scores

Bindings for protocols::frag_picker::scores namespace

class pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

scores a fragment by the root mean square deviation of Phi and Psi angles.

__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.frag_picker.scores.AmbigCSScore, : int, : float, : bool, : pyrosetta.rosetta.protocols.frag_picker.CSTalosIO, : pyrosetta.rosetta.protocols.frag_picker.CSTalosIO) → 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.frag_picker.scores.CachingScoringMethod, : pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod) → pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

C++: protocols::frag_picker::scores::CachingScoringMethod::operator=(const class protocols::frag_picker::scores::CachingScoringMethod &) –> class protocols::frag_picker::scores::CachingScoringMethod &

cached_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::AmbigCSScore::cached_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore) → None

C++: protocols::frag_picker::scores::AmbigCSScore::clean_up() –> void

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

C++: protocols::frag_picker::scores::AmbigCSScore::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::AmbigCSScore::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

A base class for all scoring methods that need atom coordinates

The base class provides an access to atom coordinates from the current chunk It takes care of caching proper atoms from the pose for fast access.

__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.frag_picker.scores.AtomBasedConstraintsScore, : int, : float, : bool, : int, : pyrosetta.rosetta.utility.vector1_std_string, : str) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore, : int, : float, : bool, : int, : str) -> None
3. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore) -> 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.frag_picker.scores.AtomBasedConstraintsScore, : pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore) → pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore

C++: protocols::frag_picker::scores::AtomBasedConstraintsScore::operator=(const class protocols::frag_picker::scores::AtomBasedConstraintsScore &) –> class protocols::frag_picker::scores::AtomBasedConstraintsScore &

cached_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::CachingScoringMethod::cached_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore) → None

Erases the internal array of coordinates

C++: protocols::frag_picker::scores::AtomBasedConstraintsScore::clean_up() –> void

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

In this case caching means copying coordinates of relevant atoms from a chunk’s pose

C++: protocols::frag_picker::scores::AtomBasedConstraintsScore::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_atom_coordinates(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore, residue_id: int, atom_id: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

Returns coordinates for a given atom

the residue order number. The first is 1,

the last one depends on the size of a pose i.e. the size of the current chunk

the residue order number, the first is 1

C++: protocols::frag_picker::scores::AtomBasedConstraintsScore::get_atom_coordinates(unsigned long, unsigned long) –> class numeric::xyzVector<double>

get_constrainable_atoms_map(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore) → pyrosetta.rosetta.std.map_std_string_unsigned_long

Returns a map that defines all constrained atoms used by this scoring method

Returned map defines the order of atoms as they are stored inside this object. Indexes defined y this map can be used as arguments for has_atom() and get_atom_coordinates() methods.

C++: protocols::frag_picker::scores::AtomBasedConstraintsScore::get_constrainable_atoms_map() –> class std::map<std::string, unsigned long, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, unsigned long> > >

get_constrained_atom_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore, atom_name: str) → int

returns an internal ID assigned to a given atom name

this ID remains the same for all residues

C++: protocols::frag_picker::scores::AtomBasedConstraintsScore::get_constrained_atom_id(class std::basic_string<char>) –> unsigned long

get_constrained_atom_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore, atom_id: int) → str

returns a name of a constrained atom when its internal ID is known

this is the oposite to get_constrained_atom_id(std::string)

C++: protocols::frag_picker::scores::AtomBasedConstraintsScore::get_constrained_atom_name(unsigned long) –> std::string

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_query_size(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore) → int

provides an access to the size of the length of a query sequence

C++: protocols::frag_picker::scores::AtomBasedConstraintsScore::get_query_size() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

has_atom(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore, residue_id: int, atom_id: int) → bool

Returns true if a given atom has been successfully cached and one can use its coordinates

the residue order number. The first is 1,

the last one depends on the size of a pose i.e. the size of the current chunk

the residue order number, the first is 1

C++: protocols::frag_picker::scores::AtomBasedConstraintsScore::has_atom(unsigned long, unsigned long) –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::CachingScoringMethod::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData

Bases: pybind11_builtins.pybind11_object

Holds data about a single distance constraint in the form AtomPairConstraintsScore needs

This class is used by AtomPairConstraintsScore to store data obtained from file

__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.frag_picker.scores.AtomPairConstraintsData, function: pyrosetta.rosetta.core.scoring.func.Func, offset: int, first_atom: int, second_atom: int) → None

__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData, : pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData) → pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData

C++: protocols::frag_picker::scores::AtomPairConstraintsData::operator=(const class protocols::frag_picker::scores::AtomPairConstraintsData &) –> class protocols::frag_picker::scores::AtomPairConstraintsData &

get_first_atom(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData) → int

C++: protocols::frag_picker::scores::AtomPairConstraintsData::get_first_atom() –> unsigned long

get_function(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData) → pyrosetta.rosetta.core.scoring.func.Func

C++: protocols::frag_picker::scores::AtomPairConstraintsData::get_function() –> class std::shared_ptr<class core::scoring::func::Func>

get_offset(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData) → int

C++: protocols::frag_picker::scores::AtomPairConstraintsData::get_offset() –> unsigned long

get_second_atom(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData) → int

C++: protocols::frag_picker::scores::AtomPairConstraintsData::get_second_atom() –> unsigned long

class pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore

Scores a fragment with a set of AtomPair constraints

__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.frag_picker.scores.AtomPairConstraintsScore, : int, : float, : bool, : str, : int, : pyrosetta.rosetta.utility.vector1_std_string) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore, : int, : float, : bool, : str, : int) -> None
3. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore) -> 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.frag_picker.scores.AtomPairConstraintsScore, : pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore) → pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore

C++: protocols::frag_picker::scores::AtomPairConstraintsScore::operator=(const class protocols::frag_picker::scores::AtomPairConstraintsScore &) –> class protocols::frag_picker::scores::AtomPairConstraintsScore &

cached_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::AtomPairConstraintsScore::cached_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore) → None

Erases the internal array of coordinates

C++: protocols::frag_picker::scores::AtomBasedConstraintsScore::clean_up() –> void

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

In this case caching means copying coordinates of relevant atoms from a chunk’s pose

C++: protocols::frag_picker::scores::AtomBasedConstraintsScore::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_atom_coordinates(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore, residue_id: int, atom_id: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

Returns coordinates for a given atom

the residue order number. The first is 1,

the last one depends on the size of a pose i.e. the size of the current chunk

the residue order number, the first is 1

C++: protocols::frag_picker::scores::AtomBasedConstraintsScore::get_atom_coordinates(unsigned long, unsigned long) –> class numeric::xyzVector<double>

get_constrainable_atoms_map(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore) → pyrosetta.rosetta.std.map_std_string_unsigned_long

Returns a map that defines all constrained atoms used by this scoring method

Returned map defines the order of atoms as they are stored inside this object. Indexes defined y this map can be used as arguments for has_atom() and get_atom_coordinates() methods.

C++: protocols::frag_picker::scores::AtomBasedConstraintsScore::get_constrainable_atoms_map() –> class std::map<std::string, unsigned long, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, unsigned long> > >

get_constrained_atom_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore, atom_name: str) → int

returns an internal ID assigned to a given atom name

this ID remains the same for all residues

C++: protocols::frag_picker::scores::AtomBasedConstraintsScore::get_constrained_atom_id(class std::basic_string<char>) –> unsigned long

get_constrained_atom_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore, atom_id: int) → str

returns a name of a constrained atom when its internal ID is known

this is the oposite to get_constrained_atom_id(std::string)

C++: protocols::frag_picker::scores::AtomBasedConstraintsScore::get_constrained_atom_name(unsigned long) –> std::string

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_query_size(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore) → int

provides an access to the size of the length of a query sequence

C++: protocols::frag_picker::scores::AtomBasedConstraintsScore::get_query_size() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

has_atom(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore, residue_id: int, atom_id: int) → bool

Returns true if a given atom has been successfully cached and one can use its coordinates

the residue order number. The first is 1,

the last one depends on the size of a pose i.e. the size of the current chunk

the residue order number, the first is 1

C++: protocols::frag_picker::scores::AtomBasedConstraintsScore::has_atom(unsigned long, unsigned long) –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::CachingScoringMethod::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.BFactor

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

BFactor score counts identical residues

Resulting score is the number of identical residues on corresponding positions in a vall fragment and a query sequence

__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.frag_picker.scores.BFactor, priority: int, lowest_acceptable_value: float, use_lowest: bool, : str) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.BFactor, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.BFactor) -> 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.frag_picker.scores.BFactor, : pyrosetta.rosetta.protocols.frag_picker.scores.BFactor) → pyrosetta.rosetta.protocols.frag_picker.scores.BFactor

C++: protocols::frag_picker::scores::BFactor::operator=(const class protocols::frag_picker::scores::BFactor &) –> class protocols::frag_picker::scores::BFactor &

describe_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.BFactor, f: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, empty_map: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap, out: pyrosetta.rosetta.std.ostream) → bool

prints a detailed explanation how a fragment score has been computed

besides extensive output, the method should return the same result as score()

C++: protocols::frag_picker::scores::BFactor::describe_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>, class std::basic_ostream<char> &) –> bool

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.BFactor, f: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, empty_map: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::BFactor::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.CSScore

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

scores a fragment by the root mean square deviation of Phi and Psi angles.

__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.frag_picker.scores.CSScore, : int, : float, : bool, : pyrosetta.rosetta.protocols.frag_picker.CSTalosIO) → 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.frag_picker.scores.CachingScoringMethod, : pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod) → pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

C++: protocols::frag_picker::scores::CachingScoringMethod::operator=(const class protocols::frag_picker::scores::CachingScoringMethod &) –> class protocols::frag_picker::scores::CachingScoringMethod &

cached_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.CSScore, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::CSScore::cached_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.CSScore) → None

C++: protocols::frag_picker::scores::CSScore::clean_up() –> void

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.CSScore, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

C++: protocols::frag_picker::scores::CSScore::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.CSScore, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::CSScore::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

ConstScore adds a constant to the total score for each position

The total ConstScore for a fragment = n_frag_res * score_const

__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.frag_picker.scores.ConstScore, priority: int, lowest_acceptable_value: float, use_lowest: bool) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore) -> 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.frag_picker.scores.ConstScore, : pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore) → pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore

C++: protocols::frag_picker::scores::ConstScore::operator=(const class protocols::frag_picker::scores::ConstScore &) –> class protocols::frag_picker::scores::ConstScore &

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore, f: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, empty_map: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

Computes the score i.e. returns a constant times the number of residues in a fragment

the method returns ALWAYS TRUE which is inconsistent with other methods derived from FragmentScoringMethod base class. The other option (i.e. returning false when a score is too high) doesn’t make any sense in this case.

C++: protocols::frag_picker::scores::ConstScore::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore

Scores a fragment with a set of Dihedral constraints

__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.frag_picker.scores.DihedralConstraintsScore, : int, : float, : bool, : str, : int, : pyrosetta.rosetta.utility.vector1_std_string) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore, : int, : float, : bool, : str, : int) -> None
3. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore) -> 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.frag_picker.scores.DihedralConstraintsScore, : pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore) → pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore

C++: protocols::frag_picker::scores::DihedralConstraintsScore::operator=(const class protocols::frag_picker::scores::DihedralConstraintsScore &) –> class protocols::frag_picker::scores::DihedralConstraintsScore &

cached_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

Calculates the score

C++: protocols::frag_picker::scores::DihedralConstraintsScore::cached_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore) → None

Erases the internal array of coordinates

C++: protocols::frag_picker::scores::AtomBasedConstraintsScore::clean_up() –> void

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

In this case caching means copying coordinates of relevant atoms from a chunk’s pose

C++: protocols::frag_picker::scores::AtomBasedConstraintsScore::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_atom_coordinates(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore, residue_id: int, atom_id: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

Returns coordinates for a given atom

the residue order number. The first is 1,

the last one depends on the size of a pose i.e. the size of the current chunk

the residue order number, the first is 1

C++: protocols::frag_picker::scores::AtomBasedConstraintsScore::get_atom_coordinates(unsigned long, unsigned long) –> class numeric::xyzVector<double>

get_constrainable_atoms_map(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore) → pyrosetta.rosetta.std.map_std_string_unsigned_long

Returns a map that defines all constrained atoms used by this scoring method

Returned map defines the order of atoms as they are stored inside this object. Indexes defined y this map can be used as arguments for has_atom() and get_atom_coordinates() methods.

C++: protocols::frag_picker::scores::AtomBasedConstraintsScore::get_constrainable_atoms_map() –> class std::map<std::string, unsigned long, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, unsigned long> > >

get_constrained_atom_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore, atom_name: str) → int

returns an internal ID assigned to a given atom name

this ID remains the same for all residues

C++: protocols::frag_picker::scores::AtomBasedConstraintsScore::get_constrained_atom_id(class std::basic_string<char>) –> unsigned long

get_constrained_atom_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore, atom_id: int) → str

returns a name of a constrained atom when its internal ID is known

this is the oposite to get_constrained_atom_id(std::string)

C++: protocols::frag_picker::scores::AtomBasedConstraintsScore::get_constrained_atom_name(unsigned long) –> std::string

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_query_size(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore) → int

provides an access to the size of the length of a query sequence

C++: protocols::frag_picker::scores::AtomBasedConstraintsScore::get_query_size() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

has_atom(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore, residue_id: int, atom_id: int) → bool

Returns true if a given atom has been successfully cached and one can use its coordinates

the residue order number. The first is 1,

the last one depends on the size of a pose i.e. the size of the current chunk

the residue order number, the first is 1

C++: protocols::frag_picker::scores::AtomBasedConstraintsScore::has_atom(unsigned long, unsigned long) –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::CachingScoringMethod::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

scores a fragment by the root mean square deviation of Phi and Psi angles.

__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.frag_picker.scores.DisulfideDistance, priority: int, lowest_acceptable_value: float, use_lowest: bool, disulfide_data: pyrosetta.rosetta.utility.vector1_unsigned_long, largest_fragment: int) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance) -> 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.frag_picker.scores.DisulfideDistance, : pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance) → pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance

C++: protocols::frag_picker::scores::DisulfideDistance::operator=(const class protocols::frag_picker::scores::DisulfideDistance &) –> class protocols::frag_picker::scores::DisulfideDistance &

cached_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::DisulfideDistance::cached_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance) → None

C++: protocols::frag_picker::scores::DisulfideDistance::clean_up() –> void

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

C++: protocols::frag_picker::scores::DisulfideDistance::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::DisulfideDistance::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

DisulfideIdentity score counts identical residues

Resulting score is the number of identical residues on corresponding positions in a vall fragment and a query sequence

__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.frag_picker.scores.DisulfideIdentity, priority: int, lowest_acceptable_value: float, use_lowest: bool, fastaQueryDisulfide: str) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity) -> 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.frag_picker.scores.FragmentScoringMethod, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::FragmentScoringMethod::operator=(const class protocols::frag_picker::scores::FragmentScoringMethod &) –> class protocols::frag_picker::scores::FragmentScoringMethod &

describe_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity, f: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, empty_map: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap, out: pyrosetta.rosetta.std.ostream) → bool

prints a detailed explanation how a fragment score has been computed

besides extensive output, the method should return the same result as score()

C++: protocols::frag_picker::scores::DisulfideIdentity::describe_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>, class std::basic_ostream<char> &) –> bool

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity, f: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, empty_map: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::DisulfideIdentity::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData

Bases: pybind11_builtins.pybind11_object

Holds data about a single four-body constraint in the form usefull for InterbondAngleScore and DihedralConstraintsScore classes

This class is used to store data obtained from file before score method is created

__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.frag_picker.scores.FourAtomsConstraintData, function: pyrosetta.rosetta.core.scoring.func.Func, first_atom: int, second_offset: int, second_atom: int, third_offset: int, third_atom: int, fourth_offset: int, fourth_atom: int) → None

__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData, : pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData) → pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData

C++: protocols::frag_picker::scores::FourAtomsConstraintData::operator=(const class protocols::frag_picker::scores::FourAtomsConstraintData &) –> class protocols::frag_picker::scores::FourAtomsConstraintData &

get_first_atom(self: pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData) → int

C++: protocols::frag_picker::scores::FourAtomsConstraintData::get_first_atom() –> unsigned long

get_fourth_atom(self: pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData) → int

C++: protocols::frag_picker::scores::FourAtomsConstraintData::get_fourth_atom() –> unsigned long

get_fourth_offset(self: pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData) → int

C++: protocols::frag_picker::scores::FourAtomsConstraintData::get_fourth_offset() –> unsigned long

get_function(self: pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData) → pyrosetta.rosetta.core.scoring.func.Func

C++: protocols::frag_picker::scores::FourAtomsConstraintData::get_function() –> class std::shared_ptr<class core::scoring::func::Func>

get_second_atom(self: pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData) → int

C++: protocols::frag_picker::scores::FourAtomsConstraintData::get_second_atom() –> unsigned long

get_second_offset(self: pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData) → int

C++: protocols::frag_picker::scores::FourAtomsConstraintData::get_second_offset() –> unsigned long

get_third_atom(self: pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData) → int

C++: protocols::frag_picker::scores::FourAtomsConstraintData::get_third_atom() –> unsigned long

get_third_offset(self: pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData) → int

C++: protocols::frag_picker::scores::FourAtomsConstraintData::get_third_offset() –> unsigned long

class pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

scores a fragment by its crmsd to the given reference 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__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd, : int, : float, : bool, : str, : pyrosetta.rosetta.core.pose.Pose) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd, : int, : float, : bool, : str, : pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) -> None
3. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd) -> 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.frag_picker.scores.FragmentAllAtomCrmsd, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd

C++: protocols::frag_picker::scores::FragmentAllAtomCrmsd::operator=(const class protocols::frag_picker::scores::FragmentAllAtomCrmsd &) –> class protocols::frag_picker::scores::FragmentAllAtomCrmsd &

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::FragmentAllAtomCrmsd::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

scores a fragment by its tmscore to the given reference 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__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms, : int, : float, : bool, : str, : pyrosetta.rosetta.core.pose.Pose, : ObjexxFCL::FArray1D<int>) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms) -> 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.frag_picker.scores.FragmentChunkCrms, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms

C++: protocols::frag_picker::scores::FragmentChunkCrms::operator=(const class protocols::frag_picker::scores::FragmentChunkCrms &) –> class protocols::frag_picker::scores::FragmentChunkCrms &

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::FragmentChunkCrms::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

scores a fragment by its crmsd to the given reference 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__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd, : int, : float, : bool, : pyrosetta.rosetta.core.pose.Pose) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd, : int, : float, : bool, : pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) -> None
3. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd) -> 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.frag_picker.scores.FragmentCrmsd, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd

C++: protocols::frag_picker::scores::FragmentCrmsd::operator=(const class protocols::frag_picker::scores::FragmentCrmsd &) –> class protocols::frag_picker::scores::FragmentCrmsd &

cached_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::FragmentCrmsd::cached_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd) → None

C++: protocols::frag_picker::scores::FragmentCrmsd::clean_up() –> void

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

C++: protocols::frag_picker::scores::FragmentCrmsd::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::FragmentCrmsd::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

scores a fragment by its crmsd to the given reference 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__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth, : int, : float, : bool, : pyrosetta.rosetta.core.pose.Pose, query_residue_depth: pyrosetta.rosetta.utility.vector1_double) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth, : int, : float, : bool, : pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, query_residue_depth: pyrosetta.rosetta.utility.vector1_double) -> None
3. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth) -> 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.frag_picker.scores.FragmentCrmsdResDepth, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth

C++: protocols::frag_picker::scores::FragmentCrmsdResDepth::operator=(const class protocols::frag_picker::scores::FragmentCrmsdResDepth &) –> class protocols::frag_picker::scores::FragmentCrmsdResDepth &

cached_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::FragmentCrmsdResDepth::cached_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth) → None

C++: protocols::frag_picker::scores::FragmentCrmsdResDepth::clean_up() –> void

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

C++: protocols::frag_picker::scores::FragmentCrmsdResDepth::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::FragmentCrmsdResDepth::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

scores a fragment by its DME to the given reference 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__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME, : int, : float, : bool, : pyrosetta.rosetta.core.pose.Pose) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME, : int, : float, : bool, : pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) -> None
3. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME) -> 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.frag_picker.scores.FragmentDME, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME

C++: protocols::frag_picker::scores::FragmentDME::operator=(const class protocols::frag_picker::scores::FragmentDME &) –> class protocols::frag_picker::scores::FragmentDME &

cached_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::FragmentDME::cached_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME) → None

C++: protocols::frag_picker::scores::FragmentDME::clean_up() –> void

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

C++: protocols::frag_picker::scores::FragmentDME::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::FragmentDME::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager

Bases: pybind11_builtins.pybind11_object

holds particular score components, weights and calculates the total score for a fragment candidate

a fragment picker object needs exactly one fragment manager to pick fragments. Adding new scoring methods is supposed to be done FragmentPicker, which calls proper method from this class.

__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.frag_picker.scores.FragmentScoreManager) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager) -> 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_scoring_method(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, : float) → None

registers a new scoring method in this manager

C++: protocols::frag_picker::scores::FragmentScoreManager::add_scoring_method(class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>, double) –> void

assign(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager

C++: protocols::frag_picker::scores::FragmentScoreManager::operator=(const class protocols::frag_picker::scores::FragmentScoreManager &) –> class protocols::frag_picker::scores::FragmentScoreManager &

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager) → None

calls clean_up() for each FragmentScoringMethod object, if it is possible

FragmentPicker calls this method when a given chunk has been processed

C++: protocols::frag_picker::scores::FragmentScoreManager::clean_up() –> void

count_components(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager) → int

says how many scoring methods have already been registered

C++: protocols::frag_picker::scores::FragmentScoreManager::count_components() –> unsigned long

create_empty_map(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap

creates an empty score map

C++: protocols::frag_picker::scores::FragmentScoreManager::create_empty_map() –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>

create_scores(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager, : str, : protocols::frag_picker::FragmentPicker) → None

reads a config file and creates scoring methods

C++: protocols::frag_picker::scores::FragmentScoreManager::create_scores(const class std::basic_string<char> &, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>) –> void

create_scoring_method(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager, : str, : int, : float, : float, : bool, : protocols::frag_picker::FragmentPicker, : str) → None

creates a new scoring method object

C++: protocols::frag_picker::scores::FragmentScoreManager::create_scoring_method(const class std::basic_string<char> &, unsigned long, double, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> void

describe_fragments(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager, : pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t, : pyrosetta.rosetta.std.ostream) → None

prints a flat table with all scores for all the fragments in a given vector

C++: protocols::frag_picker::scores::FragmentScoreManager::describe_fragments(const class utility::vector1<struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> >, class std::allocator<struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> > > > &, class std::basic_ostream<char> &) –> void

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager, chunk: pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

calls do_caching() for each FragmentScoringMethod object, if it is possible

FragmentPicker calls this method when a new chunk is to be processed

C++: protocols::frag_picker::scores::FragmentScoreManager::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_component(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager, index: int) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

Returns a desired scoring method

Allowed index values are [1,count_components()]

C++: protocols::frag_picker::scores::FragmentScoreManager::get_component(unsigned long) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

get_weights(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager) → pyrosetta.rosetta.utility.vector1_double

returns a vector of weights that are used to compute the total score

C++: protocols::frag_picker::scores::FragmentScoreManager::get_weights() –> class utility::vector1<double, class std::allocator<double> >

if_late_scoring_for_zeros(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager) → bool

says if late scoring is used or not

late scoring means that some scores (those with weight=0, such as crmsd) are evaluated only for the selected fragments rather than for all the candidates

C++: protocols::frag_picker::scores::FragmentScoreManager::if_late_scoring_for_zeros() –> bool

register_score_maker(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager, : pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → None

registers a maker object that will be used to create a scoring method object

C++: protocols::frag_picker::scores::FragmentScoreManager::register_score_maker(class std::shared_ptr<class protocols::frag_picker::scores::MakeFragmentScoringMethod>) –> void

score_fragment(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager, : protocols::frag_picker::FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

calculates all the small scores for a given fragment

results are properly stored inside a FragmentScoreMap object

C++: protocols::frag_picker::scores::FragmentScoreManager::score_fragment(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

score_fragment_from_cache(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager, : protocols::frag_picker::FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

calculates all the small scores for a given fragment

results are properly stored inside a FragmentScoreMap object

C++: protocols::frag_picker::scores::FragmentScoreManager::score_fragment_from_cache(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

score_zero_scores(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager, : protocols::frag_picker::FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

calculates all these small scores for a given fragment whose weight is 0.0

When use_late_scoring_for_zeros() was used to set the flag to true, all fragment scoring methods neglects zero-weighted scores. These will be evaluated by this function, that may be called after fragments are picked. This way some time consuming computations (e.g. crmsd for fragments) may be computed only for the selected fragments rather than for all of them

C++: protocols::frag_picker::scores::FragmentScoreManager::score_zero_scores(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_precision(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager, which_score: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, precision: int) → None

sets up a new precision used to print fragment score value

C++: protocols::frag_picker::scores::FragmentScoreManager::set_precision(class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>, unsigned long) –> void

set_width(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager, which_score: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, width: int) → None

sets up a new number of characters spend to print fragment score value

C++: protocols::frag_picker::scores::FragmentScoreManager::set_width(class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>, unsigned long) –> void

show_scoring_methods(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager, out: pyrosetta.rosetta.std.ostream) → None

prints a nice table showing the registered scores

the table shows also the order in which the scores are evaluated

C++: protocols::frag_picker::scores::FragmentScoreManager::show_scoring_methods(class std::basic_ostream<char> &) –> void

total_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → float

calculates the total score

C++: protocols::frag_picker::scores::FragmentScoreManager::total_score(class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> double

use_late_scoring_for_zeros(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager, if_true: bool) → None

those score metohods that have weight = 0.0 will be computed after the fragments are picked

if weight for a score is 0.0 than it does not affect the total score and thus has no

effect on fragments sorting, quota, etc. Such scores may be computed after fragment picking is finished

C++: protocols::frag_picker::scores::FragmentScoreManager::use_late_scoring_for_zeros(const bool) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap

Bases: pybind11_builtins.pybind11_object

holds all small scores (score components) for a given fragment

each scoring method puts its own result into the map. The total score is a dot product of the vector from this map and a vector of weights

__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.frag_picker.scores.FragmentScoreMap, n_componens: int) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) -> 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.frag_picker.scores.FragmentScoreMap, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap

C++: protocols::frag_picker::scores::FragmentScoreMap::operator=(const class protocols::frag_picker::scores::FragmentScoreMap &) –> class protocols::frag_picker::scores::FragmentScoreMap &

at(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap, score_index: int) → float

C++: protocols::frag_picker::scores::FragmentScoreMap::at(unsigned long) const –> double

clone(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap

creates a new deep copy of this map

C++: protocols::frag_picker::scores::FragmentScoreMap::clone() const –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>

get_most_recent_total_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → float

returns the total score that has been evaluated recently

the method does not compute anything. You must check if the map has been modified after the last total score calculation. If so, you must recompute the total again

C++: protocols::frag_picker::scores::FragmentScoreMap::get_most_recent_total_score() –> double

get_quota_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → float

C++: protocols::frag_picker::scores::FragmentScoreMap::get_quota_score() –> double

get_score_components(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → pyrosetta.rosetta.utility.vector1_double

returns the vector of score components

C++: protocols::frag_picker::scores::FragmentScoreMap::get_score_components() const –> class utility::vector1<double, class std::allocator<double> > &

set_quota_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap, quota_score: float) → None

C++: protocols::frag_picker::scores::FragmentScoreMap::set_quota_score(double) –> void

set_score_component(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap, score_value: float, component_id: int) → None

sets a new score value for a given component

C++: protocols::frag_picker::scores::FragmentScoreMap::set_score_component(double, unsigned long) –> void

size(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → int

C++: protocols::frag_picker::scores::FragmentScoreMap::size() const –> unsigned long

was_modified(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

If the map has been modified, the total score it holds is not up-to-date and must be recalculated

C++: protocols::frag_picker::scores::FragmentScoreMap::was_modified() –> bool

class pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

Bases: pybind11_builtins.pybind11_object

a fragment candidate score

__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.frag_picker.scores.FragmentScoringMethod, priority: int, lowest_acceptable_value: float, use_lowest: bool, name: str) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) -> 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.frag_picker.scores.FragmentScoringMethod, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::FragmentScoringMethod::operator=(const class protocols::frag_picker::scores::FragmentScoringMethod &) –> class protocols::frag_picker::scores::FragmentScoringMethod &

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, : protocols::frag_picker::FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::FragmentScoringMethod::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

scores a fragment by its crmsd to the given reference 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__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore, : int, : float, : bool, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_unsigned_long, : int) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore) -> 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.frag_picker.scores.GunnCostScore, : pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore) → pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore

C++: protocols::frag_picker::scores::GunnCostScore::operator=(const class protocols::frag_picker::scores::GunnCostScore &) –> class protocols::frag_picker::scores::GunnCostScore &

cached_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::GunnCostScore::cached_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore) → None

C++: protocols::frag_picker::scores::GunnCostScore::clean_up() –> void

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

C++: protocols::frag_picker::scores::GunnCostScore::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::GunnCostScore::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

scores a fragment by its hydrophobicity similarity

__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.frag_picker.scores.HydrophobicityProfileSimilarity, priority: int, lowest_acceptable_value: float, use_lowest: bool, fastaQuerySequence: str, query_profile: pyrosetta.rosetta.core.sequence.SequenceProfile) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity) -> 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.frag_picker.scores.CachingScoringMethod, : pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod) → pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

C++: protocols::frag_picker::scores::CachingScoringMethod::operator=(const class protocols::frag_picker::scores::CachingScoringMethod &) –> class protocols::frag_picker::scores::CachingScoringMethod &

cached_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::HydrophobicityProfileSimilarity::cached_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity) → None

C++: protocols::frag_picker::scores::HydrophobicityProfileSimilarity::clean_up() –> void

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

C++: protocols::frag_picker::scores::HydrophobicityProfileSimilarity::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::HydrophobicityProfileSimilarity::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

scores a fragment by its hydrophobicity similarity

__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.frag_picker.scores.HydrophobicitySimilarity, priority: int, lowest_acceptable_value: float, use_lowest: bool, fastaQuerySequence: str) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity) -> 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.frag_picker.scores.CachingScoringMethod, : pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod) → pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

C++: protocols::frag_picker::scores::CachingScoringMethod::operator=(const class protocols::frag_picker::scores::CachingScoringMethod &) –> class protocols::frag_picker::scores::CachingScoringMethod &

cached_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::HydrophobicitySimilarity::cached_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity) → None

C++: protocols::frag_picker::scores::HydrophobicitySimilarity::clean_up() –> void

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

C++: protocols::frag_picker::scores::HydrophobicitySimilarity::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::HydrophobicitySimilarity::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore

Scores a fragment with a set of Dihedral constraints

__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.frag_picker.scores.InterbondAngleScore, : int, : float, : bool, : str, : int, : pyrosetta.rosetta.utility.vector1_std_string) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore, : int, : float, : bool, : str, : int) -> None
3. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore) -> 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.frag_picker.scores.InterbondAngleScore, : pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore) → pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore

C++: protocols::frag_picker::scores::InterbondAngleScore::operator=(const class protocols::frag_picker::scores::InterbondAngleScore &) –> class protocols::frag_picker::scores::InterbondAngleScore &

cached_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

Calculates the score

C++: protocols::frag_picker::scores::InterbondAngleScore::cached_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore) → None

Erases the internal array of coordinates

C++: protocols::frag_picker::scores::AtomBasedConstraintsScore::clean_up() –> void

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

In this case caching means copying coordinates of relevant atoms from a chunk’s pose

C++: protocols::frag_picker::scores::AtomBasedConstraintsScore::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_atom_coordinates(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore, residue_id: int, atom_id: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

Returns coordinates for a given atom

the residue order number. The first is 1,

the last one depends on the size of a pose i.e. the size of the current chunk

the residue order number, the first is 1

C++: protocols::frag_picker::scores::AtomBasedConstraintsScore::get_atom_coordinates(unsigned long, unsigned long) –> class numeric::xyzVector<double>

get_constrainable_atoms_map(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore) → pyrosetta.rosetta.std.map_std_string_unsigned_long

Returns a map that defines all constrained atoms used by this scoring method

Returned map defines the order of atoms as they are stored inside this object. Indexes defined y this map can be used as arguments for has_atom() and get_atom_coordinates() methods.

C++: protocols::frag_picker::scores::AtomBasedConstraintsScore::get_constrainable_atoms_map() –> class std::map<std::string, unsigned long, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, unsigned long> > >

get_constrained_atom_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore, atom_name: str) → int

returns an internal ID assigned to a given atom name

this ID remains the same for all residues

C++: protocols::frag_picker::scores::AtomBasedConstraintsScore::get_constrained_atom_id(class std::basic_string<char>) –> unsigned long

get_constrained_atom_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore, atom_id: int) → str

returns a name of a constrained atom when its internal ID is known

this is the oposite to get_constrained_atom_id(std::string)

C++: protocols::frag_picker::scores::AtomBasedConstraintsScore::get_constrained_atom_name(unsigned long) –> std::string

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_query_size(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore) → int

provides an access to the size of the length of a query sequence

C++: protocols::frag_picker::scores::AtomBasedConstraintsScore::get_query_size() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

has_atom(self: pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore, residue_id: int, atom_id: int) → bool

Returns true if a given atom has been successfully cached and one can use its coordinates

the residue order number. The first is 1,

the last one depends on the size of a pose i.e. the size of the current chunk

the residue order number, the first is 1

C++: protocols::frag_picker::scores::AtomBasedConstraintsScore::has_atom(unsigned long, unsigned long) –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::CachingScoringMethod::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

scores a fragment by the JCouplings

__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.frag_picker.scores.JCoupling, : int, : float, : bool, : pyrosetta.rosetta.protocols.frag_picker.JCouplingIO) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling) -> 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.frag_picker.scores.JCoupling, : pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling) → pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling

C++: protocols::frag_picker::scores::JCoupling::operator=(const class protocols::frag_picker::scores::JCoupling &) –> class protocols::frag_picker::scores::JCoupling &

cached_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::JCoupling::cached_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling) → None

C++: protocols::frag_picker::scores::JCoupling::clean_up() –> void

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

C++: protocols::frag_picker::scores::JCoupling::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::JCoupling::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

scores a fragment by torsion bin similarity

__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.frag_picker.scores.LAMBEGO_Similarity, priority: int, lowest_acceptable_value: float, use_lowest: bool, query_bin_probs: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, sequence_length: int, longest_vall_chunk: int) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity) -> 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.frag_picker.scores.LAMBEGO_Similarity, : pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity) → pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity

C++: protocols::frag_picker::scores::LAMBEGO_Similarity::operator=(const class protocols::frag_picker::scores::LAMBEGO_Similarity &) –> class protocols::frag_picker::scores::LAMBEGO_Similarity &

cached_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

Computes the score

C++: protocols::frag_picker::scores::LAMBEGO_Similarity::cached_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity) → None

C++: protocols::frag_picker::scores::LAMBEGO_Similarity::clean_up() –> void

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

C++: protocols::frag_picker::scores::LAMBEGO_Similarity::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::CachingScoringMethod::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.MakeABEGO_SS_Score

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Maker class that produces a new ABEGO_SS_Score object

__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.frag_picker.scores.MakeABEGO_SS_Score) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeABEGO_SS_Score, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakeABEGO_SS_Score) -> 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.frag_picker.scores.MakeABEGO_SS_Score, : pyrosetta.rosetta.protocols.frag_picker.scores.MakeABEGO_SS_Score) → pyrosetta.rosetta.protocols.frag_picker.scores.MakeABEGO_SS_Score

C++: protocols::frag_picker::scores::MakeABEGO_SS_Score::operator=(const class protocols::frag_picker::scores::MakeABEGO_SS_Score &) –> class protocols::frag_picker::scores::MakeABEGO_SS_Score &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeABEGO_SS_Score, : int, : float, : bool, : pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakeABEGO_SS_Score::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MakeAmbigCSScore

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Maker class that produces a new AmbigCSScore object

__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.frag_picker.scores.MakeAmbigCSScore) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeAmbigCSScore, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakeAmbigCSScore) -> 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.frag_picker.scores.MakeAmbigCSScore, : pyrosetta.rosetta.protocols.frag_picker.scores.MakeAmbigCSScore) → pyrosetta.rosetta.protocols.frag_picker.scores.MakeAmbigCSScore

C++: protocols::frag_picker::scores::MakeAmbigCSScore::operator=(const class protocols::frag_picker::scores::MakeAmbigCSScore &) –> class protocols::frag_picker::scores::MakeAmbigCSScore &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeAmbigCSScore, : int, : float, : bool, : pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakeAmbigCSScore::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MakeAtomPairConstraintsScore

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Maker class that produces a new AtomPairConstraintsScore object

__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.frag_picker.scores.MakeAtomPairConstraintsScore) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeAtomPairConstraintsScore, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakeAtomPairConstraintsScore) -> 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.frag_picker.scores.MakeAtomPairConstraintsScore, : pyrosetta.rosetta.protocols.frag_picker.scores.MakeAtomPairConstraintsScore) → pyrosetta.rosetta.protocols.frag_picker.scores.MakeAtomPairConstraintsScore

C++: protocols::frag_picker::scores::MakeAtomPairConstraintsScore::operator=(const class protocols::frag_picker::scores::MakeAtomPairConstraintsScore &) –> class protocols::frag_picker::scores::MakeAtomPairConstraintsScore &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeAtomPairConstraintsScore, : int, : float, : bool, : protocols::frag_picker::FragmentPicker, : str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakeAtomPairConstraintsScore::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MakeBFactor

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Maker class that produces a new BFactor object

__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.frag_picker.scores.MakeBFactor) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeBFactor, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakeBFactor) -> 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.frag_picker.scores.MakeBFactor, : pyrosetta.rosetta.protocols.frag_picker.scores.MakeBFactor) → pyrosetta.rosetta.protocols.frag_picker.scores.MakeBFactor

C++: protocols::frag_picker::scores::MakeBFactor::operator=(const class protocols::frag_picker::scores::MakeBFactor &) –> class protocols::frag_picker::scores::MakeBFactor &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeBFactor, priority: int, lowest_acceptable_value: float, use_lowest: bool, picker: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakeBFactor::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MakeCSScore

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Maker class that produces a new CSScore object

__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.frag_picker.scores.MakeCSScore) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeCSScore, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakeCSScore) -> 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.frag_picker.scores.MakeCSScore, : pyrosetta.rosetta.protocols.frag_picker.scores.MakeCSScore) → pyrosetta.rosetta.protocols.frag_picker.scores.MakeCSScore

C++: protocols::frag_picker::scores::MakeCSScore::operator=(const class protocols::frag_picker::scores::MakeCSScore &) –> class protocols::frag_picker::scores::MakeCSScore &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeCSScore, : int, : float, : bool, : pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakeCSScore::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MakeConstScore

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Maker class that produces a new ConstScore object

__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.frag_picker.scores.MakeConstScore) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeConstScore, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakeConstScore) -> 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.frag_picker.scores.MakeConstScore, : pyrosetta.rosetta.protocols.frag_picker.scores.MakeConstScore) → pyrosetta.rosetta.protocols.frag_picker.scores.MakeConstScore

C++: protocols::frag_picker::scores::MakeConstScore::operator=(const class protocols::frag_picker::scores::MakeConstScore &) –> class protocols::frag_picker::scores::MakeConstScore &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeConstScore, priority: int, lowest_acceptable_value: float, use_lowest: bool, : pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakeConstScore::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MakeDihedralConstraintsScore

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Maker class that produces a new DihedralConstraintsScore object

__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.frag_picker.scores.MakeDihedralConstraintsScore) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeDihedralConstraintsScore, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakeDihedralConstraintsScore) -> 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.frag_picker.scores.MakeDihedralConstraintsScore, : pyrosetta.rosetta.protocols.frag_picker.scores.MakeDihedralConstraintsScore) → pyrosetta.rosetta.protocols.frag_picker.scores.MakeDihedralConstraintsScore

C++: protocols::frag_picker::scores::MakeDihedralConstraintsScore::operator=(const class protocols::frag_picker::scores::MakeDihedralConstraintsScore &) –> class protocols::frag_picker::scores::MakeDihedralConstraintsScore &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeDihedralConstraintsScore, : int, : float, : bool, : pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakeDihedralConstraintsScore::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideDistance

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Matker class that produces a new DisulfideDistance object

__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.frag_picker.scores.MakeDisulfideDistance) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideDistance, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideDistance) -> 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.frag_picker.scores.MakeDisulfideDistance, : pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideDistance) → pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideDistance

C++: protocols::frag_picker::scores::MakeDisulfideDistance::operator=(const class protocols::frag_picker::scores::MakeDisulfideDistance &) –> class protocols::frag_picker::scores::MakeDisulfideDistance &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideDistance, : int, : float, : bool, : pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakeDisulfideDistance::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideIdentity

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Maker class that produces a new DisulfideIdentity object

__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.frag_picker.scores.MakeDisulfideIdentity) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideIdentity, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideIdentity) -> 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.frag_picker.scores.MakeDisulfideIdentity, : pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideIdentity) → pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideIdentity

C++: protocols::frag_picker::scores::MakeDisulfideIdentity::operator=(const class protocols::frag_picker::scores::MakeDisulfideIdentity &) –> class protocols::frag_picker::scores::MakeDisulfideIdentity &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideIdentity, priority: int, lowest_acceptable_value: float, use_lowest: bool, picker: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakeDisulfideIdentity::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentAllAtomCrmsd

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Maker class that produces a new FragmentAllAtomCrmsd object

__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.frag_picker.scores.MakeFragmentAllAtomCrmsd) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentAllAtomCrmsd, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentAllAtomCrmsd) -> 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.frag_picker.scores.MakeFragmentAllAtomCrmsd, : pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentAllAtomCrmsd) → pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentAllAtomCrmsd

C++: protocols::frag_picker::scores::MakeFragmentAllAtomCrmsd::operator=(const class protocols::frag_picker::scores::MakeFragmentAllAtomCrmsd &) –> class protocols::frag_picker::scores::MakeFragmentAllAtomCrmsd &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentAllAtomCrmsd, : int, : float, : bool, : pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakeFragmentAllAtomCrmsd::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentChunkCrms

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Maker class that produces a new FragmentChunkCrms object

__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.frag_picker.scores.MakeFragmentChunkCrms) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentChunkCrms, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentChunkCrms) -> 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.frag_picker.scores.MakeFragmentChunkCrms, : pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentChunkCrms) → pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentChunkCrms

C++: protocols::frag_picker::scores::MakeFragmentChunkCrms::operator=(const class protocols::frag_picker::scores::MakeFragmentChunkCrms &) –> class protocols::frag_picker::scores::MakeFragmentChunkCrms &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentChunkCrms, : int, : float, : bool, : pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakeFragmentChunkCrms::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsd

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Maker class that produces a new FragmentCrmsd object

__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.frag_picker.scores.MakeFragmentCrmsd) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsd, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsd) -> 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.frag_picker.scores.MakeFragmentCrmsd, : pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsd) → pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsd

C++: protocols::frag_picker::scores::MakeFragmentCrmsd::operator=(const class protocols::frag_picker::scores::MakeFragmentCrmsd &) –> class protocols::frag_picker::scores::MakeFragmentCrmsd &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsd, : int, : float, : bool, : pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakeFragmentCrmsd::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsdResDepth

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Maker class that produces a new FragmentCrmsdResDepth object

__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.frag_picker.scores.MakeFragmentCrmsdResDepth) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsdResDepth, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsdResDepth) -> 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.frag_picker.scores.MakeFragmentCrmsdResDepth, : pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsdResDepth) → pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsdResDepth

C++: protocols::frag_picker::scores::MakeFragmentCrmsdResDepth::operator=(const class protocols::frag_picker::scores::MakeFragmentCrmsdResDepth &) –> class protocols::frag_picker::scores::MakeFragmentCrmsdResDepth &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsdResDepth, : int, : float, : bool, : pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakeFragmentCrmsdResDepth::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentDME

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Maker class that produces a new FragmentDME object

__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.frag_picker.scores.MakeFragmentDME) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentDME, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentDME) -> 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.frag_picker.scores.MakeFragmentDME, : pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentDME) → pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentDME

C++: protocols::frag_picker::scores::MakeFragmentDME::operator=(const class protocols::frag_picker::scores::MakeFragmentDME &) –> class protocols::frag_picker::scores::MakeFragmentDME &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentDME, : int, : float, : bool, : pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakeFragmentDME::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Bases: pybind11_builtins.pybind11_object

a fragment candidate

__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.frag_picker.scores.MakeFragmentScoringMethod, name: str) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) -> 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.frag_picker.scores.MakeFragmentScoringMethod, : pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::operator=(const class protocols::frag_picker::scores::MakeFragmentScoringMethod &) –> class protocols::frag_picker::scores::MakeFragmentScoringMethod &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod, : int, : float, : bool, : protocols::frag_picker::FragmentPicker, : str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MakeGunnCostScore

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Maker class that produces a new GunnCostScore object

__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.frag_picker.scores.MakeGunnCostScore) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeGunnCostScore, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakeGunnCostScore) -> 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.frag_picker.scores.MakeGunnCostScore, : pyrosetta.rosetta.protocols.frag_picker.scores.MakeGunnCostScore) → pyrosetta.rosetta.protocols.frag_picker.scores.MakeGunnCostScore

C++: protocols::frag_picker::scores::MakeGunnCostScore::operator=(const class protocols::frag_picker::scores::MakeGunnCostScore &) –> class protocols::frag_picker::scores::MakeGunnCostScore &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeGunnCostScore, : int, : float, : bool, : pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakeGunnCostScore::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicityProfileSimilarity

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Maker class that produces a new HydrophobicityProfileSimilarity object

__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.frag_picker.scores.MakeHydrophobicityProfileSimilarity) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicityProfileSimilarity, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicityProfileSimilarity) -> 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.frag_picker.scores.MakeHydrophobicityProfileSimilarity, : pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicityProfileSimilarity) → pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicityProfileSimilarity

C++: protocols::frag_picker::scores::MakeHydrophobicityProfileSimilarity::operator=(const class protocols::frag_picker::scores::MakeHydrophobicityProfileSimilarity &) –> class protocols::frag_picker::scores::MakeHydrophobicityProfileSimilarity &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicityProfileSimilarity, priority: int, lowest_acceptable_value: float, use_lowest: bool, picker: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakeHydrophobicityProfileSimilarity::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicitySimilarity

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Maker class that produces a new HydrophobicitySimilarity object

__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.frag_picker.scores.MakeHydrophobicitySimilarity) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicitySimilarity, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicitySimilarity) -> 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.frag_picker.scores.MakeHydrophobicitySimilarity, : pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicitySimilarity) → pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicitySimilarity

C++: protocols::frag_picker::scores::MakeHydrophobicitySimilarity::operator=(const class protocols::frag_picker::scores::MakeHydrophobicitySimilarity &) –> class protocols::frag_picker::scores::MakeHydrophobicitySimilarity &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicitySimilarity, priority: int, lowest_acceptable_value: float, use_lowest: bool, picker: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakeHydrophobicitySimilarity::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MakeInterbondAngleScore

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Maker class that produces a new InterbondAngleScore object

__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.frag_picker.scores.MakeInterbondAngleScore) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeInterbondAngleScore, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakeInterbondAngleScore) -> 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.frag_picker.scores.MakeInterbondAngleScore, : pyrosetta.rosetta.protocols.frag_picker.scores.MakeInterbondAngleScore) → pyrosetta.rosetta.protocols.frag_picker.scores.MakeInterbondAngleScore

C++: protocols::frag_picker::scores::MakeInterbondAngleScore::operator=(const class protocols::frag_picker::scores::MakeInterbondAngleScore &) –> class protocols::frag_picker::scores::MakeInterbondAngleScore &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeInterbondAngleScore, : int, : float, : bool, : pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakeInterbondAngleScore::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MakeJCoupling

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Matker class that produces a new JCoupling object

__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.frag_picker.scores.MakeJCoupling) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeJCoupling, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakeJCoupling) -> 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.frag_picker.scores.MakeJCoupling, : pyrosetta.rosetta.protocols.frag_picker.scores.MakeJCoupling) → pyrosetta.rosetta.protocols.frag_picker.scores.MakeJCoupling

C++: protocols::frag_picker::scores::MakeJCoupling::operator=(const class protocols::frag_picker::scores::MakeJCoupling &) –> class protocols::frag_picker::scores::MakeJCoupling &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeJCoupling, : int, : float, : bool, : pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakeJCoupling::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MakeLAMBEGO_Similarity

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Maker class that produces a new TorsionBin object

__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.frag_picker.scores.MakeLAMBEGO_Similarity) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeLAMBEGO_Similarity, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakeLAMBEGO_Similarity) -> 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.frag_picker.scores.MakeLAMBEGO_Similarity, : pyrosetta.rosetta.protocols.frag_picker.scores.MakeLAMBEGO_Similarity) → pyrosetta.rosetta.protocols.frag_picker.scores.MakeLAMBEGO_Similarity

C++: protocols::frag_picker::scores::MakeLAMBEGO_Similarity::operator=(const class protocols::frag_picker::scores::MakeLAMBEGO_Similarity &) –> class protocols::frag_picker::scores::MakeLAMBEGO_Similarity &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeLAMBEGO_Similarity, priority: int, lowest_acceptable_value: float, use_lowest: bool, picker: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakeLAMBEGO_Similarity::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPhiOut

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Matker class that produces a new MidPhiOut object

__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.frag_picker.scores.MakeMidPhiOut) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPhiOut, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPhiOut) -> 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.frag_picker.scores.MakeMidPhiOut, : pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPhiOut) → pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPhiOut

C++: protocols::frag_picker::scores::MakeMidPhiOut::operator=(const class protocols::frag_picker::scores::MakeMidPhiOut &) –> class protocols::frag_picker::scores::MakeMidPhiOut &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPhiOut, : int, : float, : bool, : pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakeMidPhiOut::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPsiOut

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Matker class that produces a new MidPsiOut object

__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.frag_picker.scores.MakeMidPsiOut) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPsiOut, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPsiOut) -> 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.frag_picker.scores.MakeMidPsiOut, : pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPsiOut) → pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPsiOut

C++: protocols::frag_picker::scores::MakeMidPsiOut::operator=(const class protocols::frag_picker::scores::MakeMidPsiOut &) –> class protocols::frag_picker::scores::MakeMidPsiOut &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPsiOut, : int, : float, : bool, : pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakeMidPsiOut::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MakePCS_FragDistance

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Matker class that produces a new PCS_FragDistance object

__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.frag_picker.scores.MakePCS_FragDistance) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakePCS_FragDistance, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakePCS_FragDistance) -> 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.frag_picker.scores.MakePCS_FragDistance, : pyrosetta.rosetta.protocols.frag_picker.scores.MakePCS_FragDistance) → pyrosetta.rosetta.protocols.frag_picker.scores.MakePCS_FragDistance

C++: protocols::frag_picker::scores::MakePCS_FragDistance::operator=(const class protocols::frag_picker::scores::MakePCS_FragDistance &) –> class protocols::frag_picker::scores::MakePCS_FragDistance &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakePCS_FragDistance, : int, : float, : bool, : pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakePCS_FragDistance::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MakePartialSecondarySimilarity

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Maker class that produces a new PartialSecondarySimilarity object

__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.frag_picker.scores.MakePartialSecondarySimilarity) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakePartialSecondarySimilarity, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakePartialSecondarySimilarity) -> 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.frag_picker.scores.MakePartialSecondarySimilarity, : pyrosetta.rosetta.protocols.frag_picker.scores.MakePartialSecondarySimilarity) → pyrosetta.rosetta.protocols.frag_picker.scores.MakePartialSecondarySimilarity

C++: protocols::frag_picker::scores::MakePartialSecondarySimilarity::operator=(const class protocols::frag_picker::scores::MakePartialSecondarySimilarity &) –> class protocols::frag_picker::scores::MakePartialSecondarySimilarity &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakePartialSecondarySimilarity, priority: int, lowest_acceptable_value: float, use_lowest: bool, picker: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, prediction_id: str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakePartialSecondarySimilarity::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MakePhi

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Maker class that produces a new Phi object

__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.frag_picker.scores.MakePhi) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakePhi, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakePhi) -> 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.frag_picker.scores.MakePhi, : pyrosetta.rosetta.protocols.frag_picker.scores.MakePhi) → pyrosetta.rosetta.protocols.frag_picker.scores.MakePhi

C++: protocols::frag_picker::scores::MakePhi::operator=(const class protocols::frag_picker::scores::MakePhi &) –> class protocols::frag_picker::scores::MakePhi &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakePhi, priority: int, lowest_acceptable_value: float, use_lowest: bool, picker: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakePhi::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiRmsd

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Matker class that produces a new PhiPsiRmsd object

__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.frag_picker.scores.MakePhiPsiRmsd) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiRmsd, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiRmsd) -> 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.frag_picker.scores.MakePhiPsiRmsd, : pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiRmsd) → pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiRmsd

C++: protocols::frag_picker::scores::MakePhiPsiRmsd::operator=(const class protocols::frag_picker::scores::MakePhiPsiRmsd &) –> class protocols::frag_picker::scores::MakePhiPsiRmsd &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiRmsd, : int, : float, : bool, : pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakePhiPsiRmsd::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiSquareWell

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Matker class that produces a new PhiPsiSquareWell object

__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.frag_picker.scores.MakePhiPsiSquareWell) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiSquareWell, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiSquareWell) -> 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.frag_picker.scores.MakePhiPsiSquareWell, : pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiSquareWell) → pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiSquareWell

C++: protocols::frag_picker::scores::MakePhiPsiSquareWell::operator=(const class protocols::frag_picker::scores::MakePhiPsiSquareWell &) –> class protocols::frag_picker::scores::MakePhiPsiSquareWell &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiSquareWell, : int, : float, : bool, : pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakePhiPsiSquareWell::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MakeProlinePhiScore

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Maker class that produces a new ProlinePhiScore object

__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.frag_picker.scores.MakeProlinePhiScore) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeProlinePhiScore, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakeProlinePhiScore) -> 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.frag_picker.scores.MakeProlinePhiScore, : pyrosetta.rosetta.protocols.frag_picker.scores.MakeProlinePhiScore) → pyrosetta.rosetta.protocols.frag_picker.scores.MakeProlinePhiScore

C++: protocols::frag_picker::scores::MakeProlinePhiScore::operator=(const class protocols::frag_picker::scores::MakeProlinePhiScore &) –> class protocols::frag_picker::scores::MakeProlinePhiScore &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeProlinePhiScore, priority: int, lowest_acceptable_value: float, use_lowest: bool, picker: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakeProlinePhiScore::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MakePsi

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Maker class that produces a new Psi object

__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.frag_picker.scores.MakePsi) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakePsi, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakePsi) -> 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.frag_picker.scores.MakePsi, : pyrosetta.rosetta.protocols.frag_picker.scores.MakePsi) → pyrosetta.rosetta.protocols.frag_picker.scores.MakePsi

C++: protocols::frag_picker::scores::MakePsi::operator=(const class protocols::frag_picker::scores::MakePsi &) –> class protocols::frag_picker::scores::MakePsi &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakePsi, priority: int, lowest_acceptable_value: float, use_lowest: bool, picker: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakePsi::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MakeRDCScore

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Maker class that produces a new RDCScore object

__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.frag_picker.scores.MakeRDCScore) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeRDCScore, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakeRDCScore) -> 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.frag_picker.scores.MakeRDCScore, : pyrosetta.rosetta.protocols.frag_picker.scores.MakeRDCScore) → pyrosetta.rosetta.protocols.frag_picker.scores.MakeRDCScore

C++: protocols::frag_picker::scores::MakeRDCScore::operator=(const class protocols::frag_picker::scores::MakeRDCScore &) –> class protocols::frag_picker::scores::MakeRDCScore &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeRDCScore, : int, : float, : bool, : pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakeRDCScore::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MakeRamaScore

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Maker class that produces a new RamaScore object

__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.frag_picker.scores.MakeRamaScore) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeRamaScore, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakeRamaScore) -> 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.frag_picker.scores.MakeRamaScore, : pyrosetta.rosetta.protocols.frag_picker.scores.MakeRamaScore) → pyrosetta.rosetta.protocols.frag_picker.scores.MakeRamaScore

C++: protocols::frag_picker::scores::MakeRamaScore::operator=(const class protocols::frag_picker::scores::MakeRamaScore &) –> class protocols::frag_picker::scores::MakeRamaScore &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeRamaScore, priority: int, lowest_acceptable_value: float, use_lowest: bool, picker: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, prediction_id: str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakeRamaScore::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondaryIdentity

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Maker class that produces a new SecondaryIdentity object

__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.frag_picker.scores.MakeSecondaryIdentity) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondaryIdentity, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondaryIdentity) -> 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.frag_picker.scores.MakeSecondaryIdentity, : pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondaryIdentity) → pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondaryIdentity

C++: protocols::frag_picker::scores::MakeSecondaryIdentity::operator=(const class protocols::frag_picker::scores::MakeSecondaryIdentity &) –> class protocols::frag_picker::scores::MakeSecondaryIdentity &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondaryIdentity, priority: int, lowest_acceptable_value: float, use_lowest: bool, picker: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, prediction_id: str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakeSecondaryIdentity::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondarySimilarity

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Maker class that produces a new SecondarySimilarity object

__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.frag_picker.scores.MakeSecondarySimilarity) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondarySimilarity, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondarySimilarity) -> 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.frag_picker.scores.MakeSecondarySimilarity, : pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondarySimilarity) → pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondarySimilarity

C++: protocols::frag_picker::scores::MakeSecondarySimilarity::operator=(const class protocols::frag_picker::scores::MakeSecondarySimilarity &) –> class protocols::frag_picker::scores::MakeSecondarySimilarity &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondarySimilarity, priority: int, lowest_acceptable_value: float, use_lowest: bool, picker: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, prediction_id: str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakeSecondarySimilarity::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MakeSequenceIdentity

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Maker class that produces a new SequenceIdentity object

__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.frag_picker.scores.MakeSequenceIdentity) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeSequenceIdentity, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakeSequenceIdentity) -> 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.frag_picker.scores.MakeSequenceIdentity, : pyrosetta.rosetta.protocols.frag_picker.scores.MakeSequenceIdentity) → pyrosetta.rosetta.protocols.frag_picker.scores.MakeSequenceIdentity

C++: protocols::frag_picker::scores::MakeSequenceIdentity::operator=(const class protocols::frag_picker::scores::MakeSequenceIdentity &) –> class protocols::frag_picker::scores::MakeSequenceIdentity &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeSequenceIdentity, priority: int, lowest_acceptable_value: float, use_lowest: bool, picker: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakeSequenceIdentity::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MakeSolventAccessibility

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Maker class that produces a new SolventAccessibility object

__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.frag_picker.scores.MakeSolventAccessibility) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeSolventAccessibility, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakeSolventAccessibility) -> 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.frag_picker.scores.MakeSolventAccessibility, : pyrosetta.rosetta.protocols.frag_picker.scores.MakeSolventAccessibility) → pyrosetta.rosetta.protocols.frag_picker.scores.MakeSolventAccessibility

C++: protocols::frag_picker::scores::MakeSolventAccessibility::operator=(const class protocols::frag_picker::scores::MakeSolventAccessibility &) –> class protocols::frag_picker::scores::MakeSolventAccessibility &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeSolventAccessibility, priority: int, lowest_acceptable_value: float, use_lowest: bool, picker: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakeSolventAccessibility::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MakeTalosSSSimilarity

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Maker class that produces a new TalosSSSimilarity object

__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.frag_picker.scores.MakeTalosSSSimilarity) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeTalosSSSimilarity, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakeTalosSSSimilarity) -> 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.frag_picker.scores.MakeTalosSSSimilarity, : pyrosetta.rosetta.protocols.frag_picker.scores.MakeTalosSSSimilarity) → pyrosetta.rosetta.protocols.frag_picker.scores.MakeTalosSSSimilarity

C++: protocols::frag_picker::scores::MakeTalosSSSimilarity::operator=(const class protocols::frag_picker::scores::MakeTalosSSSimilarity &) –> class protocols::frag_picker::scores::MakeTalosSSSimilarity &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeTalosSSSimilarity, priority: int, lowest_acceptable_value: float, use_lowest: bool, picker: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, prediction_id: str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakeTalosSSSimilarity::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MakeTorsionBinSimilarity

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod

Maker class that produces a new TorsionBin object

__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.frag_picker.scores.MakeTorsionBinSimilarity) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeTorsionBinSimilarity, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MakeTorsionBinSimilarity) -> 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.frag_picker.scores.MakeTorsionBinSimilarity, : pyrosetta.rosetta.protocols.frag_picker.scores.MakeTorsionBinSimilarity) → pyrosetta.rosetta.protocols.frag_picker.scores.MakeTorsionBinSimilarity

C++: protocols::frag_picker::scores::MakeTorsionBinSimilarity::operator=(const class protocols::frag_picker::scores::MakeTorsionBinSimilarity &) –> class protocols::frag_picker::scores::MakeTorsionBinSimilarity &

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → str

C++: protocols::frag_picker::scores::MakeFragmentScoringMethod::get_score_name() –> std::string &

make(self: pyrosetta.rosetta.protocols.frag_picker.scores.MakeTorsionBinSimilarity, priority: int, lowest_acceptable_value: float, use_lowest: bool, picker: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : str) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::MakeTorsionBinSimilarity::make(unsigned long, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

class pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

scores a fragment by the root mean square deviation of Phi and Psi angles.

__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.frag_picker.scores.MidPhiOut, priority: int, lowest_acceptable_value: float, use_lowest: bool) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut) -> 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.frag_picker.scores.MidPhiOut, : pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut) → pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut

C++: protocols::frag_picker::scores::MidPhiOut::operator=(const class protocols::frag_picker::scores::MidPhiOut &) –> class protocols::frag_picker::scores::MidPhiOut &

cached_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::MidPhiOut::cached_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut) → None

C++: protocols::frag_picker::scores::MidPhiOut::clean_up() –> void

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

C++: protocols::frag_picker::scores::MidPhiOut::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::MidPhiOut::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

scores a fragment by the root mean square deviation of Psi and Psi angles.

__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.frag_picker.scores.MidPsiOut, priority: int, lowest_acceptable_value: float, use_lowest: bool) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut) -> 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.frag_picker.scores.MidPsiOut, : pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut) → pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut

C++: protocols::frag_picker::scores::MidPsiOut::operator=(const class protocols::frag_picker::scores::MidPsiOut &) –> class protocols::frag_picker::scores::MidPsiOut &

cached_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::MidPsiOut::cached_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut) → None

C++: protocols::frag_picker::scores::MidPsiOut::clean_up() –> void

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

C++: protocols::frag_picker::scores::MidPsiOut::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::MidPsiOut::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

scores a fragment by the root mean square deviation of Phi and Psi angles.

__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.frag_picker.scores.PCS_FragDistance, priority: int, lowest_acceptable_value: float, use_lowest: bool, target_ca_dev: ObjexxFCL::FArray2D<double>, target_ca_dist: ObjexxFCL::FArray2D<double>, largest_fragment: int, max_length: int) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance) -> 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.frag_picker.scores.PCS_FragDistance, : pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance) → pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance

C++: protocols::frag_picker::scores::PCS_FragDistance::operator=(const class protocols::frag_picker::scores::PCS_FragDistance &) –> class protocols::frag_picker::scores::PCS_FragDistance &

cached_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::PCS_FragDistance::cached_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance) → None

C++: protocols::frag_picker::scores::PCS_FragDistance::clean_up() –> void

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

C++: protocols::frag_picker::scores::PCS_FragDistance::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::PCS_FragDistance::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager

holds particular score components, weights and calculates the total score for a fragment candidate

a fragment picker object needs exactly one fragment manager to pick fragments. Adding new scoring methods is supposed to be done FragmentPicker, which calls proper method from this class.

__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.frag_picker.scores.PValuedFragmentScoreManager) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager) -> 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_scoring_method(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, : float) → None

registers a new scoring method in this manager

C++: protocols::frag_picker::scores::FragmentScoreManager::add_scoring_method(class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>, double) –> void

assign(self: pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager, : pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager) → pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager

C++: protocols::frag_picker::scores::PValuedFragmentScoreManager::operator=(const class protocols::frag_picker::scores::PValuedFragmentScoreManager &) –> class protocols::frag_picker::scores::PValuedFragmentScoreManager &

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager) → None

calls clean_up() for each FragmentScoringMethod object, if it is possible

FragmentPicker calls this method when a given chunk has been processed

C++: protocols::frag_picker::scores::FragmentScoreManager::clean_up() –> void

count_components(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager) → int

says how many scoring methods have already been registered

C++: protocols::frag_picker::scores::FragmentScoreManager::count_components() –> unsigned long

create_empty_map(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap

creates an empty score map

C++: protocols::frag_picker::scores::FragmentScoreManager::create_empty_map() –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>

create_scores(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager, : str, : protocols::frag_picker::FragmentPicker) → None

reads a config file and creates scoring methods

C++: protocols::frag_picker::scores::FragmentScoreManager::create_scores(const class std::basic_string<char> &, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>) –> void

create_scoring_method(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager, : str, : int, : float, : float, : bool, : protocols::frag_picker::FragmentPicker, : str) → None

creates a new scoring method object

C++: protocols::frag_picker::scores::FragmentScoreManager::create_scoring_method(const class std::basic_string<char> &, unsigned long, double, double, bool, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>, class std::basic_string<char>) –> void

describe_fragments(self: pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager, : pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t, : pyrosetta.rosetta.std.ostream) → None

prints a flat table with all scores for all the fragments in a given vector

If the manager allows for annotations, they will be printed as well

C++: protocols::frag_picker::scores::PValuedFragmentScoreManager::describe_fragments(const class utility::vector1<struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> >, class std::allocator<struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> > > > &, class std::basic_ostream<char> &) –> void

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager, chunk: pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

calls do_caching() for each FragmentScoringMethod object, if it is possible

FragmentPicker calls this method when a new chunk is to be processed

C++: protocols::frag_picker::scores::FragmentScoreManager::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_component(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager, index: int) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

Returns a desired scoring method

Allowed index values are [1,count_components()]

C++: protocols::frag_picker::scores::FragmentScoreManager::get_component(unsigned long) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>

get_weights(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager) → pyrosetta.rosetta.utility.vector1_double

returns a vector of weights that are used to compute the total score

C++: protocols::frag_picker::scores::FragmentScoreManager::get_weights() –> class utility::vector1<double, class std::allocator<double> >

if_late_scoring_for_zeros(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager) → bool

says if late scoring is used or not

late scoring means that some scores (those with weight=0, such as crmsd) are evaluated only for the selected fragments rather than for all the candidates

C++: protocols::frag_picker::scores::FragmentScoreManager::if_late_scoring_for_zeros() –> bool

register_score_maker(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager, : pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod) → None

registers a maker object that will be used to create a scoring method object

C++: protocols::frag_picker::scores::FragmentScoreManager::register_score_maker(class std::shared_ptr<class protocols::frag_picker::scores::MakeFragmentScoringMethod>) –> void

score_fragment(self: pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

calculates all the small scores for a given fragment

results are properly stored inside a FragmentScoreMap object

C++: protocols::frag_picker::scores::PValuedFragmentScoreManager::score_fragment(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

score_fragment_from_cache(self: pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

calculates all the small scores for a given fragment

results are properly stored inside a FragmentScoreMap object

C++: protocols::frag_picker::scores::PValuedFragmentScoreManager::score_fragment_from_cache(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

score_zero_scores(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager, : protocols::frag_picker::FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

calculates all these small scores for a given fragment whose weight is 0.0

When use_late_scoring_for_zeros() was used to set the flag to true, all fragment scoring methods neglects zero-weighted scores. These will be evaluated by this function, that may be called after fragments are picked. This way some time consuming computations (e.g. crmsd for fragments) may be computed only for the selected fragments rather than for all of them

C++: protocols::frag_picker::scores::FragmentScoreManager::score_zero_scores(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_precision(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager, which_score: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, precision: int) → None

sets up a new precision used to print fragment score value

C++: protocols::frag_picker::scores::FragmentScoreManager::set_precision(class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>, unsigned long) –> void

set_width(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager, which_score: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, width: int) → None

sets up a new number of characters spend to print fragment score value

C++: protocols::frag_picker::scores::FragmentScoreManager::set_width(class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>, unsigned long) –> void

show_scoring_methods(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager, out: pyrosetta.rosetta.std.ostream) → None

prints a nice table showing the registered scores

the table shows also the order in which the scores are evaluated

C++: protocols::frag_picker::scores::FragmentScoreManager::show_scoring_methods(class std::basic_ostream<char> &) –> void

total_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → float

calculates the total score

C++: protocols::frag_picker::scores::FragmentScoreManager::total_score(class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> double

use_late_scoring_for_zeros(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager, if_true: bool) → None

those score metohods that have weight = 0.0 will be computed after the fragments are picked

if weight for a score is 0.0 than it does not affect the total score and thus has no

effect on fragments sorting, quota, etc. Such scores may be computed after fragment picking is finished

C++: protocols::frag_picker::scores::FragmentScoreManager::use_late_scoring_for_zeros(const bool) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

scores a fragment by secondary structure similarity

The score for each position is P(H), P(L) or P(E) if a vall residue is within Helix, Loop or Extended secondary stucture element, respectively. P(H), P(L) and P(E) denotes the probability that a given residue in a query is within Helix, Loop or Extended secondary stucture element. The total score of a fragment is a simple sum of all positions; for N-mer fragment is a sum of N terms If P(H), P(L) and P(E) probabilities takes only 1.0 and 0.0 values, result of this scoring function should be the same as SecondaryIdentity, although the later one is faster.

__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.frag_picker.scores.PartialSecondarySimilarity, priority: int, lowest_acceptable_value: float, use_lowest: bool, query_prediction: pyrosetta.rosetta.core.fragment.SecondaryStructure, prediction_name: str, sequence_length: int, longest_vall_chunk: int) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity) -> 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.frag_picker.scores.PartialSecondarySimilarity, : pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity) → pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity

C++: protocols::frag_picker::scores::PartialSecondarySimilarity::operator=(const class protocols::frag_picker::scores::PartialSecondarySimilarity &) –> class protocols::frag_picker::scores::PartialSecondarySimilarity &

cached_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity, f: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, empty_map: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::PartialSecondarySimilarity::cached_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity) → None

C++: protocols::frag_picker::scores::PartialSecondarySimilarity::clean_up() –> void

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

C++: protocols::frag_picker::scores::PartialSecondarySimilarity::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_prediction_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity) → str

C++: protocols::frag_picker::scores::PartialSecondarySimilarity::get_prediction_name() –> std::string &

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

Computes the score

C++: protocols::frag_picker::scores::PartialSecondarySimilarity::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.Phi

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

scores a fragment by its predicted phi similarity

__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.frag_picker.scores.Phi, priority: int, lowest_acceptable_value: float, use_lowest: bool, fastaQuerySequence: str, query_phi_prediction: pyrosetta.rosetta.utility.vector1_double, query_phi_prediction_conf: pyrosetta.rosetta.utility.vector1_double) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.Phi, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.Phi) -> 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.frag_picker.scores.CachingScoringMethod, : pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod) → pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

C++: protocols::frag_picker::scores::CachingScoringMethod::operator=(const class protocols::frag_picker::scores::CachingScoringMethod &) –> class protocols::frag_picker::scores::CachingScoringMethod &

cached_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.Phi, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::Phi::cached_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.Phi) → None

C++: protocols::frag_picker::scores::Phi::clean_up() –> void

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.Phi, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

C++: protocols::frag_picker::scores::Phi::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.Phi, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::Phi::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

scores a fragment by the root mean square deviation of Phi and Psi angles.

__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.frag_picker.scores.PhiPsiRmsd, priority: int, lowest_acceptable_value: float, use_lowest: bool, reference_pose: pyrosetta.rosetta.core.pose.Pose) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd, : int, : float, : bool, : pyrosetta.rosetta.protocols.frag_picker.PhiPsiTalosIO) -> None
3. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd) -> 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.frag_picker.scores.PhiPsiRmsd, : pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd) → pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd

C++: protocols::frag_picker::scores::PhiPsiRmsd::operator=(const class protocols::frag_picker::scores::PhiPsiRmsd &) –> class protocols::frag_picker::scores::PhiPsiRmsd &

cached_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::PhiPsiRmsd::cached_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd) → None

C++: protocols::frag_picker::scores::PhiPsiRmsd::clean_up() –> void

describe_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap, : pyrosetta.rosetta.std.ostream) → bool

Print debugging informations about a score for a given fragment

C++: protocols::frag_picker::scores::PhiPsiRmsd::describe_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>, class std::basic_ostream<char> &) –> bool

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

C++: protocols::frag_picker::scores::PhiPsiRmsd::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::PhiPsiRmsd::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

scores a fragment by the root mean square deviation of Phi and Psi angles.

__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.frag_picker.scores.PhiPsiSquareWell, : int, : float, : bool, : pyrosetta.rosetta.protocols.frag_picker.PhiPsiTalosIO) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell, : int, : float, : bool, : pyrosetta.rosetta.core.pose.Pose) -> None
3. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell) -> 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.frag_picker.scores.PhiPsiSquareWell, : pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell) → pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell

C++: protocols::frag_picker::scores::PhiPsiSquareWell::operator=(const class protocols::frag_picker::scores::PhiPsiSquareWell &) –> class protocols::frag_picker::scores::PhiPsiSquareWell &

cached_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::PhiPsiSquareWell::cached_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell) → None

C++: protocols::frag_picker::scores::PhiPsiSquareWell::clean_up() –> void

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

C++: protocols::frag_picker::scores::PhiPsiSquareWell::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::PhiPsiSquareWell::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

a fragment candidate

__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.frag_picker.scores.ProfileScore, priority: int, lowest_acceptable_value: float, use_lowest: bool, query_profile: pyrosetta.rosetta.core.sequence.SequenceProfile, profile_scoring: pyrosetta.rosetta.core.sequence.ScoringScheme, longest_vall_chunk: int) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore) -> 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.frag_picker.scores.ProfileScore, : pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore) → pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore

C++: protocols::frag_picker::scores::ProfileScore::operator=(const class protocols::frag_picker::scores::ProfileScore &) –> class protocols::frag_picker::scores::ProfileScore &

cached_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::ProfileScore::cached_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore) → None

C++: protocols::frag_picker::scores::ProfileScore::clean_up() –> void

describe_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore, f: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, empty_map: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap, out: pyrosetta.rosetta.std.ostream) → bool

C++: protocols::frag_picker::scores::ProfileScore::describe_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>, class std::basic_ostream<char> &) –> bool

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

C++: protocols::frag_picker::scores::ProfileScore::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::CachingScoringMethod::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

a fragment candidate

__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.frag_picker.scores.ProfileScoreBlosum62, priority: int, lowest_acceptable_value: float, use_lowest: bool, query_profile: pyrosetta.rosetta.core.sequence.SequenceProfile, longest_vall_chunk: int) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62) -> 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.frag_picker.scores.ProfileScoreBlosum62, : pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62) → pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62

C++: protocols::frag_picker::scores::ProfileScoreBlosum62::operator=(const class protocols::frag_picker::scores::ProfileScoreBlosum62 &) –> class protocols::frag_picker::scores::ProfileScoreBlosum62 &

cached_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::ProfileScoreBlosum62::cached_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62) → None

C++: protocols::frag_picker::scores::ProfileScoreBlosum62::clean_up() –> void

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

C++: protocols::frag_picker::scores::ProfileScoreBlosum62::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::ProfileScoreBlosum62::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

a fragment candidate

__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.frag_picker.scores.ProfileScoreDistWeight, priority: int, lowest_acceptable_value: float, use_lowest: bool, query_profile: pyrosetta.rosetta.core.sequence.SequenceProfile, query_ss_prediction: pyrosetta.rosetta.core.fragment.SecondaryStructure, query_sequence: str, longest_vall_chunk: int) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight) -> 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.frag_picker.scores.ProfileScoreDistWeight, : pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight) → pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight

C++: protocols::frag_picker::scores::ProfileScoreDistWeight::operator=(const class protocols::frag_picker::scores::ProfileScoreDistWeight &) –> class protocols::frag_picker::scores::ProfileScoreDistWeight &

cached_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::ProfileScoreDistWeight::cached_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight) → None

C++: protocols::frag_picker::scores::ProfileScoreDistWeight::clean_up() –> void

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

C++: protocols::frag_picker::scores::ProfileScoreDistWeight::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::CachingScoringMethod::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

a fragment candidate

__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.frag_picker.scores.ProfileScoreL1, : int, : float, : bool, : pyrosetta.rosetta.core.sequence.SequenceProfile, : pyrosetta.rosetta.utility.vector1_unsigned_long, : int) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1) -> 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.frag_picker.scores.ProfileScoreL1, : pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1) → pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1

C++: protocols::frag_picker::scores::ProfileScoreL1::operator=(const class protocols::frag_picker::scores::ProfileScoreL1 &) –> class protocols::frag_picker::scores::ProfileScoreL1 &

cached_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::ProfileScoreL1::cached_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1) → None

C++: protocols::frag_picker::scores::ProfileScoreL1::clean_up() –> void

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

C++: protocols::frag_picker::scores::ProfileScoreL1::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

do_caching_simple(self: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

C++: protocols::frag_picker::scores::ProfileScoreL1::do_caching_simple(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::ProfileScoreL1::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

a fragment candidate

__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.frag_picker.scores.ProfileScoreStructL1, : int, : float, : bool, : pyrosetta.rosetta.core.sequence.SequenceProfile, : pyrosetta.rosetta.utility.vector1_unsigned_long, : int) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1) -> 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.frag_picker.scores.ProfileScoreStructL1, : pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1) → pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1

C++: protocols::frag_picker::scores::ProfileScoreStructL1::operator=(const class protocols::frag_picker::scores::ProfileScoreStructL1 &) –> class protocols::frag_picker::scores::ProfileScoreStructL1 &

cached_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::ProfileScoreStructL1::cached_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1) → None

C++: protocols::frag_picker::scores::ProfileScoreStructL1::clean_up() –> void

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

C++: protocols::frag_picker::scores::ProfileScoreStructL1::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

do_caching_simple(self: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

C++: protocols::frag_picker::scores::ProfileScoreStructL1::do_caching_simple(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::ProfileScoreStructL1::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

a fragment candidate

__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.frag_picker.scores.ProfileScoreSubMatrix, priority: int, lowest_acceptable_value: float, use_lowest: bool, sequence: str, longest_vall_chunk: int, subMatrixFile: str) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix) -> 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.frag_picker.scores.ProfileScoreSubMatrix, : pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix) → pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix

C++: protocols::frag_picker::scores::ProfileScoreSubMatrix::operator=(const class protocols::frag_picker::scores::ProfileScoreSubMatrix &) –> class protocols::frag_picker::scores::ProfileScoreSubMatrix &

cached_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::ProfileScoreSubMatrix::cached_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix) → None

C++: protocols::frag_picker::scores::ProfileScoreSubMatrix::clean_up() –> void

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

C++: protocols::frag_picker::scores::ProfileScoreSubMatrix::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::ProfileScoreSubMatrix::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

ProlinePhiScore score counts identical residues

Resulting score is the number of identical residues on corresponding positions in a vall fragment and a query sequence

__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.frag_picker.scores.ProlinePhiScore, priority: int, lowest_acceptable_value: float, use_lowest: bool, fastaQueryDisulfide: str) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore) -> 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.frag_picker.scores.FragmentScoringMethod, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::FragmentScoringMethod::operator=(const class protocols::frag_picker::scores::FragmentScoringMethod &) –> class protocols::frag_picker::scores::FragmentScoringMethod &

describe_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore, f: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, empty_map: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap, out: pyrosetta.rosetta.std.ostream) → bool

prints a detailed explanation how a fragment score has been computed

besides extensive output, the method should return the same result as score()

C++: protocols::frag_picker::scores::ProlinePhiScore::describe_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>, class std::basic_ostream<char> &) –> bool

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore, f: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, empty_map: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::ProlinePhiScore::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.Psi

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

scores a fragment by its predicted psi similarity

__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.frag_picker.scores.Psi, priority: int, lowest_acceptable_value: float, use_lowest: bool, fastaQuerySequence: str, query_psi_prediction: pyrosetta.rosetta.utility.vector1_double, query_psi_prediction_conf: pyrosetta.rosetta.utility.vector1_double) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.Psi, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.Psi) -> 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.frag_picker.scores.CachingScoringMethod, : pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod) → pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

C++: protocols::frag_picker::scores::CachingScoringMethod::operator=(const class protocols::frag_picker::scores::CachingScoringMethod &) –> class protocols::frag_picker::scores::CachingScoringMethod &

cached_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.Psi, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::Psi::cached_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.Psi) → None

C++: protocols::frag_picker::scores::Psi::clean_up() –> void

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.Psi, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

C++: protocols::frag_picker::scores::Psi::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.Psi, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::Psi::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

scores a fragment by its crmsd to the given reference 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__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore, : int, : float, : bool) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore) -> 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.frag_picker.scores.RDCScore, : pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore) → pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore

C++: protocols::frag_picker::scores::RDCScore::operator=(const class protocols::frag_picker::scores::RDCScore &) –> class protocols::frag_picker::scores::RDCScore &

cached_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::RDCScore::cached_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore) → None

C++: protocols::frag_picker::scores::RDCScore::clean_up() –> void

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

C++: protocols::frag_picker::scores::RDCScore::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::RDCScore::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

RamaScore score counts identical residues

Resulting score is the number of identical residues on corresponding positions in a vall fragment and a query sequence

SetupRamaTables(self: pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore) → None

C++: protocols::frag_picker::scores::RamaScore::SetupRamaTables() –> void

__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.frag_picker.scores.RamaScore, : int, : float, : bool, : str, : str) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore, : int, : float, : bool, : str, : pyrosetta.rosetta.core.fragment.SecondaryStructure, : str) -> None
3. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore) -> 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.frag_picker.scores.CachingScoringMethod, : pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod) → pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

C++: protocols::frag_picker::scores::CachingScoringMethod::operator=(const class protocols::frag_picker::scores::CachingScoringMethod &) –> class protocols::frag_picker::scores::CachingScoringMethod &

cached_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore, f: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, empty_map: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::RamaScore::cached_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore) → None

C++: protocols::frag_picker::scores::RamaScore::clean_up() –> void

describe_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore, f: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, empty_map: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap, out: pyrosetta.rosetta.std.ostream) → bool

prints a detailed explanation how a fragment score has been computed

besides extensive output, the method should return the same result as score()

C++: protocols::frag_picker::scores::RamaScore::describe_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>, class std::basic_ostream<char> &) –> bool

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

C++: protocols::frag_picker::scores::RamaScore::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_prediction_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore) → str

C++: protocols::frag_picker::scores::RamaScore::get_prediction_name() –> std::string &

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore, f: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, empty_map: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::RamaScore::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore

Computes E-Value for a Profile object

__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.frag_picker.scores.ScoreEValuator, priority: int, lowest_acceptable_value: float, use_lowest: bool, query_profile: pyrosetta.rosetta.core.sequence.SequenceProfile, profile_scoring: pyrosetta.rosetta.core.sequence.ScoringScheme, largest_chunk_size: int) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator) -> 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.frag_picker.scores.ScoreEValuator, : pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator) → pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator

C++: protocols::frag_picker::scores::ScoreEValuator::operator=(const class protocols::frag_picker::scores::ScoreEValuator &) –> class protocols::frag_picker::scores::ScoreEValuator &

cached_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::ProfileScore::cached_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator) → None

C++: protocols::frag_picker::scores::ScoreEValuator::clean_up() –> void

describe_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore, f: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, empty_map: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap, out: pyrosetta.rosetta.std.ostream) → bool

C++: protocols::frag_picker::scores::ProfileScore::describe_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>, class std::basic_ostream<char> &) –> bool

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

C++: protocols::frag_picker::scores::ScoreEValuator::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::ScoreEValuator::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

SequenceIdentity score counts how many residues share the same secondary structure

Resulting score is the number of residues on corresponding positions in a vall fragment and a query sequence that are annotated with the same 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__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity, priority: int, lowest_acceptable_value: float, use_lowest: bool, query_secondary_structure: str, prediction_name: str) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity) -> 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.frag_picker.scores.FragmentScoringMethod, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::FragmentScoringMethod::operator=(const class protocols::frag_picker::scores::FragmentScoringMethod &) –> class protocols::frag_picker::scores::FragmentScoringMethod &

describe_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap, : pyrosetta.rosetta.std.ostream) → bool

prints a detailed explanation how a fragment score has been computed

besides extensive output, the method should return the same result as score()

C++: protocols::frag_picker::scores::SecondaryIdentity::describe_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>, class std::basic_ostream<char> &) –> bool

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_prediction_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity) → str

C++: protocols::frag_picker::scores::SecondaryIdentity::get_prediction_name() –> std::string &

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

Computes the score

C++: protocols::frag_picker::scores::SecondaryIdentity::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

scores a fragment by secondary structure similarity

The score for each position is P(H), P(L) or P(E) if a vall residue is within Helix, Loop or Extended secondary stucture element, respectively. P(H), P(L) and P(E) denotes the probability that a given residue in a query is within Helix, Loop or Extended secondary stucture element. The total score of a fragment is a simple sum of all positions; for N-mer fragment is a sum of N terms If P(H), P(L) and P(E) probabilities takes only 1.0 and 0.0 values, result of this scoring function should be the same as SecondaryIdentity, although the later one is faster.

__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.frag_picker.scores.SecondarySimilarity, priority: int, lowest_acceptable_value: float, use_lowest: bool, query_prediction: pyrosetta.rosetta.core.fragment.SecondaryStructure, prediction_name: str, sequence_length: int, frag_sizes: pyrosetta.rosetta.utility.vector1_unsigned_long, longest_vall_chunk: int) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity) -> 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.frag_picker.scores.SecondarySimilarity, : pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity) → pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity

C++: protocols::frag_picker::scores::SecondarySimilarity::operator=(const class protocols::frag_picker::scores::SecondarySimilarity &) –> class protocols::frag_picker::scores::SecondarySimilarity &

cached_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity, f: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, empty_map: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::SecondarySimilarity::cached_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity) → None

C++: protocols::frag_picker::scores::SecondarySimilarity::clean_up() –> void

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

C++: protocols::frag_picker::scores::SecondarySimilarity::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

do_caching_simple(self: pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

C++: protocols::frag_picker::scores::SecondarySimilarity::do_caching_simple(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_prediction_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity) → str

C++: protocols::frag_picker::scores::SecondarySimilarity::get_prediction_name() –> std::string &

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_secondary_prediction(self: pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity) → pyrosetta.rosetta.core.fragment.SecondaryStructure

returns the secondary structure porediction object that is used by this score

C++: protocols::frag_picker::scores::SecondarySimilarity::get_secondary_prediction() –> class std::shared_ptr<class core::fragment::SecondaryStructure>

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

Computes the score

C++: protocols::frag_picker::scores::SecondarySimilarity::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

SequenceIdentity score counts identical residues

Resulting score is the number of identical residues on corresponding positions in a vall fragment and a query sequence

__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.frag_picker.scores.SequenceIdentity, priority: int, lowest_acceptable_value: float, use_lowest: bool, fastaQuerySequence: str) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity) -> 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.frag_picker.scores.FragmentScoringMethod, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod

C++: protocols::frag_picker::scores::FragmentScoringMethod::operator=(const class protocols::frag_picker::scores::FragmentScoringMethod &) –> class protocols::frag_picker::scores::FragmentScoringMethod &

describe_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity, f: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, empty_map: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap, out: pyrosetta.rosetta.std.ostream) → bool

prints a detailed explanation how a fragment score has been computed

besides extensive output, the method should return the same result as score()

C++: protocols::frag_picker::scores::SequenceIdentity::describe_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>, class std::basic_ostream<char> &) –> bool

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity, f: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, empty_map: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::SequenceIdentity::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

scores a fragment by its predicted solvent accessibility

__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.frag_picker.scores.SolventAccessibility, priority: int, lowest_acceptable_value: float, use_lowest: bool, fastaQuerySequence: str, predicted_sa: pyrosetta.rosetta.utility.vector1_double) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility) -> 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.frag_picker.scores.CachingScoringMethod, : pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod) → pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

C++: protocols::frag_picker::scores::CachingScoringMethod::operator=(const class protocols::frag_picker::scores::CachingScoringMethod &) –> class protocols::frag_picker::scores::CachingScoringMethod &

cached_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::SolventAccessibility::cached_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility) → None

C++: protocols::frag_picker::scores::SolventAccessibility::clean_up() –> void

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

C++: protocols::frag_picker::scores::SolventAccessibility::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::SolventAccessibility::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

scores a fragment by secondary structure similarity

The score for each position is P(H), P(L) or P(E) if a vall residue is within Helix, Loop or Extended secondary stucture element, respectively. P(H), P(L) and P(E) denotes the probability that a given residue in a query is within Helix, Loop or Extended secondary stucture element. The total score of a fragment is a simple sum of all positions; for N-mer fragment is a sum of N terms If P(H), P(L) and P(E) probabilities takes only 1.0 and 0.0 values, result of this scoring function should be the same as SecondaryIdentity, although the later one is faster.

__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.frag_picker.scores.TalosSSSimilarity, priority: int, lowest_acceptable_value: float, use_lowest: bool, query_prediction: pyrosetta.rosetta.core.fragment.SecondaryStructure, prediction_name: str, sequence_length: int, frag_sizes: pyrosetta.rosetta.utility.vector1_unsigned_long, longest_vall_chunk: int) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity) -> 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.frag_picker.scores.TalosSSSimilarity, : pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity) → pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity

C++: protocols::frag_picker::scores::TalosSSSimilarity::operator=(const class protocols::frag_picker::scores::TalosSSSimilarity &) –> class protocols::frag_picker::scores::TalosSSSimilarity &

cached_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity, f: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, empty_map: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::TalosSSSimilarity::cached_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity) → None

C++: protocols::frag_picker::scores::TalosSSSimilarity::clean_up() –> void

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

C++: protocols::frag_picker::scores::TalosSSSimilarity::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

do_caching_simple(self: pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

C++: protocols::frag_picker::scores::TalosSSSimilarity::do_caching_simple(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_prediction_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity) → str

C++: protocols::frag_picker::scores::TalosSSSimilarity::get_prediction_name() –> std::string &

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_secondary_prediction(self: pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity) → pyrosetta.rosetta.core.fragment.SecondaryStructure

returns the secondary structure porediction object that is used by this score

C++: protocols::frag_picker::scores::TalosSSSimilarity::get_secondary_prediction() –> class std::shared_ptr<class core::fragment::SecondaryStructure>

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

Computes the score

C++: protocols::frag_picker::scores::TalosSSSimilarity::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

class pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity

Bases: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod

scores a fragment by torsion bin similarity

__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.frag_picker.scores.TorsionBinSimilarity, priority: int, lowest_acceptable_value: float, use_lowest: bool, query_bin_probs: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, sequence_length: int, longest_vall_chunk: int) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity, arg0: pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity) -> 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.frag_picker.scores.TorsionBinSimilarity, : pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity) → pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity

C++: protocols::frag_picker::scores::TorsionBinSimilarity::operator=(const class protocols::frag_picker::scores::TorsionBinSimilarity &) –> class protocols::frag_picker::scores::TorsionBinSimilarity &

cached_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

Computes the score

C++: protocols::frag_picker::scores::TorsionBinSimilarity::cached_score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

clean_up(self: pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity) → None

C++: protocols::frag_picker::scores::TorsionBinSimilarity::clean_up() –> void

do_caching(self: pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) → None

C++: protocols::frag_picker::scores::TorsionBinSimilarity::do_caching(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void

get_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns an integer index assigned to this scoring method by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_id() –> unsigned long

get_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → float

Returns the lowest acceptable score value for this scoring method.

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_min_allowed_score() –> double

get_priority(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → int

Returns a priority of this scoring method.

The higher the priority, the earlier a given scoring method is evaluated

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_priority() –> unsigned long

get_score_name(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → str

Returns a name of this scoring method

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_score_name() –> std::string &

get_use_lowest(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod) → bool

Returns the boolean choice on using the above lowest acceptable score value.

False means there is no lowest acceptable score

C++: protocols::frag_picker::scores::FragmentScoringMethod::get_use_lowest() –> bool

score(self: pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) → bool

C++: protocols::frag_picker::scores::CachingScoringMethod::score(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>) –> bool

set_id(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, id: int) → None

Sets a new integer index for this scoring method.

the method should be called only by a scoring manager

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_id(unsigned long) –> void

set_min_allowed_score(self: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, lowest_acceptable_value: float) → None

Sets a new value of the lowest acceptable score

Fragments that are below the threshold will be discarded

C++: protocols::frag_picker::scores::FragmentScoringMethod::set_min_allowed_score(double) –> void

pyrosetta.rosetta.protocols.frag_picker.scores.allocate_matrix(i_size: int, j_size: int, dst: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) → None

C++: protocols::frag_picker::scores::allocate_matrix(unsigned long, unsigned long, class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &) –> void

pyrosetta.rosetta.protocols.frag_picker.scores.create_cache(frag_sizes: pyrosetta.rosetta.utility.vector1_unsigned_long, query_len: int, longest_vall_chunk: int, cache: pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t) → None

C++: protocols::frag_picker::scores::create_cache(class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, unsigned long, unsigned long, class utility::vector1<class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >, class std::allocator<class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > > > &) –> void

pyrosetta.rosetta.protocols.frag_picker.scores.do_one_line(start_i: int, start_j: int, small_scores: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, frag_len: int, frag_scores: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) → None

C++: protocols::frag_picker::scores::do_one_line(unsigned long, unsigned long, class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, unsigned long, class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &) –> void

pyrosetta.rosetta.protocols.frag_picker.scores.rolling_score(small_scores: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, frag_len: int, frag_scores: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) → None

C++: protocols::frag_picker::scores::rolling_score(class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, unsigned long, class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &) –> void