frags

Bindings for protocols::frags namespace

class pyrosetta.rosetta.protocols.frags.FragLib

Bases: pybind11_builtins.pybind11_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.frags.FragLib, frag_map: pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_protocols_frags_TorsionFragmentLibrary_t) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frags.FragLib) -> None
3. __init__(self: pyrosetta.rosetta.protocols.frags.FragLib, arg0: pyrosetta.rosetta.protocols.frags.FragLib) -> None

__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.protocols.frags.FragLib) → str

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.protocols.frags.FragLib, : pyrosetta.rosetta.protocols.frags.FragLib) → pyrosetta.rosetta.protocols.frags.FragLib

C++: protocols::frags::FragLib::operator=(const class protocols::frags::FragLib &) –> class protocols::frags::FragLib &

clear(self: pyrosetta.rosetta.protocols.frags.FragLib) → None

C++: protocols::frags::FragLib::clear() –> void

copy_fragments(self: pyrosetta.rosetta.protocols.frags.FragLib, src: pyrosetta.rosetta.protocols.frags.FragLib) → None

C++: protocols::frags::FragLib::copy_fragments(const class protocols::frags::FragLib &) –> void

delete_residue(self: pyrosetta.rosetta.protocols.frags.FragLib, seqpos: int) → None

C++: protocols::frags::FragLib::delete_residue(const unsigned long) –> void

frag_sizes(self: pyrosetta.rosetta.protocols.frags.FragLib) → pyrosetta.rosetta.utility.vector1_unsigned_long

slow

C++: protocols::frags::FragLib::frag_sizes() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

library(self: pyrosetta.rosetta.protocols.frags.FragLib, size: int) → pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary

C++: protocols::frags::FragLib::library(const unsigned long) –> class protocols::frags::TorsionFragmentLibrary &

shift(self: pyrosetta.rosetta.protocols.frags.FragLib, current2desired_offset: int) → None

C++: protocols::frags::FragLib::shift(const int) –> void

class pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary

Bases: pybind11_builtins.pybind11_object

a class for collection of fragments for a single residue position

essentially a vector of TorsionFragment (owning pointers)

__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).

__getitem__(self: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary, index: int) → pyrosetta.rosetta.protocols.frags.TorsionFragment

overloaded [] operator to get single piece of fragment (actual object, not owning pointers)

C++: protocols::frags::SingleResidueTorsionFragmentLibrary::operator[](const unsigned long) const –> const class protocols::frags::TorsionFragment &

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary, arg0: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary) -> None

__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary) → str

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

append_fragment(self: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary, fragment: pyrosetta.rosetta.protocols.frags.TorsionFragment) → None

append one piece of fragment at the end

C++: protocols::frags::SingleResidueTorsionFragmentLibrary::append_fragment(class std::shared_ptr<class protocols::frags::TorsionFragment>) –> void

assign(self: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary, : pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary) → pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary

C++: protocols::frags::SingleResidueTorsionFragmentLibrary::operator=(const class protocols::frags::SingleResidueTorsionFragmentLibrary &) –> class protocols::frags::SingleResidueTorsionFragmentLibrary &

clear(self: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary) → None

C++: protocols::frags::SingleResidueTorsionFragmentLibrary::clear() –> void

copy_fragments(self: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary, src: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary) → None

C++: protocols::frags::SingleResidueTorsionFragmentLibrary::copy_fragments(const class protocols::frags::SingleResidueTorsionFragmentLibrary &) –> void

erase(self: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary, index: int) → None

erase a single fragment

C++: protocols::frags::SingleResidueTorsionFragmentLibrary::erase(const unsigned long) –> void

insert_fragment(self: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary, fragment: pyrosetta.rosetta.protocols.frags.TorsionFragment) → None

insert one piece of fragment in the front

C++: protocols::frags::SingleResidueTorsionFragmentLibrary::insert_fragment(class std::shared_ptr<class protocols::frags::TorsionFragment>) –> void

size(self: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary) → int

number of available fragment pieces for this position

C++: protocols::frags::SingleResidueTorsionFragmentLibrary::size() const –> unsigned long

class pyrosetta.rosetta.protocols.frags.TorsionFragment

Bases: pybind11_builtins.pybind11_object

a class for single piece of torsion fragment

It stores torsion angles and secondary structure. Torsions are stored as vector of vector, such as TorsionFragment[frag_size][n_bb_torsion]; SS are stored as vector, such as TorsionFragment[frag_length]

__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.frags.TorsionFragment) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frags.TorsionFragment, arg0: pyrosetta.rosetta.protocols.frags.TorsionFragment) -> None
3. __init__(self: pyrosetta.rosetta.protocols.frags.TorsionFragment, size_in: int, nbb_in: 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__(self: pyrosetta.rosetta.protocols.frags.TorsionFragment) → str

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.protocols.frags.TorsionFragment, : pyrosetta.rosetta.protocols.frags.TorsionFragment) → pyrosetta.rosetta.protocols.frags.TorsionFragment

C++: protocols::frags::TorsionFragment::operator=(const class protocols::frags::TorsionFragment &) –> class protocols::frags::TorsionFragment &

clone(self: pyrosetta.rosetta.protocols.frags.TorsionFragment) → pyrosetta.rosetta.protocols.frags.TorsionFragment

C++: protocols::frags::TorsionFragment::clone() const –> class std::shared_ptr<class protocols::frags::TorsionFragment>

get_secstruct(self: pyrosetta.rosetta.protocols.frags.TorsionFragment, pos: int) → str

C++: protocols::frags::TorsionFragment::get_secstruct(const unsigned long) const –> char

get_sequence(self: pyrosetta.rosetta.protocols.frags.TorsionFragment, pos: int) → str

C++: protocols::frags::TorsionFragment::get_sequence(const unsigned long) const –> char

get_torsion(self: pyrosetta.rosetta.protocols.frags.TorsionFragment, pos: int, tor: int) → float

get value for specific torsion in this piece of fragment

C++: protocols::frags::TorsionFragment::get_torsion(const unsigned long, const unsigned long) const –> double

insert(self: pyrosetta.rosetta.protocols.frags.TorsionFragment, pose: pyrosetta.rosetta.core.pose.Pose, begin: int) → None

C++: protocols::frags::TorsionFragment::insert(class core::pose::Pose &, const unsigned long) const –> void

nbb(self: pyrosetta.rosetta.protocols.frags.TorsionFragment) → int

number of backbone torsions.

C++: protocols::frags::TorsionFragment::nbb() const –> unsigned long

set_secstruct(self: pyrosetta.rosetta.protocols.frags.TorsionFragment, pos: int, setting: str) → None

set secstruct for this position

C++: protocols::frags::TorsionFragment::set_secstruct(const unsigned long, const char) –> void

set_sequence(self: pyrosetta.rosetta.protocols.frags.TorsionFragment, pos: int, setting: str) → None

set seq for this position

C++: protocols::frags::TorsionFragment::set_sequence(const unsigned long, const char) –> void

set_size_and_nbb(self: pyrosetta.rosetta.protocols.frags.TorsionFragment, size: int, nbb: int) → None

C++: protocols::frags::TorsionFragment::set_size_and_nbb(const unsigned long, const unsigned long) –> void

set_torsion(self: pyrosetta.rosetta.protocols.frags.TorsionFragment, pos: int, tor: int, setting: float) → None

set value for specific torsion in this piece of fragment.

C++: protocols::frags::TorsionFragment::set_torsion(const unsigned long, const unsigned long, const double) –> void

size(self: pyrosetta.rosetta.protocols.frags.TorsionFragment) → int

fragment size, 3mer or 9mer?

C++: protocols::frags::TorsionFragment::size() const –> unsigned long

class pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary

Bases: pybind11_builtins.pybind11_object

a class for classic Rosetta fragment library

essentially a collection of SingleResidueTorsionFragmentLibrary (indexed by residue position)

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getitem__(self: pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary, pos: int) → pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary

overloaded [] operator to get framgnet pieces for a certain residue position

C++: protocols::frags::TorsionFragmentLibrary::operator[](const unsigned long) –> class protocols::frags::SingleResidueTorsionFragmentLibrary &

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary, size_in: 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__(self: pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary) → str

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary, : pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary) → pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary

C++: protocols::frags::TorsionFragmentLibrary::operator=(const class protocols::frags::TorsionFragmentLibrary &) –> class protocols::frags::TorsionFragmentLibrary &

clear(self: pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary) → None

C++: protocols::frags::TorsionFragmentLibrary::clear() –> void

copy_fragments(self: pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary, src: pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary) → None

C++: protocols::frags::TorsionFragmentLibrary::copy_fragments(const class protocols::frags::TorsionFragmentLibrary &) –> void

delete_residue(self: pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary, seqpos: int) → None

C++: protocols::frags::TorsionFragmentLibrary::delete_residue(const unsigned long) –> void

derive_from_src_lib(*args, **kwargs)

Overloaded function.

1. derive_from_src_lib(self: pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary, my_size: int, src_size: int, src_lib_op: pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary) -> bool

C++: protocols::frags::TorsionFragmentLibrary::derive_from_src_lib(const unsigned long, const unsigned long, class std::shared_ptr<const class protocols::frags::TorsionFragmentLibrary>) –> bool

2. derive_from_src_lib(self: pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary, my_size: int, src_size: int, src_lib: pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary) -> bool

C++: protocols::frags::TorsionFragmentLibrary::derive_from_src_lib(const unsigned long, const unsigned long, const class protocols::frags::TorsionFragmentLibrary &) –> bool

print(self: pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary, os: pyrosetta.rosetta.std.ostream) → None

Show some info – right now just for debugging, ie not a full dump of the library

C++: protocols::frags::TorsionFragmentLibrary::print(class std::basic_ostream<char> &) const –> void

read_file(self: pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary, name: str, frag_size: int, nbb: int) → bool

C++: protocols::frags::TorsionFragmentLibrary::read_file(const class std::basic_string<char> &, const unsigned long, const unsigned long) –> bool

resize(self: pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary, new_size: int) → None

change the size of fragment library

C++: protocols::frags::TorsionFragmentLibrary::resize(const unsigned long) –> void

shift(self: pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary, current2desired_offset: int) → None

C++: protocols::frags::TorsionFragmentLibrary::shift(const int) –> void

size(self: pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary) → int

number of residues

C++: protocols::frags::TorsionFragmentLibrary::size() const –> unsigned long

class pyrosetta.rosetta.protocols.frags.VallData

Bases: pybind11_builtins.pybind11_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.frags.VallData) -> None
2. __init__(self: pyrosetta.rosetta.protocols.frags.VallData, filename: str) -> 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_line(self: pyrosetta.rosetta.protocols.frags.VallData, sq: str, ss: str, ph: float, ps: float, om: float) → None

read in one more line from Vall input file

C++: protocols::frags::VallData::add_line(const char, const char, const double, const double, const double) –> void

bigbin(self: pyrosetta.rosetta.protocols.frags.VallData) → pyrosetta.rosetta.utility.vector1_char

C++: protocols::frags::VallData::bigbin() const –> const class utility::vector1<char, class std::allocator<char> > &

chain(self: pyrosetta.rosetta.protocols.frags.VallData) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::frags::VallData::chain() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

get_cheating_frags(self: pyrosetta.rosetta.protocols.frags.VallData, nfrags: int, target_seq: str, target_ss: str, target_phi: pyrosetta.rosetta.utility.vector1_double, target_psi: pyrosetta.rosetta.utility.vector1_double, target_omega: pyrosetta.rosetta.utility.vector1_double, seq_weight: float, ss_weight: float, torsion_weight: float, min_torsion_dev: float, max_torsion_dev: float, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long, library: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary) → None

C++: protocols::frags::VallData::get_cheating_frags(const unsigned long, const class std::basic_string<char> &, const class std::basic_string<char> &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, const double, const double, const double, const double, const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class protocols::frags::SingleResidueTorsionFragmentLibrary &) const –> void

get_frags(*args, **kwargs)

Overloaded function.

1. get_frags(self: pyrosetta.rosetta.protocols.frags.VallData, nfrags: int, target_seq: str, target_ss: str, seq_weight: float, ss_weight: float, exclude_gly: bool, exclude_pro: bool, exclude_cis_peptides: bool, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long, library: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary) -> None
2. get_frags(self: pyrosetta.rosetta.protocols.frags.VallData, nfrags: int, target_seq: str, target_ss: str, seq_weight: float, ss_weight: float, exclude_gly: bool, exclude_pro: bool, exclude_cis_peptides: bool, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long, library: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary, bb_weight: float) -> None
3. get_frags(self: pyrosetta.rosetta.protocols.frags.VallData, nfrags: int, target_seq: str, target_ss: str, seq_weight: float, ss_weight: float, exclude_gly: bool, exclude_pro: bool, exclude_cis_peptides: bool, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long, library: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary, bb_weight: float, target_bb: str) -> None

C++: protocols::frags::VallData::get_frags(const unsigned long, const class std::basic_string<char> &, const class std::basic_string<char> &, const double, const double, const bool, const bool, const bool, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class protocols::frags::SingleResidueTorsionFragmentLibrary &, const double, const class std::basic_string<char> &) const –> void

num_chains(self: pyrosetta.rosetta.protocols.frags.VallData) → int

number of chains

C++: protocols::frags::VallData::num_chains() const –> unsigned long

omega(self: pyrosetta.rosetta.protocols.frags.VallData) → pyrosetta.rosetta.utility.vector1_double

C++: protocols::frags::VallData::omega() const –> const class utility::vector1<double, class std::allocator<double> > &

phi(self: pyrosetta.rosetta.protocols.frags.VallData) → pyrosetta.rosetta.utility.vector1_double

C++: protocols::frags::VallData::phi() const –> const class utility::vector1<double, class std::allocator<double> > &

psi(self: pyrosetta.rosetta.protocols.frags.VallData) → pyrosetta.rosetta.utility.vector1_double

C++: protocols::frags::VallData::psi() const –> const class utility::vector1<double, class std::allocator<double> > &

read_file(self: pyrosetta.rosetta.protocols.frags.VallData, filename: str) → None

C++: protocols::frags::VallData::read_file(const class std::basic_string<char> &) –> void

secstruct(self: pyrosetta.rosetta.protocols.frags.VallData) → pyrosetta.rosetta.utility.vector1_char

C++: protocols::frags::VallData::secstruct() const –> const class utility::vector1<char, class std::allocator<char> > &

sequence(self: pyrosetta.rosetta.protocols.frags.VallData) → pyrosetta.rosetta.utility.vector1_char

C++: protocols::frags::VallData::sequence() const –> const class utility::vector1<char, class std::allocator<char> > &

shrink(self: pyrosetta.rosetta.protocols.frags.VallData) → None

removes excess storage capacity to minimize memory usage

C++: protocols::frags::VallData::shrink() –> void

size(self: pyrosetta.rosetta.protocols.frags.VallData) → int

number of lines in Vall database

C++: protocols::frags::VallData::size() const –> int

pyrosetta.rosetta.protocols.frags.add_vall_cheating_fragments(*args, **kwargs)

Overloaded function.

1. add_vall_cheating_fragments(frag_sizes: pyrosetta.rosetta.utility.vector1_unsigned_long, nfrags: int, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap, secstruct: str, seq_weight: float, ss_weight: float, torsion_weight: float, min_torsion_dev: float, max_torsion_dev: float, frag_lib: pyrosetta.rosetta.protocols.frags.FragLib) -> None
2. add_vall_cheating_fragments(frag_sizes: pyrosetta.rosetta.utility.vector1_unsigned_long, nfrags: int, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap, secstruct: str, seq_weight: float, ss_weight: float, torsion_weight: float, min_torsion_dev: float, max_torsion_dev: float, frag_lib: pyrosetta.rosetta.protocols.frags.FragLib, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: protocols::frags::add_vall_cheating_fragments(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const unsigned long, const class core::pose::Pose &, const class core::kinematics::MoveMap &, const class std::basic_string<char> &, const double, const double, const double, const double, const double, class protocols::frags::FragLib &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

pyrosetta.rosetta.protocols.frags.add_vall_fragments(*args, **kwargs)

Overloaded function.

1. add_vall_fragments(frag_sizes: pyrosetta.rosetta.utility.vector1_unsigned_long, nfrags: int, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap, secstruct: str, seq_weight: float, ss_weight: float, frag_lib: pyrosetta.rosetta.protocols.frags.FragLib) -> None
2. add_vall_fragments(frag_sizes: pyrosetta.rosetta.utility.vector1_unsigned_long, nfrags: int, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap, secstruct: str, seq_weight: float, ss_weight: float, frag_lib: pyrosetta.rosetta.protocols.frags.FragLib, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
3. add_vall_fragments(frag_sizes: pyrosetta.rosetta.utility.vector1_unsigned_long, nfrags: int, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap, secstruct: str, seq_weight: float, ss_weight: float, frag_lib: pyrosetta.rosetta.protocols.frags.FragLib, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long, bb_weight: float) -> None
4. add_vall_fragments(frag_sizes: pyrosetta.rosetta.utility.vector1_unsigned_long, nfrags: int, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap, secstruct: str, seq_weight: float, ss_weight: float, frag_lib: pyrosetta.rosetta.protocols.frags.FragLib, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long, bb_weight: float, bigbins: str) -> None
5. add_vall_fragments(frag_sizes: pyrosetta.rosetta.utility.vector1_unsigned_long, nfrags: int, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap, secstruct: str, seq_weight: float, ss_weight: float, frag_lib: pyrosetta.rosetta.protocols.frags.FragLib, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long, bb_weight: float, bigbins: str, inputseq: str) -> None

C++: protocols::frags::add_vall_fragments(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const unsigned long, const class core::pose::Pose &, const class core::kinematics::MoveMap &, const class std::basic_string<char> &, const double, const double, class protocols::frags::FragLib &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

pyrosetta.rosetta.protocols.frags.dump_vall_fasta(fasta_filename: str) → None

C++: protocols::frags::dump_vall_fasta(const class std::basic_string<char> &) –> void

pyrosetta.rosetta.protocols.frags.fill_in_gaps(*args, **kwargs)

Overloaded function.

1. fill_in_gaps(nfrags: int, pose: pyrosetta.rosetta.core.pose.Pose, secstruct: str, seq_weight: float, ss_weight: float, frag_lib: pyrosetta.rosetta.protocols.frags.FragLib) -> None
2. fill_in_gaps(nfrags: int, pose: pyrosetta.rosetta.core.pose.Pose, secstruct: str, seq_weight: float, ss_weight: float, frag_lib: pyrosetta.rosetta.protocols.frags.FragLib, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
3. fill_in_gaps(nfrags: int, pose: pyrosetta.rosetta.core.pose.Pose, secstruct: str, seq_weight: float, ss_weight: float, frag_lib: pyrosetta.rosetta.protocols.frags.FragLib, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long, allow_uninitialized_secstruct: bool) -> None

C++: protocols::frags::fill_in_gaps(const unsigned long, const class core::pose::Pose &, const class std::basic_string<char> &, const double, const double, class protocols::frags::FragLib &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

pyrosetta.rosetta.protocols.frags.get_cheating_frags(nfrags: int, target_seq: str, target_ss: str, target_phi: pyrosetta.rosetta.utility.vector1_double, target_psi: pyrosetta.rosetta.utility.vector1_double, target_omega: pyrosetta.rosetta.utility.vector1_double, seq_weight: float, ss_weight: float, torsion_weight: float, min_torsion_dev: float, max_torsion_dev: float, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long, library: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary) → None

C++: protocols::frags::get_cheating_frags(const unsigned long, const class std::basic_string<char> &, const class std::basic_string<char> &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, const double, const double, const double, const double, const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class protocols::frags::SingleResidueTorsionFragmentLibrary &) –> void

pyrosetta.rosetta.protocols.frags.get_frags(*args, **kwargs)

Overloaded function.

1. get_frags(nfrags: int, target_seq: str, target_ss: str, seq_weight: float, ss_weight: float, exclude_gly: bool, exclude_pro: bool, exclude_cis_peptides: bool, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long, library: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary) -> None
2. get_frags(nfrags: int, target_seq: str, target_ss: str, seq_weight: float, ss_weight: float, exclude_gly: bool, exclude_pro: bool, exclude_cis_peptides: bool, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long, library: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary, bb_weight: float) -> None
3. get_frags(nfrags: int, target_seq: str, target_ss: str, seq_weight: float, ss_weight: float, exclude_gly: bool, exclude_pro: bool, exclude_cis_peptides: bool, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long, library: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary, bb_weight: float, target_bb: str) -> None

handles loading the vall if necessary

C++: protocols::frags::get_frags(const unsigned long, const class std::basic_string<char> &, const class std::basic_string<char> &, const double, const double, const bool, const bool, const bool, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class protocols::frags::SingleResidueTorsionFragmentLibrary &, const double, const class std::basic_string<char> &) –> void

pyrosetta.rosetta.protocols.frags.heap_down(heap: ObjexxFCL::FArray1A<int>, coheap: ObjexxFCL::FArray1A<float>, index_in: int) → None

C++: protocols::frags::heap_down(class ObjexxFCL::FArray1A<int>, class ObjexxFCL::FArray1A<float>, int) –> void

pyrosetta.rosetta.protocols.frags.heap_extract(heap: ObjexxFCL::FArray1A<int>, coheap: ObjexxFCL::FArray1A<float>, val: int, coval: float, err: bool) → None

C++: protocols::frags::heap_extract(class ObjexxFCL::FArray1A<int>, class ObjexxFCL::FArray1A<float>, int &, float &, bool &) –> void

pyrosetta.rosetta.protocols.frags.heap_init(heap: ObjexxFCL::FArray1A<int>, coheap: ObjexxFCL::FArray1A<float>, max_items: int) → None

C++: protocols::frags::heap_init(class ObjexxFCL::FArray1A<int>, class ObjexxFCL::FArray1A<float>, int) –> void

pyrosetta.rosetta.protocols.frags.heap_insert(heap: ObjexxFCL::FArray1A<int>, coheap: ObjexxFCL::FArray1A<float>, val: int, coval: float, err: bool) → None

C++: protocols::frags::heap_insert(class ObjexxFCL::FArray1A<int>, class ObjexxFCL::FArray1A<float>, int, float, bool &) –> void

pyrosetta.rosetta.protocols.frags.heap_replace(heap: ObjexxFCL::FArray1A<int>, coheap: ObjexxFCL::FArray1A<float>, val: int, coval: float) → None

C++: protocols::frags::heap_replace(class ObjexxFCL::FArray1A<int>, class ObjexxFCL::FArray1A<float>, int, float) –> void

pyrosetta.rosetta.protocols.frags.heap_up(heap: ObjexxFCL::FArray1A<int>, coheap: ObjexxFCL::FArray1A<float>, index_in: int) → None

C++: protocols::frags::heap_up(class ObjexxFCL::FArray1A<int>, class ObjexxFCL::FArray1A<float>, int &) –> void

pyrosetta.rosetta.protocols.frags.insert_fragment(*args, **kwargs)

Overloaded function.

1. insert_fragment(begin: int, end: int, pose: pyrosetta.rosetta.core.pose.Pose, lib: pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary) -> None
2. insert_fragment(begin: int, end: int, pose: pyrosetta.rosetta.core.pose.Pose, lib: pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary, desired_insert_pos: int) -> None

C++: protocols::frags::insert_fragment(const int, const int, class core::pose::Pose &, const class protocols::frags::TorsionFragmentLibrary &, const int) –> void

pyrosetta.rosetta.protocols.frags.insert_random_fragments_in_flexible_protein_regions(flex_protein: pyrosetta.rosetta.utility.vector1_unsigned_long, frag_lib: pyrosetta.rosetta.protocols.frags.FragLib, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::frags::insert_random_fragments_in_flexible_protein_regions(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class protocols::frags::FragLib &, class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.frags.setup_vall_cheating_fragments(*args, **kwargs)

Overloaded function.

1. setup_vall_cheating_fragments(frag_sizes: pyrosetta.rosetta.utility.vector1_unsigned_long, nfrags: int, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap, secstruct: str, seq_weight: float, ss_weight: float, torsion_weight: float, min_torsion_dev: float, max_torsion_dev: float) -> pyrosetta.rosetta.protocols.frags.FragLib
2. setup_vall_cheating_fragments(frag_sizes: pyrosetta.rosetta.utility.vector1_unsigned_long, nfrags: int, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap, secstruct: str, seq_weight: float, ss_weight: float, torsion_weight: float, min_torsion_dev: float, max_torsion_dev: float, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long) -> pyrosetta.rosetta.protocols.frags.FragLib

C++: protocols::frags::setup_vall_cheating_fragments(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const unsigned long, const class core::pose::Pose &, const class core::kinematics::MoveMap &, const class std::basic_string<char> &, const double, const double, const double, const double, const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> class std::shared_ptr<class protocols::frags::FragLib>

pyrosetta.rosetta.protocols.frags.setup_vall_fragments(*args, **kwargs)

Overloaded function.

1. setup_vall_fragments(frag_sizes: pyrosetta.rosetta.utility.vector1_unsigned_long, nfrags: int, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap, secstruct: str, seq_weight: float, ss_weight: float) -> pyrosetta.rosetta.protocols.frags.FragLib
2. setup_vall_fragments(frag_sizes: pyrosetta.rosetta.utility.vector1_unsigned_long, nfrags: int, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap, secstruct: str, seq_weight: float, ss_weight: float, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long) -> pyrosetta.rosetta.protocols.frags.FragLib

C++: protocols::frags::setup_vall_fragments(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const unsigned long, const class core::pose::Pose &, const class core::kinematics::MoveMap &, const class std::basic_string<char> &, const double, const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> class std::shared_ptr<class protocols::frags::FragLib>

pyrosetta.rosetta.protocols.frags.ss_length_check(min_len_helix: int, min_len_strand: int, pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::frags::ss_length_check(const unsigned long, const unsigned long, const class core::pose::Pose &) –> bool

pyrosetta.rosetta.protocols.frags.torsion2big_bin(phi: float, psi: float, omega: float) → str

C++: protocols::frags::torsion2big_bin(const double, const double, const double) –> char