pose_metric_calculators

Bindings for protocols::toolbox::pose_metric_calculators namespace

class pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.InterGroupNeighborsCalculator

Bases: pyrosetta.rosetta.core.pose.metrics.StructureDependentCalculator

This is complicated, so pay attention. You define groups of residues within a protein (say, the N and C terminal domains). You then define which pairs of groups you are interested in. This calculator returns the union of the sets of residues at the interfaces between these domains/groups. Functionally it is intended for “interface design” at the non-chainbreak interface between domains of multidomain proteins. It contains a superset of the functionality of some of the other calculators (so I’ll be obsoleting them, maybe?). The pose does NOT have to have been scored.

“groups” string returns the input groups; of type utility::vector1< std::pair< std::set< core::Size >, std::set< core::Size > > > (not a calculated value)

“dist_cutoff” returns the input cutoff distance for neighbor finding (not a calculated value)

“neighbors” returns a std::set<core::Size> of the neighbors calculated between the group pairs.

“num_neighbors” returns the size of the neighbors set.

__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.

1. __init__(self: pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.InterGroupNeighborsCalculator, arg0: pyrosetta.rosetta.utility.vector1_std_pair_std_set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_std_set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t) -> None

doc

2. __init__(self: pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.InterGroupNeighborsCalculator, groups: pyrosetta.rosetta.utility.vector1_std_pair_std_set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_std_set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t, dist_cutoff: float) -> None
3. __init__(self: pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.InterGroupNeighborsCalculator, arg0: pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.InterGroupNeighborsCalculator) -> 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.toolbox.pose_metric_calculators.InterGroupNeighborsCalculator, : pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.InterGroupNeighborsCalculator) → pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.InterGroupNeighborsCalculator

C++: protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator::operator=(const class protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator &) –> class protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator &

clone(self: pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.InterGroupNeighborsCalculator) → pyrosetta.rosetta.core.pose.metrics.PoseMetricCalculator

C++: protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator::clone() const –> class std::shared_ptr<class core::pose::metrics::PoseMetricCalculator>

dist_cutoff(self: pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.InterGroupNeighborsCalculator) → float

return distance cutoff

C++: protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator::dist_cutoff() const –> double

get(*args, **kwargs)

Overloaded function.

1. get(self: pyrosetta.rosetta.core.pose.metrics.StructureDependentCalculator, key: str, val: pyrosetta.rosetta.basic.MetricValueBase, this_pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: core::pose::metrics::StructureDependentCalculator::get(const class std::basic_string<char> &, class basic::MetricValueBase &, const class core::pose::Pose &) –> void

2. get(self: pyrosetta.rosetta.core.pose.metrics.StructureDependentCalculator, key: str, this_pose: pyrosetta.rosetta.core.pose.Pose) -> str

C++: core::pose::metrics::StructureDependentCalculator::get(const class std::basic_string<char> &, const class core::pose::Pose &) –> std::string

groups(self: pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.InterGroupNeighborsCalculator) → pyrosetta.rosetta.utility.vector1_std_pair_std_set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_std_set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t

return groups

C++: protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator::groups() const –> const class utility::vector1<struct std::pair<class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >, class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > >, class std::allocator<struct std::pair<class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >, class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > > > > &

notify_energy_change(self: pyrosetta.rosetta.core.pose.metrics.PoseMetricCalculator) → None

C++: core::pose::metrics::PoseMetricCalculator::notify_energy_change() –> void

notify_structure_change(self: pyrosetta.rosetta.core.pose.metrics.StructureDependentCalculator) → None

C++: core::pose::metrics::StructureDependentCalculator::notify_structure_change() –> void

class pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborhoodByDistanceCalculator

Bases: pyrosetta.rosetta.core.pose.metrics.StructureDependentCalculator

this calculator determines the number and resids of residues within X angstroms of a group of given residues. Its intended purpose is the backend for a TaskOperation that allows one to construct a PackerTask based on neighborhoods around a set of particular residues. It can return its set of central residues, the total count of their neighbors as determined by the sub-calculators (inclusive of the central residues), and the identities of those neighbors.

__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.

1. __init__(self: pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborhoodByDistanceCalculator, central_residues: pyrosetta.rosetta.std.set_unsigned_long_t) -> None
2. __init__(self: pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborhoodByDistanceCalculator, central_residues: pyrosetta.rosetta.std.set_unsigned_long_t, dist_cutoff: float) -> None
3. __init__(self: pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborhoodByDistanceCalculator, arg0: pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborhoodByDistanceCalculator) -> 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.core.pose.metrics.StructureDependentCalculator, : pyrosetta.rosetta.core.pose.metrics.StructureDependentCalculator) → pyrosetta.rosetta.core.pose.metrics.StructureDependentCalculator

C++: core::pose::metrics::StructureDependentCalculator::operator=(const class core::pose::metrics::StructureDependentCalculator &) –> class core::pose::metrics::StructureDependentCalculator &

central_residues(self: pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborhoodByDistanceCalculator) → pyrosetta.rosetta.std.set_unsigned_long_t

return central residues set

C++: protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator::central_residues() const –> const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &

clone(self: pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborhoodByDistanceCalculator) → pyrosetta.rosetta.core.pose.metrics.PoseMetricCalculator

C++: protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator::clone() const –> class std::shared_ptr<class core::pose::metrics::PoseMetricCalculator>

dist_cutoff(self: pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborhoodByDistanceCalculator) → float

return distance cutoff

C++: protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator::dist_cutoff() const –> double

get(*args, **kwargs)

Overloaded function.

1. get(self: pyrosetta.rosetta.core.pose.metrics.StructureDependentCalculator, key: str, val: pyrosetta.rosetta.basic.MetricValueBase, this_pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: core::pose::metrics::StructureDependentCalculator::get(const class std::basic_string<char> &, class basic::MetricValueBase &, const class core::pose::Pose &) –> void

2. get(self: pyrosetta.rosetta.core.pose.metrics.StructureDependentCalculator, key: str, this_pose: pyrosetta.rosetta.core.pose.Pose) -> str

C++: core::pose::metrics::StructureDependentCalculator::get(const class std::basic_string<char> &, const class core::pose::Pose &) –> std::string

notify_energy_change(self: pyrosetta.rosetta.core.pose.metrics.PoseMetricCalculator) → None

C++: core::pose::metrics::PoseMetricCalculator::notify_energy_change() –> void

notify_structure_change(self: pyrosetta.rosetta.core.pose.metrics.StructureDependentCalculator) → None

C++: core::pose::metrics::StructureDependentCalculator::notify_structure_change() –> void

class pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborsByDistanceCalculator

Bases: pyrosetta.rosetta.core.pose.metrics.StructureDependentCalculator

this calculator determines the number and resids of residues within X angstroms of the given residue. Its intended purpose is the backend for a TaskOperation that allows one to construct a PackerTask based on neighborhoods around a set of particular residues. (It combines with a NeighborhoodByDistanceCalculator for that purpose). It can return the identity of its seeded central residue and distance (just get functions) and calculate the neighbors and count of neighbors around that residue within that distance. It uses the PointGraph class to do this; if you have a better/faster implementation please code it up and replace this one. Note that returned data is INCLUSIVE of the central residue - it is part of the count and part of the std::set.

__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.

1. __init__(self: pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborsByDistanceCalculator, arg0: int) -> None

doc

2. __init__(self: pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborsByDistanceCalculator, central_residue: int, dist_cutoff: float) -> None
3. __init__(self: pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborsByDistanceCalculator, arg0: pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborsByDistanceCalculator) -> 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.core.pose.metrics.StructureDependentCalculator, : pyrosetta.rosetta.core.pose.metrics.StructureDependentCalculator) → pyrosetta.rosetta.core.pose.metrics.StructureDependentCalculator

C++: core::pose::metrics::StructureDependentCalculator::operator=(const class core::pose::metrics::StructureDependentCalculator &) –> class core::pose::metrics::StructureDependentCalculator &

central_residue(self: pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborsByDistanceCalculator) → int

return central residue

C++: protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator::central_residue() const –> unsigned long

clone(self: pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborsByDistanceCalculator) → pyrosetta.rosetta.core.pose.metrics.PoseMetricCalculator

C++: protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator::clone() const –> class std::shared_ptr<class core::pose::metrics::PoseMetricCalculator>

dist_cutoff(self: pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborsByDistanceCalculator) → float

return distance cutoff

C++: protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator::dist_cutoff() const –> double

get(*args, **kwargs)

Overloaded function.

1. get(self: pyrosetta.rosetta.core.pose.metrics.StructureDependentCalculator, key: str, val: pyrosetta.rosetta.basic.MetricValueBase, this_pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: core::pose::metrics::StructureDependentCalculator::get(const class std::basic_string<char> &, class basic::MetricValueBase &, const class core::pose::Pose &) –> void

2. get(self: pyrosetta.rosetta.core.pose.metrics.StructureDependentCalculator, key: str, this_pose: pyrosetta.rosetta.core.pose.Pose) -> str

C++: core::pose::metrics::StructureDependentCalculator::get(const class std::basic_string<char> &, const class core::pose::Pose &) –> std::string

notify_energy_change(self: pyrosetta.rosetta.core.pose.metrics.PoseMetricCalculator) → None

C++: core::pose::metrics::PoseMetricCalculator::notify_energy_change() –> void

notify_structure_change(self: pyrosetta.rosetta.core.pose.metrics.StructureDependentCalculator) → None

C++: core::pose::metrics::StructureDependentCalculator::notify_structure_change() –> void

pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.choose_hbond_parameter_set() → str

use the “score12_params” set if the -restore_pre_talaris_2013_behavior flag is on the command line

and otherwise use the new and improved sp2_elec_params parameter set

C++: protocols::toolbox::pose_metric_calculators::choose_hbond_parameter_set() –> std::string

pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.residue_subset(setf: str, rset: pyrosetta.rosetta.utility.vector1_unsigned_long, ps: pyrosetta.rosetta.core.pose.Pose) → None

extracts the pose indexes of a selected subset of residues

C++: protocols::toolbox::pose_metric_calculators::residue_subset(class std::basic_string<char>, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class core::pose::Pose &) –> void