output¶

Bindings for protocols::match::output namespace

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

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.match.output.CloudPDBWriter, grouper: pyrosetta.rosetta.protocols.match.output.MatchGrouper) -> None
__init__(self: pyrosetta.rosetta.protocols.match.output.CloudPDBWriter, arg0: pyrosetta.rosetta.protocols.match.output.CloudPDBWriter) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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

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.

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

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 class std::basic_string<char> &) –> 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.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.

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.

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

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.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

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.match.output.MatchScoreWriter) -> None
__init__(self: pyrosetta.rosetta.protocols.match.output.MatchScoreWriter, arg0: pyrosetta.rosetta.protocols.match.output.MatchScoreWriter) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.protocols.match.output.MatchScoreWriter) → str¶

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

add_match(*args, **kwargs)¶

Overloaded function.

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(class std::basic_string<char>, double) –> void

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(class std::basic_string<char>) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.match.output.MatchScoreWriter) -> None
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(class std::basic_ostream<char> &) 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.PoseMatchOutputWriter¶

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

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

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter, grouper: pyrosetta.rosetta.protocols.match.output.MatchGrouper) -> None
__init__(self: pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter, arg0: pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.

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

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

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.

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

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 class std::basic_string<char> &) –> 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.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

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper) -> None
__init__(self: pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper, ncst: int) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper) -> None
__init__(self: pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper, ncst: int) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.

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

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.

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter) -> None
__init__(self: pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter, arg0: pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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 class std::basic_string<char> &) –> 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 &, class std::basic_ostream<char> &) const –> 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

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter, filter_name: str, coordinate_cacher: protocols::match::output::UpstreamHitCacher) -> None
__init__(self: pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter, arg0: pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.

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

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.

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

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.

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter, filter_name: str, coordinate_cacher: pyrosetta.rosetta.protocols.match.output.UpstreamHitCacher) -> None
__init__(self: pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter, arg0: pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.

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

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.

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

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