match

Bindings for protocols::match namespace

class pyrosetta.rosetta.protocols.match.AddAllPositionsMPM

Bases: pyrosetta.rosetta.protocols.match.MatchPositionModifier

MPM that returns a vector of all protein positions in the pose i.e. allowing matching everywhere

__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.AddAllPositionsMPM) → 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.AddAllPositionsMPM, : pyrosetta.rosetta.protocols.match.AddAllPositionsMPM) → pyrosetta.rosetta.protocols.match.AddAllPositionsMPM

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

modified_match_positions(self: pyrosetta.rosetta.protocols.match.AddAllPositionsMPM, original_positions: pyrosetta.rosetta.utility.vector1_unsigned_long, match_pose: pyrosetta.rosetta.core.pose.Pose, mtask: protocols::match::MatcherTask) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::match::AddAllPositionsMPM::modified_match_positions(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class core::pose::Pose &, class std::shared_ptr<const class protocols::match::MatcherTask>) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

class pyrosetta.rosetta.protocols.match.BfactorMPM

Bases: pyrosetta.rosetta.protocols.match.MatchPositionModifier

removes positions at which the bfactors for c-alpha atoms are above a desired cutoff. bfactors stored in the pose pdbinfo are taken. if relative bfactors are used, all bfactors are divided by the largest observed bfactor

__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.match.BfactorMPM, input_tokens: pyrosetta.rosetta.utility.vector1_std_string) -> None
  2. __init__(self: pyrosetta.rosetta.protocols.match.BfactorMPM, arg0: pyrosetta.rosetta.protocols.match.BfactorMPM) -> 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.BfactorMPM, : pyrosetta.rosetta.protocols.match.BfactorMPM) → pyrosetta.rosetta.protocols.match.BfactorMPM

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

get_ca_bfactors(self: pyrosetta.rosetta.protocols.match.BfactorMPM, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_double

C++: protocols::match::BfactorMPM::get_ca_bfactors(const class core::pose::Pose &) const –> class utility::vector1<double, class std::allocator<double> >

modified_match_positions(self: pyrosetta.rosetta.protocols.match.BfactorMPM, original_positions: pyrosetta.rosetta.utility.vector1_unsigned_long, match_pose: pyrosetta.rosetta.core.pose.Pose, mtask: protocols::match::MatcherTask) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::match::BfactorMPM::modified_match_positions(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class core::pose::Pose &, class std::shared_ptr<const class protocols::match::MatcherTask>) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

class pyrosetta.rosetta.protocols.match.HitHasher

Bases: pybind11_builtins.pybind11_object

This object hashes hits into 6D voxels. This hash can then be traversed to retrieve the hits that hash to the same voxel (matches!). There are 64 hashes representing the 2^6 ways to perturb the bins in 6D by 1/2 of their bin width.

The hit hasher expects someone else to own the hits. It takes as input constant pointers to the hits that exist and uses their addresses to hash upon. The hit hasher should only be used if you can guarantee that the hits it points to will outlive the hasher.

__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.HitHasher) → 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.HitHasher, : pyrosetta.rosetta.protocols.match.HitHasher) → pyrosetta.rosetta.protocols.match.HitHasher

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

binner(self: pyrosetta.rosetta.protocols.match.HitHasher, which_hash_map: int) → pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner

C++: protocols::match::HitHasher::binner(unsigned long) const –> const class numeric::geometry::hashing::SixDCoordinateBinner &

clear_hash_map(self: pyrosetta.rosetta.protocols.match.HitHasher, which_hash_map: int) → None

C++: protocols::match::HitHasher::clear_hash_map(unsigned long) –> void

initialize(self: pyrosetta.rosetta.protocols.match.HitHasher) → None

C++: protocols::match::HitHasher::initialize() –> void

insert_hit(*args, **kwargs)

Overloaded function.

  1. insert_hit(self: pyrosetta.rosetta.protocols.match.HitHasher, geometric_constraint_id: int, hit: pyrosetta.rosetta.protocols.match.Hit) -> None

Insert a hits into all 64 hash maps

C++: protocols::match::HitHasher::insert_hit(unsigned long, const class protocols::match::Hit *) –> void

  1. insert_hit(self: pyrosetta.rosetta.protocols.match.HitHasher, which_hash_map: int, geometric_constraint_id: int, hit: pyrosetta.rosetta.protocols.match.Hit) -> None

Insert a hits into a particular hash maps

C++: protocols::match::HitHasher::insert_hit(unsigned long, unsigned long, const class protocols::match::Hit *) –> void

set_bounding_box(self: pyrosetta.rosetta.protocols.match.HitHasher, bb: pyrosetta.rosetta.numeric.geometry.BoundingBox_numeric_xyzVector_double_t) → None

C++: protocols::match::HitHasher::set_bounding_box(const class numeric::geometry::BoundingBox<class numeric::xyzVector<double> > &) –> void

set_euler_bin_widths(self: pyrosetta.rosetta.protocols.match.HitHasher, euler_bin_widths: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

C++: protocols::match::HitHasher::set_euler_bin_widths(const class numeric::xyzVector<double> &) –> void

set_nhits_per_match(self: pyrosetta.rosetta.protocols.match.HitHasher, num_geometric_constraints: int) → None

C++: protocols::match::HitHasher::set_nhits_per_match(unsigned long) –> void

set_uniform_euler_angle_bin_width(self: pyrosetta.rosetta.protocols.match.HitHasher, bin_width_degrees: float) → None

C++: protocols::match::HitHasher::set_uniform_euler_angle_bin_width(double) –> void

set_uniform_xyz_bin_width(self: pyrosetta.rosetta.protocols.match.HitHasher, bin_width: float) → None

C++: protocols::match::HitHasher::set_uniform_xyz_bin_width(double) –> void

set_xyz_bin_widths(self: pyrosetta.rosetta.protocols.match.HitHasher, bin_widths: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

C++: protocols::match::HitHasher::set_xyz_bin_widths(const class numeric::xyzVector<double> &) –> void

class pyrosetta.rosetta.protocols.match.HitNeighborFinder

Bases: pybind11_builtins.pybind11_object

Class for finding hit neighbors in 6D considering all 64 origin definitions (but without forming all 64 hashes).

__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.HitNeighborFinder) → 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).

add_hits(*args, **kwargs)

Overloaded function.

  1. add_hits(self: pyrosetta.rosetta.protocols.match.HitNeighborFinder, hitlist: pyrosetta.rosetta.std.list_protocols_match_Hit_t) -> None

Add all hits (using hit pointers!) from one list of hits

C++: protocols::match::HitNeighborFinder::add_hits(const class std::list<class protocols::match::Hit, class std::allocator<class protocols::match::Hit> > &) –> void

  1. add_hits(self: pyrosetta.rosetta.protocols.match.HitNeighborFinder, hitptrlist: pyrosetta.rosetta.std.list_const_protocols_match_Hit_*_t) -> None

Add hit pointers from the input list

C++: protocols::match::HitNeighborFinder::add_hits(const class std::list<const class protocols::match::Hit *, class std::allocator<const class protocols::match::Hit *> > &) –> void

assign(self: pyrosetta.rosetta.protocols.match.HitNeighborFinder, : pyrosetta.rosetta.protocols.match.HitNeighborFinder) → pyrosetta.rosetta.protocols.match.HitNeighborFinder

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

initialize(self: pyrosetta.rosetta.protocols.match.HitNeighborFinder) → None
Call this after the bounding-box and the bin-widths have been set up. Must
be called before “add_hits” it called. This initializes the SixDCoordinateBinner.

C++: protocols::match::HitNeighborFinder::initialize() –> void

neighbor_hits(self: pyrosetta.rosetta.protocols.match.HitNeighborFinder, queryhits: pyrosetta.rosetta.std.list_const_protocols_match_Hit_*_t) → pyrosetta.rosetta.std.list_const_protocols_match_Hit_*_t
Find the neighbors of the given set of query hits. This search iterates
across both the upper and the lower neighbors of the query hits (3^6 neighbors).

C++: protocols::match::HitNeighborFinder::neighbor_hits(const class std::list<const class protocols::match::Hit *, class std::allocator<const class protocols::match::Hit *> > &) const –> class std::list<const class protocols::match::Hit *, class std::allocator<const class protocols::match::Hit *> >

set_bounding_box(self: pyrosetta.rosetta.protocols.match.HitNeighborFinder, bb: pyrosetta.rosetta.numeric.geometry.BoundingBox_numeric_xyzVector_double_t) → None

Use the same bounding box as the HitHasher / OccupiedSpaceHash

C++: protocols::match::HitNeighborFinder::set_bounding_box(const class numeric::geometry::BoundingBox<class numeric::xyzVector<double> > &) –> void

set_euler_bin_widths(self: pyrosetta.rosetta.protocols.match.HitNeighborFinder, euler_bin_widths: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

Give the same euler-angle bin witdhs given to the HitHasher / OccupiedSpaceHash.

C++: protocols::match::HitNeighborFinder::set_euler_bin_widths(const class numeric::xyzVector<double> &) –> void

set_uniform_euler_angle_bin_width(self: pyrosetta.rosetta.protocols.match.HitNeighborFinder, bin_width_degrees: float) → None

Give the same euler-angle bin witdh given to the HitHasher / OccupiedSpaceHash.

C++: protocols::match::HitNeighborFinder::set_uniform_euler_angle_bin_width(double) –> void

set_uniform_xyz_bin_width(self: pyrosetta.rosetta.protocols.match.HitNeighborFinder, bin_width: float) → None

Give the same xyz bin witdh given to the HitHasher / OccupiedSpaceHash.

C++: protocols::match::HitNeighborFinder::set_uniform_xyz_bin_width(double) –> void

set_xyz_bin_widths(self: pyrosetta.rosetta.protocols.match.HitNeighborFinder, bin_widths: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

Give the same xyz bin witdhs given to the HitHasher / OccupiedSpaceHash.

C++: protocols::match::HitNeighborFinder::set_xyz_bin_widths(const class numeric::xyzVector<double> &) –> void

class pyrosetta.rosetta.protocols.match.MatchCounter

Bases: pybind11_builtins.pybind11_object

Class for counting the number of matches given a particular discretization level.

__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.MatchCounter) → 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).

add_hits(*args, **kwargs)

Overloaded function.

  1. add_hits(self: pyrosetta.rosetta.protocols.match.MatchCounter, geomcst_id: int, hitlist: pyrosetta.rosetta.std.list_protocols_match_Hit_t) -> None

Add hits from a list of hits for a particular geometric constraint.

C++: protocols::match::MatchCounter::add_hits(unsigned long, const class std::list<class protocols::match::Hit, class std::allocator<class protocols::match::Hit> > &) –> void

  1. add_hits(self: pyrosetta.rosetta.protocols.match.MatchCounter, geomcst_id: int, hitptrlist: pyrosetta.rosetta.std.list_const_protocols_match_Hit_*_t) -> None

Add hit from the input list of hits for a particular geometric constraint.

C++: protocols::match::MatchCounter::add_hits(unsigned long, const class std::list<const class protocols::match::Hit *, class std::allocator<const class protocols::match::Hit *> > &) –> void

assign(self: pyrosetta.rosetta.protocols.match.MatchCounter, : pyrosetta.rosetta.protocols.match.MatchCounter) → pyrosetta.rosetta.protocols.match.MatchCounter

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

count_n_matches(self: pyrosetta.rosetta.protocols.match.MatchCounter) → int
Possibly slow method to predict the total number of matches given a set of
hits and a particular grid resolution. (The main function that this class provides).

C++: protocols::match::MatchCounter::count_n_matches() const –> unsigned long

initialize(self: pyrosetta.rosetta.protocols.match.MatchCounter) → None
Call this after the bounding-box and the bin-widths have been set up. Must
be called before “add_hits” it called. This initializes the SixDCoordinateBinner.

C++: protocols::match::MatchCounter::initialize() –> void

set_bounding_box(self: pyrosetta.rosetta.protocols.match.MatchCounter, bb: pyrosetta.rosetta.numeric.geometry.BoundingBox_numeric_xyzVector_double_t) → None

Use the same bounding box as the HitHasher / OccupiedSpaceHash

C++: protocols::match::MatchCounter::set_bounding_box(const class numeric::geometry::BoundingBox<class numeric::xyzVector<double> > &) –> void

set_euler_bin_widths(self: pyrosetta.rosetta.protocols.match.MatchCounter, euler_bin_widths: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

Give the same euler-angle bin witdhs given to the HitHasher / OccupiedSpaceHash.

C++: protocols::match::MatchCounter::set_euler_bin_widths(const class numeric::xyzVector<double> &) –> void

set_n_geometric_constraints(self: pyrosetta.rosetta.protocols.match.MatchCounter, ngeomcsts: int) → None

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

set_uniform_euler_angle_bin_width(self: pyrosetta.rosetta.protocols.match.MatchCounter, bin_width_degrees: float) → None

Give the same euler-angle bin witdh given to the HitHasher / OccupiedSpaceHash.

C++: protocols::match::MatchCounter::set_uniform_euler_angle_bin_width(double) –> void

set_uniform_xyz_bin_width(self: pyrosetta.rosetta.protocols.match.MatchCounter, bin_width: float) → None

Give the same xyz bin witdh given to the HitHasher / OccupiedSpaceHash.

C++: protocols::match::MatchCounter::set_uniform_xyz_bin_width(double) –> void

set_xyz_bin_widths(self: pyrosetta.rosetta.protocols.match.MatchCounter, bin_widths: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

Give the same xyz bin witdhs given to the HitHasher / OccupiedSpaceHash.

C++: protocols::match::MatchCounter::set_xyz_bin_widths(const class numeric::xyzVector<double> &) –> void

class pyrosetta.rosetta.protocols.match.MatchPositionModifier

Bases: pybind11_builtins.pybind11_object

base class for objects that modify the match positions based on some criterion

__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.match.MatchPositionModifier) -> None
  2. __init__(self: pyrosetta.rosetta.protocols.match.MatchPositionModifier, arg0: pyrosetta.rosetta.protocols.match.MatchPositionModifier) -> 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.MatchPositionModifier, : pyrosetta.rosetta.protocols.match.MatchPositionModifier) → pyrosetta.rosetta.protocols.match.MatchPositionModifier

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

modified_match_positions(self: pyrosetta.rosetta.protocols.match.MatchPositionModifier, original_positions: pyrosetta.rosetta.utility.vector1_unsigned_long, match_pose: pyrosetta.rosetta.core.pose.Pose, mtask: protocols::match::MatcherTask) → pyrosetta.rosetta.utility.vector1_unsigned_long
the positions in the vector1< Size > that is returned
by this function will replace the match positions in the MatcherTask.

C++: protocols::match::MatchPositionModifier::modified_match_positions(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class core::pose::Pose &, class std::shared_ptr<const class protocols::match::MatcherTask>) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

class pyrosetta.rosetta.protocols.match.Matcher

Bases: pybind11_builtins.pybind11_object

Overview: The matcher algorithm was originally concieved of within the domain of enzyme design. The transition state for the desired reqction is contacted by several amino acids each with a particular geometry. The goal of the matcher is to find a set of backbone positions on a given protein-backbone scaffold where those amino acids could be grafted such that they would contact the ligand in the desired geometry.

Consider a case where the transition state is contacted by an asparagine, an aspartate and a histadine. The user designing an enzyme for this transition state knows the geometry that describes the orientation of the transition state with respect to each of these side chains; what they do not know is into what protein and at what positions they should introduce these amino acids. The user will give the matcher a description of the geometry between the amind acids and the transition state. This geometry is in the form of 6 parameters: 3 diherals, 2 angles, and 1 distance (more on these later). Given the coordinates of a particular side chain and the geometry describing the transition state relative to the side chain, the coordinates of the transition state may be computed. In a sense, the transition state may be grown off of the end of a side chain in the desired geoemtry.

(Usually, the user will specify many different possible values for each of the 6 parameters, and the matcher will then consider all combinations of those values. E.g. the ideal distance might be 2.0 A, but the user might ask the matcher to consider the values 1.95 and 2.05 A additionally. Each assignment of values to these 6 parameters fully specifies the coordinates of the transition state.)

The matcher examines each geometric constraint one at a time. It builds rotamers for one or more amino acids capable of satisfying a desired geometry (e.g. both ASP and GLU if an acid group is needed) at each of several active-site positions, and for each rotamer, it grows the transition state. The matcher does a quick collision check between the atoms of the transition state and the backbone of the protein, rejecting transition-state conformations that collide. If the conformation is collision-free, then the matcher measures the coordinates of the transition state as a point in a 6-dimensional space. (It is no coincidence that there are 6 geometric parameters and that there are 6 dimensions in the space describing the transition state’s coordinates). With this 6-dimensional coordinate, the matcher can recover the coordinates for the transition state – the 6-D coordinate and the full euclidean coordinates of the transition state are interconvertable. The matcher can also bin the coordinate. If two coordinates in 6-D are close, they will be assigned to the same bin. This is the fundamental insight of the matching algorithm: the matcher will grow the transition state from different catalytic residues, and when the 6-d coordinates from different catalytic residues are assigned to the same bin, then the matcher has found a set of conformations of the transition state that are compatible with more than one catalytic geometry.

Each collision-free placement of the transition state is called a “hit”. If there are N geometric-constrains that the matcher is asked to satisfy, then a set of N hits, one per constraint, that fall into the same bin are called a “match”.

In the general case, the Matcher builds hits for each of several geometric constraints. The protein scaffold in the enzyme-design example generalizes to any macro-molecular polymer scaffold. The protein rotamers in the enzyme-design example generalizes to a set of conformations for the “upstream” partner. The transition state gene in the enzyme-design example generalizes to a “downstream” partner, which itself may have multiple conformations. “Upstream” and “Downstream” refer to the order in which the coordinates of the two partners are computed. The upstream coordinates are built first, the downstream coordinates second. Changes to the coordinates of the upstream partner propagate to the coordinates of the downstream partner. In the enzyme-design example, the transition state is considered to be rigid; in the general case the transition state may have multiple conformations. The downstream partner could also be an entire protein – and may have it’s own set of rotameric states. E.G. one might want to match a hydrogen-bond donor on the scaffold to a serine side-chain on the target (downstream) protein. The downstream partner should then be able to examine many serine rotamers for each conformation of the upstream rotamer.

A hit is represented in two parts: a discrete part and a continuous part. The discrete portion consists of four integers: 1. the build-point index on the scaffold, 2. the rotamer index on the upstream partner, 3. the external-geometry index, and 4. the rotamer index on the downstream partner. The continuous portion consists of 6 double-precision values representing the coordinate of the downstream partner in 6D. The first three values are the x,y and z coordinates of a particular atom in the downstream partner. The second three values are the phi, psi, and theta values describing the coordinate frame at this atom. These three “Euler angle” parameters describe three rotations: Z(psi) * X(theta) * Z(phi) * I. They are described in greater detail in src/numeric/HomogeneousTransform.hh. “Phi” and “psi” here have nothing to do with the protein-backbone angles. When a hit is binned, there are two sets of parameters that describe how wide the bins in each dimension should be: the Euclidean bin widths are for the xyz coordinates, and the Euler bin widths are for the Euler angles. The Euclidean bin widths are in Angstroms and the Euler bin widths are in degrees.

A Matcher object should be initialized from a MatcherTask object through the intialize_from_task() method. A MatcherTask will contain an EnzConstraintIO object, and the function Matcher::initialize_from_file() will be invoked as the Matcher is intialied from a MatcherTask. The documentation for Matcher::inialize_from_file() describes the format of extra data that may be included in the enzyme-design constraint file. This data should live within a ALGORITHM_INFO:: match … ALGORITHM::END block inside a CST::BEGIN … CST::END block in the constraint file.

find_hits() is the main worker function. After the matcher finishes find_hits(), the matches can be read by a MatchProcessor in a call to process_matches.

__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.Matcher) → 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).

add_external_geometry_samples_for_constraint(*args, **kwargs)

Overloaded function.

  1. add_external_geometry_samples_for_constraint(self: pyrosetta.rosetta.protocols.match.Matcher, cst_id: int, restype: pyrosetta.rosetta.core.chemical.ResidueType, upstream_launch_atoms: pyrosetta.rosetta.utility.vector1_std_string, downstream_3atoms: pyrosetta.rosetta.utility.vector1_core_id_AtomID, exgeom_list: pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_ExternalGeomSampler, exgeom_id: int) -> None
  2. add_external_geometry_samples_for_constraint(self: pyrosetta.rosetta.protocols.match.Matcher, cst_id: int, restype: pyrosetta.rosetta.core.chemical.ResidueType, upstream_launch_atoms: pyrosetta.rosetta.utility.vector1_std_string, downstream_3atoms: pyrosetta.rosetta.utility.vector1_core_id_AtomID, exgeom_list: pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_ExternalGeomSampler, exgeom_id: int, enumerate_ligand_rotamers: bool) -> None
  3. add_external_geometry_samples_for_constraint(self: pyrosetta.rosetta.protocols.match.Matcher, cst_id: int, restype: pyrosetta.rosetta.core.chemical.ResidueType, upstream_launch_atoms: pyrosetta.rosetta.utility.vector1_std_string, downstream_3atoms: pyrosetta.rosetta.utility.vector1_core_id_AtomID, exgeom_list: pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_ExternalGeomSampler, exgeom_id: int, enumerate_ligand_rotamers: bool, catalytic_bond: bool) -> None
  4. add_external_geometry_samples_for_constraint(self: pyrosetta.rosetta.protocols.match.Matcher, cst_id: int, restype: pyrosetta.rosetta.core.chemical.ResidueType, upstream_launch_atoms: pyrosetta.rosetta.utility.vector1_std_string, downstream_3atoms: pyrosetta.rosetta.utility.vector1_core_id_AtomID, exgeom_list: pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_ExternalGeomSampler, exgeom_id: int, enumerate_ligand_rotamers: bool, catalytic_bond: bool, build_round1_hits_twice: bool) -> None

C++: protocols::match::Matcher::add_external_geometry_samples_for_constraint(unsigned long, class std::shared_ptr<const class core::chemical::ResidueType>, const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &, const class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> > &, const class utility::vector1<class protocols::toolbox::match_enzdes_util::ExternalGeomSampler, class std::allocator<class protocols::toolbox::match_enzdes_util::ExternalGeomSampler> > &, const unsigned long, bool, bool, bool) –> void

add_secondary_downstream_match_geometry_for_constraint(self: pyrosetta.rosetta.protocols.match.Matcher, geom_cst_id: int, candidate_restype: pyrosetta.rosetta.core.chemical.ResidueType, downstream_restype: pyrosetta.rosetta.core.chemical.ResidueType, candidate_atids: pyrosetta.rosetta.utility.vector1_unsigned_long, target_atids: pyrosetta.rosetta.utility.vector1_unsigned_long, mcfi: protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo, SecMatchStr: str, upstream_pose: pyrosetta.rosetta.core.pose.Pose, catalytic_bond: bool) → None

C++: protocols::match::Matcher::add_secondary_downstream_match_geometry_for_constraint(unsigned long, class std::shared_ptr<const class core::chemical::ResidueType>, class std::shared_ptr<const class core::chemical::ResidueType>, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo>, class std::basic_string<char>, const class core::pose::Pose &, bool) –> void

add_secondary_upstream_match_geometry_for_constraint(self: pyrosetta.rosetta.protocols.match.Matcher, geom_cst_id: int, target_geom_cst_id: int, candidate_restype: pyrosetta.rosetta.core.chemical.ResidueType, target_restype: pyrosetta.rosetta.core.chemical.ResidueType, candidate_atids: pyrosetta.rosetta.utility.vector1_unsigned_long, target_atids: pyrosetta.rosetta.utility.vector1_unsigned_long, mcfi: protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo, SecMatchStr: str, upstream_pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::match::Matcher::add_secondary_upstream_match_geometry_for_constraint(unsigned long, unsigned long, class std::shared_ptr<const class core::chemical::ResidueType>, class std::shared_ptr<const class core::chemical::ResidueType>, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo>, class std::basic_string<char>, const class core::pose::Pose &) –> void

add_upstream_restype_for_constraint(self: pyrosetta.rosetta.protocols.match.Matcher, cst_id: int, restype: pyrosetta.rosetta.core.chemical.ResidueType) → None

C++: protocols::match::Matcher::add_upstream_restype_for_constraint(unsigned long, class std::shared_ptr<const class core::chemical::ResidueType>) –> void

build_point(self: pyrosetta.rosetta.protocols.match.Matcher, index: int) → pyrosetta.rosetta.protocols.match.upstream.ScaffoldBuildPoint

Non-const access

C++: protocols::match::Matcher::build_point(unsigned long) –> class std::shared_ptr<class protocols::match::upstream::ScaffoldBuildPoint>

desymmeterize_upstream_restype_for_constraint(self: pyrosetta.rosetta.protocols.match.Matcher, cst_id: int) → None

C++: protocols::match::Matcher::desymmeterize_upstream_restype_for_constraint(unsigned long) –> void

downstream_builder(self: pyrosetta.rosetta.protocols.match.Matcher, : int) → protocols::match::downstream::DownstreamBuilder
Return non-const access to a representative downstream builder
for a particular geometric constraint

C++: protocols::match::Matcher::downstream_builder(unsigned long) –> class std::shared_ptr<class protocols::match::downstream::DownstreamBuilder>

downstream_builders(self: pyrosetta.rosetta.protocols.match.Matcher, cst_id: int) → pyrosetta.rosetta.std.list_std_shared_ptr_protocols_match_downstream_DownstreamBuilder_std_allocator_std_shared_ptr_protocols_match_downstream_DownstreamBuilder_t
Return non-const access to all of the downstream builders
for a particular geometric constraint

C++: protocols::match::Matcher::downstream_builders(unsigned long) const –> const class std::list<class std::shared_ptr<class protocols::match::downstream::DownstreamBuilder>, class std::allocator<class std::shared_ptr<class protocols::match::downstream::DownstreamBuilder> > > &

downstream_pose(self: pyrosetta.rosetta.protocols.match.Matcher) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::match::Matcher::downstream_pose() const –> class std::shared_ptr<const class core::pose::Pose>

erase_hit(self: pyrosetta.rosetta.protocols.match.Matcher, dsalg: protocols::match::downstream::DownstreamAlgorithm, geom_cst_id_for_hit: int, iter: std::_List_iterator<protocols::match::Hit>) → None
To be invoked by a downstream algorithm. Downstream algorithms may prune their
old, inviable hits, through this method – they should pass themselves in as an argument – and they may also prune this hits for other rounds. If the should prune other-round hits, then they will trigger an update to the hit_lists_with_primary_modificiations_ list, leading to an additional pass over the geometric constraints in a primary/peripheral pattern.

C++: protocols::match::Matcher::erase_hit(const class protocols::match::downstream::DownstreamAlgorithm &, unsigned long, const struct std::_List_iterator<class protocols::match::Hit> &) –> void

find_hits(self: pyrosetta.rosetta.protocols.match.Matcher) → bool

Main worker function

C++: protocols::match::Matcher::find_hits() –> bool

get_pose_build_resids(self: pyrosetta.rosetta.protocols.match.Matcher) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::match::Matcher::get_pose_build_resids() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

has_upstream_only_geomcsts(self: pyrosetta.rosetta.protocols.match.Matcher) → bool

C++: protocols::match::Matcher::has_upstream_only_geomcsts() const –> bool

hit_list_begin(self: pyrosetta.rosetta.protocols.match.Matcher, geom_cst_id: int) → std::_List_iterator<protocols::match::Hit>
Return a non-constant iterator to a HitList for a particular geometric constraint.
DANGER DANGER DANGER. This access is intended to allow a DownstreamAlgorithm to delete its own non-viable hits and also to allow a DownstreamAlgorithm to delete another algorithm’s non-viable hits; Actual deletion requires invoking the method Matcher::erase_hit(). This non-const access is not intended for any other class.

C++: protocols::match::Matcher::hit_list_begin(unsigned long) –> struct std::_List_iterator<class protocols::match::Hit>

hit_list_end(self: pyrosetta.rosetta.protocols.match.Matcher, geom_cst_id: int) → std::_List_iterator<protocols::match::Hit>
Return a non-constant iterator to the end position for a
HitList for a particular geometric constraint. See comments for hit_list_begin()

C++: protocols::match::Matcher::hit_list_end(unsigned long) –> struct std::_List_iterator<class protocols::match::Hit>

hits(self: pyrosetta.rosetta.protocols.match.Matcher, cst_id: int) → pyrosetta.rosetta.std.list_protocols_match_Hit_t

C++: protocols::match::Matcher::hits(unsigned long) const –> const class std::list<class protocols::match::Hit, class std::allocator<class protocols::match::Hit> > &

initialize_from_file(self: pyrosetta.rosetta.protocols.match.Matcher, enz_data: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, task: protocols::match::MatcherTask) → None

Intialize the geometric constraints from the EnzConstraionIO object.

C++: protocols::match::Matcher::initialize_from_file(const class protocols::toolbox::match_enzdes_util::EnzConstraintIO &, const class protocols::match::MatcherTask &) –> void

initialize_from_task(self: pyrosetta.rosetta.protocols.match.Matcher, task: protocols::match::MatcherTask) → None

The primary way to initialize a Matcher is through a MatcherTask.

C++: protocols::match::Matcher::initialize_from_task(const class protocols::match::MatcherTask &) –> void

n_geometric_constraints(self: pyrosetta.rosetta.protocols.match.Matcher) → int

C++: protocols::match::Matcher::n_geometric_constraints() const –> unsigned long

nonconst_downstream_algorithms(self: pyrosetta.rosetta.protocols.match.Matcher, cst_id: int) → pyrosetta.rosetta.std.list_std_shared_ptr_protocols_match_downstream_DownstreamAlgorithm_std_allocator_std_shared_ptr_protocols_match_downstream_DownstreamAlgorithm_t
Non-const access to the set of downstream algorithms for a
particular geometric constraint – note that the list containing these algorithms is itself const.

C++: protocols::match::Matcher::nonconst_downstream_algorithms(unsigned long) –> const class std::list<class std::shared_ptr<class protocols::match::downstream::DownstreamAlgorithm>, class std::allocator<class std::shared_ptr<class protocols::match::downstream::DownstreamAlgorithm> > > &

occ_space_hash(self: pyrosetta.rosetta.protocols.match.Matcher) → protocols::match::OccupiedSpaceHash

C++: protocols::match::Matcher::occ_space_hash() –> class std::shared_ptr<class protocols::match::OccupiedSpaceHash>

process_matches(self: pyrosetta.rosetta.protocols.match.Matcher, processor: protocols::match::output::MatchProcessor) → None
After find_hits completes, use this function to have the
Matcher enerate the hit-combinations (matches) and send those matches to the specified match-processor. The match processor may do what it pleases with the matches.

C++: protocols::match::Matcher::process_matches(class protocols::match::output::MatchProcessor &) const –> void

representative_downstream_algorithm(self: pyrosetta.rosetta.protocols.match.Matcher, cst_id: int) → protocols::match::downstream::DownstreamAlgorithm

C++: protocols::match::Matcher::representative_downstream_algorithm(unsigned long) const –> class std::shared_ptr<const class protocols::match::downstream::DownstreamAlgorithm>

set_bump_tolerance(self: pyrosetta.rosetta.protocols.match.Matcher, permitted_overlap: float) → None

C++: protocols::match::Matcher::set_bump_tolerance(double) –> void

set_downstream_pose(self: pyrosetta.rosetta.protocols.match.Matcher, pose: pyrosetta.rosetta.core.pose.Pose, orientation_atoms: pyrosetta.rosetta.utility.vector1_core_id_AtomID) → None

C++: protocols::match::Matcher::set_downstream_pose(const class core::pose::Pose &, class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> >) –> void

set_fa_dun_cutoff_for_constraint(self: pyrosetta.rosetta.protocols.match.Matcher, cst_id: int, restype: pyrosetta.rosetta.core.chemical.ResidueType, fa_dun_cutoff: float) → None

C++: protocols::match::Matcher::set_fa_dun_cutoff_for_constraint(unsigned long, class std::shared_ptr<const class core::chemical::ResidueType>, double) –> void

set_hash_euclidean_bin_width(self: pyrosetta.rosetta.protocols.match.Matcher, width: float) → None

C++: protocols::match::Matcher::set_hash_euclidean_bin_width(double) –> void

set_hash_euclidean_bin_widths(self: pyrosetta.rosetta.protocols.match.Matcher, widths: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

C++: protocols::match::Matcher::set_hash_euclidean_bin_widths(class numeric::xyzVector<double>) –> void

set_hash_euler_bin_width(self: pyrosetta.rosetta.protocols.match.Matcher, width: float) → None

C++: protocols::match::Matcher::set_hash_euler_bin_width(double) –> void

set_hash_euler_bin_widths(self: pyrosetta.rosetta.protocols.match.Matcher, widths: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

C++: protocols::match::Matcher::set_hash_euler_bin_widths(class numeric::xyzVector<double>) –> void

set_n_geometric_constraints(self: pyrosetta.rosetta.protocols.match.Matcher, n_constraints: int) → None

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

set_occupied_space_bounding_box(self: pyrosetta.rosetta.protocols.match.Matcher, bb: pyrosetta.rosetta.numeric.geometry.BoundingBox_numeric_xyzVector_double_t) → None

C++: protocols::match::Matcher::set_occupied_space_bounding_box(const class numeric::geometry::BoundingBox<class numeric::xyzVector<double> > &) –> void

set_original_scaffold_build_points(self: pyrosetta.rosetta.protocols.match.Matcher, resids: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: protocols::match::Matcher::set_original_scaffold_build_points(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_original_scaffold_build_points_for_constraint(self: pyrosetta.rosetta.protocols.match.Matcher, cst_id: int, resids: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: protocols::match::Matcher::set_original_scaffold_build_points_for_constraint(unsigned long, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_sample_startegy_for_constraint(self: pyrosetta.rosetta.protocols.match.Matcher, cst_id: int, restype: pyrosetta.rosetta.core.chemical.ResidueType, chi: int, strat: pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData) → None

C++: protocols::match::Matcher::set_sample_startegy_for_constraint(unsigned long, class std::shared_ptr<const class core::chemical::ResidueType>, unsigned long, const class protocols::match::upstream::SampleStrategyData &) –> void

set_upstream_pose(self: pyrosetta.rosetta.protocols.match.Matcher, pose: pyrosetta.rosetta.core.pose.Pose) → None

Setup

C++: protocols::match::Matcher::set_upstream_pose(const class core::pose::Pose &) –> void

upstream_builder(self: pyrosetta.rosetta.protocols.match.Matcher, cst_id: int) → pyrosetta.rosetta.protocols.match.upstream.UpstreamBuilder

C++: protocols::match::Matcher::upstream_builder(unsigned long) –> class std::shared_ptr<class protocols::match::upstream::UpstreamBuilder>

upstream_pose(self: pyrosetta.rosetta.protocols.match.Matcher) → pyrosetta.rosetta.core.pose.Pose

Data accessors

C++: protocols::match::Matcher::upstream_pose() const –> class std::shared_ptr<const class core::pose::Pose>

class pyrosetta.rosetta.protocols.match.NumNeighborsMPM

Bases: pyrosetta.rosetta.protocols.match.MatchPositionModifier

removes positions whose numer of neighbors below a 10A cutoff is not within the desired range. if either min_neighbors_ or max_neighbors_ are unspecified (0), this means that they won’t be taken into account, i.e. if min is 5 and max is 0, every position that has more than 4 neighbors will be allowed. also offers the possibility of combining the num neighbors cutoff with the angle between the CA->CB vector of the residue and the CA->protein_center_of_mass vector, for example to only allow positions that point inward

__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.NumNeighborsMPM, input_tokens: pyrosetta.rosetta.utility.vector1_std_string) → 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.NumNeighborsMPM, : pyrosetta.rosetta.protocols.match.NumNeighborsMPM) → pyrosetta.rosetta.protocols.match.NumNeighborsMPM

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

modified_match_positions(self: pyrosetta.rosetta.protocols.match.NumNeighborsMPM, original_positions: pyrosetta.rosetta.utility.vector1_unsigned_long, match_pose: pyrosetta.rosetta.core.pose.Pose, mtask: protocols::match::MatcherTask) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::match::NumNeighborsMPM::modified_match_positions(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class core::pose::Pose &, class std::shared_ptr<const class protocols::match::MatcherTask>) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

passes_com_vector_criterion(self: pyrosetta.rosetta.protocols.match.NumNeighborsMPM, seqpos: int, pose: pyrosetta.rosetta.core.pose.Pose, com: pyrosetta.rosetta.numeric.xyzVector_double_t) → bool

C++: protocols::match::NumNeighborsMPM::passes_com_vector_criterion(unsigned long, const class core::pose::Pose &, const class numeric::xyzVector<double> &) const –> bool

class pyrosetta.rosetta.protocols.match.OccupiedSpaceHash

Bases: pybind11_builtins.pybind11_object

This class keeps track of the active voxels “up until now” with 64 hashes.

Each hash has a slightly shifted definition of the origin, so that points which are close in 6D will end up in the same hash voxel in at least one of these 64 hashes. The amount of data held in this table is intentionally small: a single boolean (32 bits). The meaning is as follows: In the first round of matching constraints, “false” is inserted into each of the hashes for each non-colliding placement of the downstream partner. The map is not altered between the end of the first round and the beginning of the second round. At the end of all rounds besides the first round, the Matcher updates the OccupiedSpaceHash object for each non-colliding placement of the dowstream partner found during that round: for each non-colliding placement of the downstream partner and for each of the 64 hashes, the 6Dofs describing the downstream partner are hashed: if the hash finds an element in the hash table, that element’s value is set to “true”. At the end of each round past the second round, the entire hash is traversed. Any element whose value is “false” represents a voxel that failed to find a match during that round. Such elements are deleted from the hash. Any element whose value is “true” DID get a hit from that round and should remain in the hash. The element’s value is set to “false”. After the OccupiedSpaceHash has cleared out the elements which failed to find a match for the previous round, the Matcher may proceed to “clean up” its older hits (from rounds previous to this one) by querying them against the hash map. Any hit in the Matcher that does not have a corresponding element in any of the 64 hashes of the OccupiedSpaceHash may be deleted, since it cannot form a complete match.

This class is intended to be accessed by multiple threads but in a controlled way: read access function “match_possible_for_hit_geometry” is accessible to all threads during the “building” stage. However, the functions note_hit_geometry and drop_unsatisfied_voxels should be called by single thread only, and no other thread should try to access the ActiveVoxelHashes object at that time.

__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.OccupiedSpaceHash) → 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.OccupiedSpaceHash, : pyrosetta.rosetta.protocols.match.OccupiedSpaceHash) → pyrosetta.rosetta.protocols.match.OccupiedSpaceHash

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

drop_unsatisfied_voxels(self: pyrosetta.rosetta.protocols.match.OccupiedSpaceHash) → None

C++: protocols::match::OccupiedSpaceHash::drop_unsatisfied_voxels() –> void

initialize(self: pyrosetta.rosetta.protocols.match.OccupiedSpaceHash) → None

C++: protocols::match::OccupiedSpaceHash::initialize() –> void

insert_hit_geometry(self: pyrosetta.rosetta.protocols.match.OccupiedSpaceHash, geom: pyrosetta.rosetta.utility.fixedsizearray1_double_6_t) → None

C++: protocols::match::OccupiedSpaceHash::insert_hit_geometry(const class utility::fixedsizearray1<double, 6> &) –> void

match_possible_for_hit_geometry(self: pyrosetta.rosetta.protocols.match.OccupiedSpaceHash, : pyrosetta.rosetta.utility.fixedsizearray1_double_6_t) → bool

C++: protocols::match::OccupiedSpaceHash::match_possible_for_hit_geometry(const class utility::fixedsizearray1<double, 6> &) const –> bool

note_hit_geometry(self: pyrosetta.rosetta.protocols.match.OccupiedSpaceHash, : pyrosetta.rosetta.utility.fixedsizearray1_double_6_t) → None

C++: protocols::match::OccupiedSpaceHash::note_hit_geometry(const class utility::fixedsizearray1<double, 6> &) –> void

prepare_to_note_hits_for_completed_round(self: pyrosetta.rosetta.protocols.match.OccupiedSpaceHash) → None

C++: protocols::match::OccupiedSpaceHash::prepare_to_note_hits_for_completed_round() –> void

previous_round_geometry_still_matchable(self: pyrosetta.rosetta.protocols.match.OccupiedSpaceHash, : pyrosetta.rosetta.utility.fixedsizearray1_double_6_t) → bool

C++: protocols::match::OccupiedSpaceHash::previous_round_geometry_still_matchable(const class utility::fixedsizearray1<double, 6> &) –> bool

reset_3d_projection(self: pyrosetta.rosetta.protocols.match.OccupiedSpaceHash) → None

C++: protocols::match::OccupiedSpaceHash::reset_3d_projection() –> void

revision_id(self: pyrosetta.rosetta.protocols.match.OccupiedSpaceHash) → int

C++: protocols::match::OccupiedSpaceHash::revision_id() const –> unsigned long

set_bounding_box(self: pyrosetta.rosetta.protocols.match.OccupiedSpaceHash, bb: pyrosetta.rosetta.numeric.geometry.BoundingBox_numeric_xyzVector_double_t) → None

C++: protocols::match::OccupiedSpaceHash::set_bounding_box(const class numeric::geometry::BoundingBox<class numeric::xyzVector<double> > &) –> void

set_euler_bin_widths(self: pyrosetta.rosetta.protocols.match.OccupiedSpaceHash, euler_bin_widths: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

C++: protocols::match::OccupiedSpaceHash::set_euler_bin_widths(const class numeric::xyzVector<double> &) –> void

set_uniform_euler_angle_bin_width(self: pyrosetta.rosetta.protocols.match.OccupiedSpaceHash, bin_width_degrees: float) → None

C++: protocols::match::OccupiedSpaceHash::set_uniform_euler_angle_bin_width(double) –> void

set_uniform_xyz_bin_width(self: pyrosetta.rosetta.protocols.match.OccupiedSpaceHash, bin_width: float) → None

C++: protocols::match::OccupiedSpaceHash::set_uniform_xyz_bin_width(double) –> void

set_xyz_bin_widths(self: pyrosetta.rosetta.protocols.match.OccupiedSpaceHash, bin_widths: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

C++: protocols::match::OccupiedSpaceHash::set_xyz_bin_widths(const class numeric::xyzVector<double> &) –> void

write_3Dprojection_kinemage(self: pyrosetta.rosetta.protocols.match.OccupiedSpaceHash, kin_file_name: str) → None

C++: protocols::match::OccupiedSpaceHash::write_3Dprojection_kinemage(const class std::basic_string<char> &) –> void

class pyrosetta.rosetta.protocols.match.ProbeRadius

Bases: pybind11_builtins.pybind11_object

The different radii types used in collision detection. These values are taken from Probe / Reduce from the Richardson lab. Code inside BumpGrid.cc assumes the radii listed here being in non-decreasing order, and that ZERO is the 0th element of this enumeration.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(*args, **kwargs)

Overloaded function.

  1. __eq__(self: pyrosetta.rosetta.protocols.match.ProbeRadius, arg0: pyrosetta.rosetta.protocols.match.ProbeRadius) -> bool
  2. __eq__(self: pyrosetta.rosetta.protocols.match.ProbeRadius, arg0: int) -> bool
__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getstate__(self: pyrosetta.rosetta.protocols.match.ProbeRadius) → tuple
__gt__

Return self>value.

__hash__(self: pyrosetta.rosetta.protocols.match.ProbeRadius) → int
__init__(self: pyrosetta.rosetta.protocols.match.ProbeRadius, arg0: 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.

__int__(self: pyrosetta.rosetta.protocols.match.ProbeRadius) → int
__le__

Return self<=value.

__lt__

Return self<value.

__ne__(*args, **kwargs)

Overloaded function.

  1. __ne__(self: pyrosetta.rosetta.protocols.match.ProbeRadius, arg0: pyrosetta.rosetta.protocols.match.ProbeRadius) -> bool
  2. __ne__(self: pyrosetta.rosetta.protocols.match.ProbeRadius, arg0: int) -> bool
__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__(self: pyrosetta.rosetta.protocols.match.ProbeRadius) → str
__setattr__

Implement setattr(self, name, value).

__setstate__(self: pyrosetta.rosetta.protocols.match.ProbeRadius, arg0: tuple) → None
__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).

class pyrosetta.rosetta.protocols.match.RemoveNorCTermMPM

Bases: pyrosetta.rosetta.protocols.match.MatchPositionModifier

added by olga and flo 1/2011 class to exclude positions at the n and c termini of proteins from matching

__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.RemoveNorCTermMPM, input_tokens: pyrosetta.rosetta.utility.vector1_std_string) → 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.RemoveNorCTermMPM, : pyrosetta.rosetta.protocols.match.RemoveNorCTermMPM) → pyrosetta.rosetta.protocols.match.RemoveNorCTermMPM

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

modified_match_positions(self: pyrosetta.rosetta.protocols.match.RemoveNorCTermMPM, original_positions: pyrosetta.rosetta.utility.vector1_unsigned_long, match_pose: pyrosetta.rosetta.core.pose.Pose, mtask: protocols::match::MatcherTask) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::match::RemoveNorCTermMPM::modified_match_positions(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class core::pose::Pose &, class std::shared_ptr<const class protocols::match::MatcherTask>) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

class pyrosetta.rosetta.protocols.match.SecondaryStructureMPM

Bases: pyrosetta.rosetta.protocols.match.MatchPositionModifier

removes positions at which the pose does not have the desired secondary structure

__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.SecondaryStructureMPM, input_tokens: pyrosetta.rosetta.utility.vector1_std_string) → 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.SecondaryStructureMPM, : pyrosetta.rosetta.protocols.match.SecondaryStructureMPM) → pyrosetta.rosetta.protocols.match.SecondaryStructureMPM

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

modified_match_positions(self: pyrosetta.rosetta.protocols.match.SecondaryStructureMPM, original_positions: pyrosetta.rosetta.utility.vector1_unsigned_long, match_pose: pyrosetta.rosetta.core.pose.Pose, mtask: protocols::match::MatcherTask) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::match::SecondaryStructureMPM::modified_match_positions(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class core::pose::Pose &, class std::shared_ptr<const class protocols::match::MatcherTask>) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

class pyrosetta.rosetta.protocols.match.TaskOperationMPM

Bases: pyrosetta.rosetta.protocols.match.MatchPositionModifier

mpm that will get a task operation as specified in the tag from the TaskOperationFactory, apply the task operation to the pose and every residue that is then set to designing in the task will be a match position

__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.TaskOperationMPM, geom_cst: int, input_tokens: pyrosetta.rosetta.utility.vector1_std_string) → 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.TaskOperationMPM, : pyrosetta.rosetta.protocols.match.TaskOperationMPM) → pyrosetta.rosetta.protocols.match.TaskOperationMPM

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

modified_match_positions(self: pyrosetta.rosetta.protocols.match.TaskOperationMPM, original_positions: pyrosetta.rosetta.utility.vector1_unsigned_long, match_pose: pyrosetta.rosetta.core.pose.Pose, mtask: protocols::match::MatcherTask) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::match::TaskOperationMPM::modified_match_positions(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class core::pose::Pose &, class std::shared_ptr<const class protocols::match::MatcherTask>) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

class pyrosetta.rosetta.protocols.match.VoxelSetIterator

Bases: pybind11_builtins.pybind11_object

Helper class for the OccupiedSpaceHasher which manages the logic for how to iterate across the 64 voxels that each 6-D point covers.

This class ensures that the bounding box for the hash is not walked outside of, that the phi and psi are wrapped at 360, and that when theta is near a gimbal-lock angle of 180 or 0, that phi and psi are appropriately wrapped to the negative rotation. This class may be rapidly allocated and deallocated on the stack – no calls to new are made anywhere.

__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.VoxelSetIterator, bb: pyrosetta.rosetta.numeric.geometry.BoundingBox_numeric_xyzVector_double_t, n_xyz_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t, n_euler_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t, xyz_bin_widths: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, euler_bin_widths: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, xyz_bin_halfwidths: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, euler_bin_halfwidths: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, point: pyrosetta.rosetta.utility.fixedsizearray1_double_6_t) → 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).

at_end(self: pyrosetta.rosetta.protocols.match.VoxelSetIterator) → bool

C++: protocols::match::VoxelSetIterator::at_end() const –> bool

get_bin_and_pos(self: pyrosetta.rosetta.protocols.match.VoxelSetIterator, bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_6_t, pos: int) → None

C++: protocols::match::VoxelSetIterator::get_bin_and_pos(class utility::fixedsizearray1<unsigned long, 6> &, unsigned long &) const –> void

plus_plus(self: pyrosetta.rosetta.protocols.match.VoxelSetIterator) → None

C++: protocols::match::VoxelSetIterator::operator++() –> void

pyrosetta.rosetta.protocols.match.advance_euler_angles(orig_angles: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, offsets: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_3_t

Increment the euler angles and then wrap them into their appropriate ranges

C++: protocols::match::advance_euler_angles(const class utility::fixedsizearray1<double, 3> &, const class utility::fixedsizearray1<double, 3> &) –> class utility::fixedsizearray1<double, 3>

pyrosetta.rosetta.protocols.match.bump_grid_to_enclose_pose(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.protocols.match.BumpGrid

C++: protocols::match::bump_grid_to_enclose_pose(const class core::pose::Pose &) –> class std::shared_ptr<class protocols::match::BumpGrid>

pyrosetta.rosetta.protocols.match.bump_grid_to_enclose_residue(residue: pyrosetta.rosetta.core.conformation.Residue, original_grid: pyrosetta.rosetta.protocols.match.BumpGrid) → pyrosetta.rosetta.protocols.match.BumpGrid
Construct a BumpGrid that encloses a single residue. Use the
original_grid as a starting point, copying over all pertinent data such that the two grids can later be merged together.

C++: protocols::match::bump_grid_to_enclose_residue(const class core::conformation::Residue &, const class protocols::match::BumpGrid &) –> class std::shared_ptr<class protocols::match::BumpGrid>

pyrosetta.rosetta.protocols.match.bump_grid_to_enclose_residue_backbone(residue: pyrosetta.rosetta.core.conformation.Residue, original_grid: pyrosetta.rosetta.protocols.match.BumpGrid) → pyrosetta.rosetta.protocols.match.BumpGrid
Construct a BumpGrid that encloses the backbone atoms for a single residue.
Use the original_grid as a starting point, copying over all pertinent data such that the two grids can later be merged together.

C++: protocols::match::bump_grid_to_enclose_residue_backbone(const class core::conformation::Residue &, const class protocols::match::BumpGrid &) –> class std::shared_ptr<class protocols::match::BumpGrid>

pyrosetta.rosetta.protocols.match.create_match_position_modifier(mpm_name: str, geom_cst: int, input_tokens: pyrosetta.rosetta.utility.vector1_std_string) → protocols::match::MatchPositionModifier

“factory” function to create the match position modifiers

C++: protocols::match::create_match_position_modifier(const class std::basic_string<char> &, unsigned long, const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> class std::shared_ptr<const class protocols::match::MatchPositionModifier>

pyrosetta.rosetta.protocols.match.fake_hit(*args, **kwargs)

Overloaded function.

  1. fake_hit(: pyrosetta.rosetta.protocols.match.upstream_hit) -> pyrosetta.rosetta.protocols.match.Hit

Create a fake hit from an upstream_hit where hit.first()[4] and hit.second() are 0’s.

C++: protocols::match::fake_hit(const class protocols::match::upstream_hit &) –> class protocols::match::Hit

  1. fake_hit(: pyrosetta.rosetta.protocols.match.downstream_hit) -> pyrosetta.rosetta.protocols.match.Hit

Create a fake hit from a downstream_hit where hit.first()[1-3] are 0’s.

C++: protocols::match::fake_hit(const class protocols::match::downstream_hit &) –> class protocols::match::Hit

pyrosetta.rosetta.protocols.match.fill_grid_with_backbone_heavyatom_spheres(residue: pyrosetta.rosetta.core.conformation.Residue, grid: pyrosetta.rosetta.protocols.match.BumpGrid) → None

C++: protocols::match::fill_grid_with_backbone_heavyatom_spheres(const class core::conformation::Residue &, class protocols::match::BumpGrid &) –> void

pyrosetta.rosetta.protocols.match.fill_grid_with_residue_heavyatom_spheres(residue: pyrosetta.rosetta.core.conformation.Residue, grid: pyrosetta.rosetta.protocols.match.BumpGrid) → None

C++: protocols::match::fill_grid_with_residue_heavyatom_spheres(const class core::conformation::Residue &, class protocols::match::BumpGrid &) –> void

pyrosetta.rosetta.protocols.match.fill_grid_with_residue_spheres(residue: pyrosetta.rosetta.core.conformation.Residue, grid: pyrosetta.rosetta.protocols.match.BumpGrid) → None

C++: protocols::match::fill_grid_with_residue_spheres(const class core::conformation::Residue &, class protocols::match::BumpGrid &) –> void

pyrosetta.rosetta.protocols.match.full_hit(m: pyrosetta.rosetta.protocols.match.match_dspos1) → pyrosetta.rosetta.protocols.match.Hit
Create a hit with the full data from a given match_dspos1 representing
the upstream conformation from the originating_geom_cst and its description of the downstream position.

C++: protocols::match::full_hit(const struct protocols::match::match_dspos1 &) –> class protocols::match::Hit

class pyrosetta.rosetta.protocols.match.match_dspos1

Bases: pybind11_builtins.pybind11_object

Describe a match as n_geometric_constraint upstream residue conformations and one positioning of the downstream partner ( “dspos1” = 1 downstrem position)

__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.match.match_dspos1) -> None
  2. __init__(self: pyrosetta.rosetta.protocols.match.match_dspos1, n_geometric_constraints: int) -> None
  3. __init__(self: pyrosetta.rosetta.protocols.match.match_dspos1, m: pyrosetta.rosetta.utility.vector1_protocols_match_Hit, geomcst_specifying_dspos: 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).

pyrosetta.rosetta.protocols.match.probe_radius_for_atom_type(atomtype: int) → pyrosetta.rosetta.protocols.match.ProbeRadius

C++: protocols::match::probe_radius_for_atom_type(unsigned long) –> enum protocols::match::ProbeRadius

pyrosetta.rosetta.protocols.match.set_ligpose_rotamer(ligpose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::match::set_ligpose_rotamer(class core::pose::Pose &) –> void