UpstreamHitCacher>) –> void

set_n_geometric_constraints(self: pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper, n_csts: int) None

C++: protocols::match::output::SameSequenceAndDSPositionGrouper::set_n_geometric_constraints(unsigned long) –> void

set_relevant_atom_ids(self: pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper, relevant_atom_ids: pyrosetta.rosetta.utility.vector1_core_id_AtomID) None

C++: protocols::match::output::SameSequenceAndDSPositionGrouper::set_relevant_atom_ids(const class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> > &) –> void

set_rms_group_cutoff(self: pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper, cutoff: float) None

C++: protocols::match::output::SameSequenceAndDSPositionGrouper::set_rms_group_cutoff(double) –> void

class pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper

Bases: pyrosetta.rosetta.protocols.match.output.MatchGrouper

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.

assign(self: pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper, : pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper) pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper

C++: protocols::match::output::SameSequenceGrouper::operator=(const class protocols::match::output::SameSequenceGrouper &) –> class protocols::match::output::SameSequenceGrouper &

assign_group_for_match(*args, **kwargs)

Overloaded function.

  1. assign_group_for_match(self: pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper, m: pyrosetta.rosetta.utility.vector1_protocols_match_Hit) -> int

C++: protocols::match::output::SameSequenceGrouper::assign_group_for_match(const class utility::vector1<class protocols::match::Hit, class std::allocator<class protocols::match::Hit> > &) –> unsigned long

  1. assign_group_for_match(self: pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper, m: pyrosetta.rosetta.protocols.match.match_dspos1) -> int

C++: protocols::match::output::SameSequenceGrouper::assign_group_for_match(const struct protocols::match::match_dspos1 &) –> unsigned long

reset(self: pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper) None

C++: protocols::match::output::SameSequenceGrouper::reset() –> void

set_hit_cacher(self: pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper, cacher: protocols::match::output::UpstreamHitCacher) None

C++: protocols::match::output::SameSequenceGrouper::set_hit_cacher(class std::shared_ptr<class protocols::match::output::UpstreamHitCacher>) –> void

set_n_geometric_constraints(self: pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper, n_csts: int) None

C++: protocols::match::output::SameSequenceGrouper::set_n_geometric_constraints(unsigned long) –> void

class pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter

Bases: pyrosetta.rosetta.protocols.match.output.DownstreamCoordinateKinemageWriter

Class for writing conformations of the downstream partner in a kinemage description.

assign(self: pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter, : pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter) pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter

C++: protocols::match::output::SingleDownstreamResidueWriter::operator=(const class protocols::match::output::SingleDownstreamResidueWriter &) –> class protocols::match::output::SingleDownstreamResidueWriter &

set_downstream_builder(self: pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter, dsbuilder: pyrosetta.rosetta.protocols.match.downstream.DownstreamBuilder) None

C++: protocols::match::output::SingleDownstreamResidueWriter::set_downstream_builder(class std::shared_ptr<const class protocols::match::downstream::DownstreamBuilder>) –> void

set_downstream_master(self: pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter, master: str) None

C++: protocols::match::output::SingleDownstreamResidueWriter::set_downstream_master(const std::string &) –> void

set_restype(self: pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter, : pyrosetta.rosetta.core.chemical.ResidueType) None

C++: protocols::match::output::SingleDownstreamResidueWriter::set_restype(class std::shared_ptr<const class core::chemical::ResidueType>) –> void

write_downstream_coordinates(self: pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter, hit: pyrosetta.rosetta.protocols.match.Hit, ostr: pyrosetta.rosetta.std.ostream) None

C++: protocols::match::output::SingleDownstreamResidueWriter::write_downstream_coordinates(const class protocols::match::Hit &, std::ostream &) const –> void

class pyrosetta.rosetta.protocols.match.output.StateAccumulatingMatchFilter

Bases: pyrosetta.rosetta.protocols.match.output.MatchFilter

assign(self: pyrosetta.rosetta.protocols.match.output.StateAccumulatingMatchFilter, : pyrosetta.rosetta.protocols.match.output.StateAccumulatingMatchFilter) pyrosetta.rosetta.protocols.match.output.StateAccumulatingMatchFilter

C++: protocols::match::output::StateAccumulatingMatchFilter::operator=(const class protocols::match::output::StateAccumulatingMatchFilter &) –> class protocols::match::output::StateAccumulatingMatchFilter &

filter_name(self: pyrosetta.rosetta.protocols.match.output.MatchFilter) str

C++: protocols::match::output::MatchFilter::filter_name() const –> std::string

note_match_accepted(*args, **kwargs)

Overloaded function.

  1. note_match_accepted(self: pyrosetta.rosetta.protocols.match.output.StateAccumulatingMatchFilter, m: pyrosetta.rosetta.utility.vector1_protocols_match_Hit) -> None

Note that a particular match has passed all the filters and will be output.

C++: protocols::match::output::StateAccumulatingMatchFilter::note_match_accepted(const class utility::vector1<class protocols::match::Hit, class std::allocator<class protocols::match::Hit> > &) –> void

  1. note_match_accepted(self: pyrosetta.rosetta.protocols.match.output.StateAccumulatingMatchFilter, m: pyrosetta.rosetta.protocols.match.match_dspos1) -> bool

C++: protocols::match::output::StateAccumulatingMatchFilter::note_match_accepted(const struct protocols::match::match_dspos1 &) const –> bool

passes_filter(*args, **kwargs)

Overloaded function.

  1. passes_filter(self: pyrosetta.rosetta.protocols.match.output.StateAccumulatingMatchFilter, m: pyrosetta.rosetta.utility.vector1_protocols_match_Hit) -> bool

Returns true if the given match passes this filter

C++: protocols::match::output::StateAccumulatingMatchFilter::passes_filter(const class utility::vector1<class protocols::match::Hit, class std::allocator<class protocols::match::Hit> > &) const –> bool

  1. passes_filter(self: pyrosetta.rosetta.protocols.match.output.StateAccumulatingMatchFilter, m: pyrosetta.rosetta.protocols.match.match_dspos1) -> bool

C++: protocols::match::output::StateAccumulatingMatchFilter::passes_filter(const struct protocols::match::match_dspos1 &) const –> bool

reset(self: pyrosetta.rosetta.protocols.match.output.StateAccumulatingMatchFilter) None

Erase all tracking data on which matches have already been output.

C++: protocols::match::output::StateAccumulatingMatchFilter::reset() –> void

class pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter

Bases: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter

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

assign(self: pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter, : pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter) pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter

C++: protocols::match::output::UpstreamCollisionFilter::operator=(const class protocols::match::output::UpstreamCollisionFilter &) –> class protocols::match::output::UpstreamCollisionFilter &

bump_grid(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter) pyrosetta.rosetta.protocols.match.BumpGrid

C++: protocols::match::output::MatchCollisionFilter::bump_grid() const –> class std::shared_ptr<const class protocols::match::BumpGrid>

empty_pose(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter) pyrosetta.rosetta.core.pose.Pose

C++: protocols::match::output::MatchCollisionFilter::empty_pose() const –> class std::shared_ptr<const class core::pose::Pose>

empty_sfxn(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter) pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::match::output::MatchCollisionFilter::empty_sfxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

etable_energy(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter) pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy

C++: protocols::match::output::MatchCollisionFilter::etable_energy() const –> class std::shared_ptr<const class core::scoring::methods::ShortRangeTwoBodyEnergy>

filter_by_lj(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter) bool

C++: protocols::match::output::MatchCollisionFilter::filter_by_lj() const –> bool

filter_name(self: pyrosetta.rosetta.protocols.match.output.MatchFilter) str

C++: protocols::match::output::MatchFilter::filter_name() const –> std::string

lj_cutoff(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter) float

C++: protocols::match::output::MatchCollisionFilter::lj_cutoff() const –> double

passes_filter(*args, **kwargs)

Overloaded function.

  1. passes_filter(self: pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter, m: pyrosetta.rosetta.utility.vector1_protocols_match_Hit) -> bool

Returns true if the given match does not contain too much residue-pair collision.

C++: protocols::match::output::UpstreamCollisionFilter::passes_filter(const class utility::vector1<class protocols::match::Hit, class std::allocator<class protocols::match::Hit> > &) const –> bool

  1. passes_filter(self: pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter, m: pyrosetta.rosetta.protocols.match.match_dspos1) -> bool

Returns true if the given match does not contain too much residue-pair collision.

C++: protocols::match::output::UpstreamCollisionFilter::passes_filter(const struct protocols::match::match_dspos1 &) const –> bool

passes_hardsphere_filter(*args, **kwargs)

Overloaded function.

  1. passes_hardsphere_filter(self: pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter, geomcst_a: int, geomcst_b: int, upstream_hit_a: pyrosetta.rosetta.protocols.match.Hit, upstream_hit_b: pyrosetta.rosetta.protocols.match.Hit) -> bool

C++: protocols::match::output::UpstreamCollisionFilter::passes_hardsphere_filter(unsigned long, unsigned long, const class protocols::match::Hit &, const class protocols::match::Hit &) const –> bool

  1. passes_hardsphere_filter(self: pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter, resA: pyrosetta.rosetta.core.conformation.Residue, resB: pyrosetta.rosetta.core.conformation.Residue) -> bool

C++: protocols::match::output::UpstreamCollisionFilter::passes_hardsphere_filter(const class core::conformation::Residue &, const class core::conformation::Residue &) const –> bool

set_filter_by_lj(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter, setting: bool) None

C++: protocols::match::output::MatchCollisionFilter::set_filter_by_lj(bool) –> void

set_lj_atr_weight(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter, setting: float) None

C++: protocols::match::output::MatchCollisionFilter::set_lj_atr_weight(double) –> void

set_lj_cutoff(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter, setting: float) None

C++: protocols::match::output::MatchCollisionFilter::set_lj_cutoff(double) –> void

set_lj_rep_weight(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter, setting: float) None

C++: protocols::match::output::MatchCollisionFilter::set_lj_rep_weight(double) –> void

set_lj_sol_weight(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter, setting: float) None

C++: protocols::match::output::MatchCollisionFilter::set_lj_sol_weight(double) –> void

set_tolerated_overlap(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter, setting: float) None

C++: protocols::match::output::MatchCollisionFilter::set_tolerated_overlap(double) –> void

tolerated_overlap(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter) float

C++: protocols::match::output::MatchCollisionFilter::tolerated_overlap() const –> double

wfa_atr(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter) float

C++: protocols::match::output::MatchCollisionFilter::wfa_atr() const –> double

wfa_rep(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter) float

C++: protocols::match::output::MatchCollisionFilter::wfa_rep() const –> double

wfa_sol(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter) float

C++: protocols::match::output::MatchCollisionFilter::wfa_sol() const –> double

class pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter

Bases: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter

This class is used to detect collisions between upstream residues and downstream poses.

assign(self: pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter, : pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter) pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter

C++: protocols::match::output::UpstreamDownstreamCollisionFilter::operator=(const class protocols::match::output::UpstreamDownstreamCollisionFilter &) –> class protocols::match::output::UpstreamDownstreamCollisionFilter &

bump_grid(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter) pyrosetta.rosetta.protocols.match.BumpGrid

C++: protocols::match::output::MatchCollisionFilter::bump_grid() const –> class std::shared_ptr<const class protocols::match::BumpGrid>

empty_pose(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter) pyrosetta.rosetta.core.pose.Pose

C++: protocols::match::output::MatchCollisionFilter::empty_pose() const –> class std::shared_ptr<const class core::pose::Pose>

empty_sfxn(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter) pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::match::output::MatchCollisionFilter::empty_sfxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

etable_energy(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter) pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy

C++: protocols::match::output::MatchCollisionFilter::etable_energy() const –> class std::shared_ptr<const class core::scoring::methods::ShortRangeTwoBodyEnergy>

filter_by_lj(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter) bool

C++: protocols::match::output::MatchCollisionFilter::filter_by_lj() const –> bool

filter_name(self: pyrosetta.rosetta.protocols.match.output.MatchFilter) str

C++: protocols::match::output::MatchFilter::filter_name() const –> std::string

lj_cutoff(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter) float

C++: protocols::match::output::MatchCollisionFilter::lj_cutoff() const –> double

passes_filter(*args, **kwargs)

Overloaded function.

  1. passes_filter(self: pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter, m: pyrosetta.rosetta.utility.vector1_protocols_match_Hit) -> bool

Returns true if there is at least one placement of the

downstream partner which does not exceed the collision tolerance with any of the upstream residues.

C++: protocols::match::output::UpstreamDownstreamCollisionFilter::passes_filter(const class utility::vector1<class protocols::match::Hit, class std::allocator<class protocols::match::Hit> > &) const –> bool

  1. passes_filter(self: pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter, m: pyrosetta.rosetta.protocols.match.match_dspos1) -> bool

Returns true if the specified downstream position does not

collide more than tolerated with any of the upstream residues

C++: protocols::match::output::UpstreamDownstreamCollisionFilter::passes_filter(const struct protocols::match::match_dspos1 &) const –> bool

passes_hardsphere_filter(*args, **kwargs)

Overloaded function.

  1. passes_hardsphere_filter(self: pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter, geomcst_up: int, geomcst_down: int, upstream_hit: pyrosetta.rosetta.protocols.match.Hit, downstream_hit: pyrosetta.rosetta.protocols.match.Hit) -> bool

C++: protocols::match::output::UpstreamDownstreamCollisionFilter::passes_hardsphere_filter(unsigned long, unsigned long, const class protocols::match::Hit &, const class protocols::match::Hit &) const –> bool

  1. passes_hardsphere_filter(self: pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter, geomcst: int, upstream_hit: pyrosetta.rosetta.protocols.match.Hit, coords: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t) -> bool

C++: protocols::match::output::UpstreamDownstreamCollisionFilter::passes_hardsphere_filter(unsigned long, const class protocols::match::Hit &, const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) const –> bool

set_chemical_bond_from_upstream_to_downstream(self: pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter, geomcst_id: int) None
Do not perform any collision detection between an upstream residue and the downstream

pose if there is a chemical bond between them

C++: protocols::match::output::UpstreamDownstreamCollisionFilter::set_chemical_bond_from_upstream_to_downstream(unsigned long) –> void

set_downstream_builder(self: pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter, geomcst_id: int, builder: pyrosetta.rosetta.protocols.match.downstream.DownstreamBuilder) None

C++: protocols::match::output::UpstreamDownstreamCollisionFilter::set_downstream_builder(unsigned long, class std::shared_ptr<const class protocols::match::downstream::DownstreamBuilder>) –> void

set_downstream_pose(self: pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter, downstream_pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::match::output::UpstreamDownstreamCollisionFilter::set_downstream_pose(const class core::pose::Pose &) –> void

set_filter_by_lj(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter, setting: bool) None

C++: protocols::match::output::MatchCollisionFilter::set_filter_by_lj(bool) –> void

set_lj_atr_weight(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter, setting: float) None

C++: protocols::match::output::MatchCollisionFilter::set_lj_atr_weight(double) –> void

set_lj_cutoff(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter, setting: float) None

C++: protocols::match::output::MatchCollisionFilter::set_lj_cutoff(double) –> void

set_lj_rep_weight(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter, setting: float) None

C++: protocols::match::output::MatchCollisionFilter::set_lj_rep_weight(double) –> void

set_lj_sol_weight(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter, setting: float) None

C++: protocols::match::output::MatchCollisionFilter::set_lj_sol_weight(double) –> void

set_num_geometric_constraints(self: pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter, n_geomcst: int) None

C++: protocols::match::output::UpstreamDownstreamCollisionFilter::set_num_geometric_constraints(unsigned long) –> void

set_tolerated_overlap(self: pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter, setting: float) None

C++: protocols::match::output::UpstreamDownstreamCollisionFilter::set_tolerated_overlap(double) –> void

tolerated_overlap(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter) float

C++: protocols::match::output::MatchCollisionFilter::tolerated_overlap() const –> double

wfa_atr(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter) float

C++: protocols::match::output::MatchCollisionFilter::wfa_atr() const –> double

wfa_rep(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter) float

C++: protocols::match::output::MatchCollisionFilter::wfa_rep() const –> double

wfa_sol(self: pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter) float

C++: protocols::match::output::MatchCollisionFilter::wfa_sol() const –> double

class pyrosetta.rosetta.protocols.match.output.UpstreamHitCacher

Bases: pyrosetta.rosetta.protocols.match.upstream.UpstreamResidueProcessor

assign(self: pyrosetta.rosetta.protocols.match.output.UpstreamHitCacher, : pyrosetta.rosetta.protocols.match.output.UpstreamHitCacher) pyrosetta.rosetta.protocols.match.output.UpstreamHitCacher

C++: protocols::match::output::UpstreamHitCacher::operator=(const class protocols::match::output::UpstreamHitCacher &) –> class protocols::match::output::UpstreamHitCacher &

process_hit(self: pyrosetta.rosetta.protocols.match.output.UpstreamHitCacher, hit: pyrosetta.rosetta.protocols.match.Hit, upstream_conformation: pyrosetta.rosetta.core.conformation.Residue) None
The method by which the UpstreamHitCacher communicates with the UpstreamBuilders.

CAUTION: this class should not be handed to an UpstreamBuilder directly. It should only hand itself to an UpstreamBuilder. Ask the UpstreamHitCacher for a particular hit, and it will call recover_rotamer() on the upstream builder; it’s doing bookkeeping in the background and that bookkeeping is important for the success of this function.

C++: protocols::match::output::UpstreamHitCacher::process_hit(const class protocols::match::Hit &, const class core::conformation::Residue &) –> void

set_cache_size(self: pyrosetta.rosetta.protocols.match.output.UpstreamHitCacher, n_rotamers_to_cache: int) None

C++: protocols::match::output::UpstreamHitCacher::set_cache_size(unsigned long) –> void

upstream_conformation_for_hit(self: pyrosetta.rosetta.protocols.match.output.UpstreamHitCacher, geometric_constraint_id: int, hit: pyrosetta.rosetta.protocols.match.Hit) pyrosetta.rosetta.core.conformation.Residue

C++: protocols::match::output::UpstreamHitCacher::upstream_conformation_for_hit(unsigned long, const class protocols::match::Hit &) –> class std::shared_ptr<const class core::conformation::Residue>

class pyrosetta.rosetta.protocols.match.output.WriteKinemageOutputter

Bases: pyrosetta.rosetta.protocols.match.output.OutputWriter

assign(self: pyrosetta.rosetta.protocols.match.output.WriteKinemageOutputter, : pyrosetta.rosetta.protocols.match.output.WriteKinemageOutputter) pyrosetta.rosetta.protocols.match.output.WriteKinemageOutputter

C++: protocols::match::output::WriteKinemageOutputter::operator=(const class protocols::match::output::WriteKinemageOutputter &) –> class protocols::match::output::WriteKinemageOutputter &

cst_io(self: pyrosetta.rosetta.protocols.match.output.OutputWriter) pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO

C++: protocols::match::output::OutputWriter::cst_io() const –> class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::EnzConstraintIO>

determine_redundant_upstream_matchres(self: pyrosetta.rosetta.protocols.match.output.OutputWriter, m: pyrosetta.rosetta.protocols.match.match_dspos1, redundant_upstream_res: pyrosetta.rosetta.std.map_unsigned_long_unsigned_long) None
determine if any upstream res are at the same scaffold

position, i.e. if one of them is a backbone interaction the redundant_upstream_res map is a mapping from the redundant geometric constraint id of the redundant residue to the geomcst_id of the “nonredundant” res i.e. if cstres 1 happens to be a cys at position 10 and cstres 3 is a gly at position 10 (and it’s backbone is used in satisfying constraint 3), the mapping will contain the 3,1 pair.

C++: protocols::match::output::OutputWriter::determine_redundant_upstream_matchres(const struct protocols::match::match_dspos1 &, class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > > &) const –> void

end_output_writing(self: pyrosetta.rosetta.protocols.match.output.OutputWriter) None

C++: protocols::match::output::OutputWriter::end_output_writing() –> void

initialize_from_matcher_task(self: pyrosetta.rosetta.protocols.match.output.OutputWriter, mtask: pyrosetta.rosetta.protocols.match.MatcherTask) None

C++: protocols::match::output::OutputWriter::initialize_from_matcher_task(class std::shared_ptr<const class protocols::match::MatcherTask>) –> void

prepare_for_output_writing(self: pyrosetta.rosetta.protocols.match.output.OutputWriter) None

C++: protocols::match::output::OutputWriter::prepare_for_output_writing() –> void

record_match(*args, **kwargs)

Overloaded function.

  1. record_match(self: pyrosetta.rosetta.protocols.match.output.WriteKinemageOutputter, m: pyrosetta.rosetta.utility.vector1_protocols_match_Hit, evaluator: pyrosetta.rosetta.protocols.match.output.MatchEvaluator, match_score_writer: pyrosetta.rosetta.protocols.match.output.MatchScoreWriter) -> None

C++: protocols::match::output::WriteKinemageOutputter::record_match(const class utility::vector1<class protocols::match::Hit, class std::allocator<class protocols::match::Hit> > &, class std::shared_ptr<class protocols::match::output::MatchEvaluator>, class std::shared_ptr<class protocols::match::output::MatchScoreWriter>) –> void

  1. record_match(self: pyrosetta.rosetta.protocols.match.output.WriteKinemageOutputter, m: pyrosetta.rosetta.protocols.match.match_dspos1) -> None

evaluator and score writer are not passed in because single-downstream-position match currently have no way of being evaluated

C++: protocols::match::output::WriteKinemageOutputter::record_match(const struct protocols::match::match_dspos1 &) –> void

set_coordinate_cacher(self: pyrosetta.rosetta.protocols.match.output.WriteKinemageOutputter, : pyrosetta.rosetta.protocols.match.output.UpstreamHitCacher) None

C++: protocols::match::output::WriteKinemageOutputter::set_coordinate_cacher(class std::shared_ptr<class protocols::match::output::UpstreamHitCacher>) –> void

set_downstream_writer(self: pyrosetta.rosetta.protocols.match.output.WriteKinemageOutputter, geomcst_id: int, ds_writer: protocols::match::output::DownstreamCoordinateKinemageWriter) None

C++: protocols::match::output::WriteKinemageOutputter::set_downstream_writer(unsigned long, class std::shared_ptr<class protocols::match::output::DownstreamCoordinateKinemageWriter>) –> void

set_kin_writer(self: pyrosetta.rosetta.protocols.match.output.WriteKinemageOutputter, us_writer: protocols::match::output::WriteUpstreamHitKinemage) None

C++: protocols::match::output::WriteKinemageOutputter::set_kin_writer(class std::shared_ptr<class protocols::match::output::WriteUpstreamHitKinemage>) –> void

set_n_geomcst(self: pyrosetta.rosetta.protocols.match.output.WriteKinemageOutputter, n_geomcst: int) None

C++: protocols::match::output::WriteKinemageOutputter::set_n_geomcst(unsigned long) –> void

class pyrosetta.rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage

Bases: pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm

are_colliding(self: pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm, us_res: pyrosetta.rosetta.core.conformation.Residue, ds_res: pyrosetta.rosetta.core.conformation.Residue, ds_atoms: pyrosetta.rosetta.utility.vector1_core_id_AtomID, catalytic_atoms: pyrosetta.rosetta.utility.vector1_unsigned_long) bool

C++: protocols::match::downstream::DownstreamAlgorithm::are_colliding(const class core::conformation::Residue &, const class core::conformation::Residue &, const class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> bool

assign(self: pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm, : pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm) pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm

C++: protocols::match::downstream::DownstreamAlgorithm::operator=(const class protocols::match::downstream::DownstreamAlgorithm &) –> const class protocols::match::downstream::DownstreamAlgorithm &

build(self: pyrosetta.rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage, scaffold_build_point_id: int, upstream_conf_id: int, upstream_residue: pyrosetta.rosetta.core.conformation.Residue) pyrosetta.rosetta.std.list_protocols_match_Hit_t

C++: protocols::match::output::WriteUpstreamCoordinateKinemage::build(const unsigned long, const unsigned long, const class core::conformation::Residue &) const –> class std::list<class protocols::match::Hit, class std::allocator<class protocols::match::Hit> >

build_hits_at_all_positions(self: pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm, matcher: pyrosetta.rosetta.protocols.match.Matcher) pyrosetta.rosetta.std.list_protocols_match_Hit_t
Main driver function for hit generation. The algorithm

is responsible for generating hits at all scaffold build points that are valid for this geometric constraint. The base class provides an iterate-across-all-positions-and-splice-together-hit-lists implementation, however, derived classes may overload this function. The base class function is parallelizable with OpenMP. The returned hit list must be in sorted order by 1) hit.scaffold_build_id() and then by 2) hit.upstream_conf_id().

C++: protocols::match::downstream::DownstreamAlgorithm::build_hits_at_all_positions(class protocols::match::Matcher &) –> class std::list<class protocols::match::Hit, class std::allocator<class protocols::match::Hit> >

clone(self: pyrosetta.rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage) pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm

C++: protocols::match::output::WriteUpstreamCoordinateKinemage::clone() const –> class std::shared_ptr<class protocols::match::downstream::DownstreamAlgorithm>

generates_primary_hits(self: pyrosetta.rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage) bool
This method returns ‘true’ since when it does return hits, it’s those generated

by the ClassicMatchAlgorithm

C++: protocols::match::output::WriteUpstreamCoordinateKinemage::generates_primary_hits() const –> bool

geom_cst_id(self: pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm) int

C++: protocols::match::downstream::DownstreamAlgorithm::geom_cst_id() const –> unsigned long

get_dsbuilder(self: pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm) protocols::match::downstream::DownstreamBuilder

C++: protocols::match::downstream::DownstreamAlgorithm::get_dsbuilder() const –> class std::shared_ptr<class protocols::match::downstream::DownstreamBuilder>

hits_to_include_with_partial_match(self: pyrosetta.rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage, m: pyrosetta.rosetta.protocols.match.match_dspos1) numeric::kdtree::WrappedPrimitive<std::list<protocols::match::Hit const*, std::allocator<protocols::match::Hit const*> > >
This method should not be invoked on this class,

since it returns “true” in its upstream_only method.

C++: protocols::match::output::WriteUpstreamCoordinateKinemage::hits_to_include_with_partial_match(const struct protocols::match::match_dspos1 &) const –> class std::shared_ptr<const class numeric::kdtree::WrappedPrimitive<class std::list<const class protocols::match::Hit *, class std::allocator<const class protocols::match::Hit *> > > >

n_possible_hits_per_upstream_conformation(self: pyrosetta.rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage) int

C++: protocols::match::output::WriteUpstreamCoordinateKinemage::n_possible_hits_per_upstream_conformation() const –> unsigned long

prepare_for_match_enumeration(self: pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm, : pyrosetta.rosetta.protocols.match.Matcher) None
Called at the conclusion of matching, the Matcher signals

to the downstream algorithm that it’s time to prepare for match generation; if the downstream algorithm needs to enumerate compatible hits in response to the invokation of its hits_to_include_with_partial_match method, then now is the time to prepare for those calls. Base class has a noop implementation.

C++: protocols::match::downstream::DownstreamAlgorithm::prepare_for_match_enumeration(const class protocols::match::Matcher &) –> void

respond_to_peripheral_hitlist_change(self: pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm, matcher: pyrosetta.rosetta.protocols.match.Matcher) None
Following the change in the number of hits of some other round – either

from the conclusion of that round in which a new set of hits has been generated, or from the cascading change to the hits from round A which were deleted after the conclusion of round B.

C++: protocols::match::downstream::DownstreamAlgorithm::respond_to_peripheral_hitlist_change(class protocols::match::Matcher &) –> void

respond_to_primary_hitlist_change(self: pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm, matcher: pyrosetta.rosetta.protocols.match.Matcher, round_just_completed: int) None
Reset appropriate Matcher data to spawn the deletion of hits from other rounds

following either hit generation by this geometric constraint, or following hit generation by another geometric constraint which caused the deletion of hits from this geometric constraint. The classic match algorithm, for example, resets the occupied-space hash so that other classic-match algorithms can delete their non-viable hits in subsequent calls to respond_to_peripheral_hitlist_change.

C++: protocols::match::downstream::DownstreamAlgorithm::respond_to_primary_hitlist_change(class protocols::match::Matcher &, unsigned long) –> void

return_pseudo_hits(*args, **kwargs)

Overloaded function.

  1. return_pseudo_hits(self: pyrosetta.rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage) -> bool

C++: protocols::match::output::WriteUpstreamCoordinateKinemage::return_pseudo_hits() const –> bool

  1. return_pseudo_hits(self: pyrosetta.rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage, setting: bool) -> None

C++: protocols::match::output::WriteUpstreamCoordinateKinemage::return_pseudo_hits(bool) –> void

set_active_site_grid(self: pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm, active_site_grid: pyrosetta.rosetta.protocols.match.downstream.ActiveSiteGrid) None

C++: protocols::match::downstream::DownstreamAlgorithm::set_active_site_grid(class std::shared_ptr<const class protocols::match::downstream::ActiveSiteGrid>) –> void

set_bb_grid(self: pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm, bbgrid: pyrosetta.rosetta.protocols.match.BumpGrid) None

C++: protocols::match::downstream::DownstreamAlgorithm::set_bb_grid(class std::shared_ptr<const class protocols::match::BumpGrid>) –> void

set_downstream_writer(self: pyrosetta.rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage, dswriter: protocols::match::output::DownstreamCoordinateKinemageWriter) None

C++: protocols::match::output::WriteUpstreamCoordinateKinemage::set_downstream_writer(class std::shared_ptr<const class protocols::match::output::DownstreamCoordinateKinemageWriter>) –> void

set_dsbuilder(self: pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm, dsbuilder: protocols::match::downstream::DownstreamBuilder) None

C++: protocols::match::downstream::DownstreamAlgorithm::set_dsbuilder(class std::shared_ptr<class protocols::match::downstream::DownstreamBuilder>) –> void

set_kinemage_file_name(self: pyrosetta.rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage, filename: str) None

C++: protocols::match::output::WriteUpstreamCoordinateKinemage::set_kinemage_file_name(const std::string &) –> void

set_match_algorithm(self: pyrosetta.rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage, algorithm: pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm) None

C++: protocols::match::output::WriteUpstreamCoordinateKinemage::set_match_algorithm(class std::shared_ptr<const class protocols::match::downstream::ClassicMatchAlgorithm>) –> void

set_n_downstream_to_output(self: pyrosetta.rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage, n_downstream_to_output: int) None

C++: protocols::match::output::WriteUpstreamCoordinateKinemage::set_n_downstream_to_output(unsigned long) –> void

upstream_only(self: pyrosetta.rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage) bool
This method returns ‘true’ whether or not it’s ClassicMatchAlgorithm is set

as it should not have its hits_to_include_with_partial_match method invoked.

C++: protocols::match::output::WriteUpstreamCoordinateKinemage::upstream_only() const –> bool

class pyrosetta.rosetta.protocols.match.output.WriteUpstreamHitKinemage

Bases: pyrosetta.rosetta.protocols.match.upstream.UpstreamResidueProcessor

animate(self: pyrosetta.rosetta.protocols.match.output.WriteUpstreamHitKinemage, setting: bool) None

C++: protocols::match::output::WriteUpstreamHitKinemage::animate(bool) –> void

assign(self: pyrosetta.rosetta.protocols.match.upstream.UpstreamResidueProcessor, : pyrosetta.rosetta.protocols.match.upstream.UpstreamResidueProcessor) pyrosetta.rosetta.protocols.match.upstream.UpstreamResidueProcessor

C++: protocols::match::upstream::UpstreamResidueProcessor::operator=(const class protocols::match::upstream::UpstreamResidueProcessor &) –> class protocols::match::upstream::UpstreamResidueProcessor &

default_master(*args, **kwargs)

Overloaded function.

  1. default_master(self: pyrosetta.rosetta.protocols.match.output.WriteUpstreamHitKinemage, setting: bool) -> None

Set whether the default master should be used, or whether the

user-defined master should be used. If the user defined master is the empty string, no master will be writen.

C++: protocols::match::output::WriteUpstreamHitKinemage::default_master(bool) –> void

  1. default_master(self: pyrosetta.rosetta.protocols.match.output.WriteUpstreamHitKinemage) -> bool

Returns whether or not the default master is being used.

C++: protocols::match::output::WriteUpstreamHitKinemage::default_master() const –> bool

dominant(self: pyrosetta.rosetta.protocols.match.output.WriteUpstreamHitKinemage, setting: bool) None

C++: protocols::match::output::WriteUpstreamHitKinemage::dominant(bool) –> void

geom_id(self: pyrosetta.rosetta.protocols.match.output.WriteUpstreamHitKinemage, setting: int) None

C++: protocols::match::output::WriteUpstreamHitKinemage::geom_id(unsigned long) –> void

group(self: pyrosetta.rosetta.protocols.match.output.WriteUpstreamHitKinemage, setting: bool) None

C++: protocols::match::output::WriteUpstreamHitKinemage::group(bool) –> void

output_hit(self: pyrosetta.rosetta.protocols.match.output.WriteUpstreamHitKinemage, hit: pyrosetta.rosetta.protocols.match.Hit, upstream_conformation: pyrosetta.rosetta.core.conformation.Residue) None

Non-virtual method to write out a kinemage for an upstream residue

C++: protocols::match::output::WriteUpstreamHitKinemage::output_hit(const class protocols::match::Hit &, const class core::conformation::Residue &) –> void

output_upstream_coordinates(self: pyrosetta.rosetta.protocols.match.output.WriteUpstreamHitKinemage, hit: pyrosetta.rosetta.protocols.match.upstream_hit, upstream_conformation: pyrosetta.rosetta.core.conformation.Residue) None
non-virtual method to write out a kinemage for an upstream residue;

without invoking dswriter_->write_downstream_coordinates(). Only information about the upstream portion of the hit is needed.

C++: protocols::match::output::WriteUpstreamHitKinemage::output_upstream_coordinates(const class protocols::match::upstream_hit &, const class core::conformation::Residue &) –> void

process_hit(self: pyrosetta.rosetta.protocols.match.output.WriteUpstreamHitKinemage, hit: pyrosetta.rosetta.protocols.match.Hit, upstream_conformation: pyrosetta.rosetta.core.conformation.Residue) None

C++: protocols::match::output::WriteUpstreamHitKinemage::process_hit(const class protocols::match::Hit &, const class core::conformation::Residue &) –> void

set_dswriter(self: pyrosetta.rosetta.protocols.match.output.WriteUpstreamHitKinemage, dswriter: protocols::match::output::DownstreamCoordinateKinemageWriter) None

C++: protocols::match::output::WriteUpstreamHitKinemage::set_dswriter(class std::shared_ptr<class protocols::match::output::DownstreamCoordinateKinemageWriter>) –> void

set_kinemage_file(self: pyrosetta.rosetta.protocols.match.output.WriteUpstreamHitKinemage, fname: str) None

C++: protocols::match::output::WriteUpstreamHitKinemage::set_kinemage_file(const std::string &) –> void

set_master(self: pyrosetta.rosetta.protocols.match.output.WriteUpstreamHitKinemage, master: str) None
Set the kinemage master for the upstream residue, overriding

the default master, which is “geom#”

C++: protocols::match::output::WriteUpstreamHitKinemage::set_master(const std::string &) –> void

start_new_match(self: pyrosetta.rosetta.protocols.match.output.WriteUpstreamHitKinemage) None

C++: protocols::match::output::WriteUpstreamHitKinemage::start_new_match() –> void

write_virtual_atoms(self: pyrosetta.rosetta.protocols.match.output.WriteUpstreamHitKinemage, setting: bool) None

C++: protocols::match::output::WriteUpstreamHitKinemage::write_virtual_atoms(bool) –> void