enzymes

Bindings for core::enzymes namespace

class pyrosetta.rosetta.core.enzymes.ConsensusSequenceType

Bases: pybind11_builtins.pybind11_object

The type of consensus sequence stored in an instance of EnzymeData.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(*args, **kwargs)

Overloaded function.

1. __eq__(self: pyrosetta.rosetta.core.enzymes.ConsensusSequenceType, arg0: pyrosetta.rosetta.core.enzymes.ConsensusSequenceType) -> bool
2. __eq__(self: pyrosetta.rosetta.core.enzymes.ConsensusSequenceType, arg0: int) -> bool

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getstate__(self: pyrosetta.rosetta.core.enzymes.ConsensusSequenceType) → tuple

__gt__

Return self>value.

__hash__(self: pyrosetta.rosetta.core.enzymes.ConsensusSequenceType) → int

__init__(self: pyrosetta.rosetta.core.enzymes.ConsensusSequenceType, arg0: int) → None

__init_subclass__()

This method is called when a class is subclassed.

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

__int__(self: pyrosetta.rosetta.core.enzymes.ConsensusSequenceType) → int

__le__

Return self<=value.

__lt__

Return self<value.

__ne__(*args, **kwargs)

Overloaded function.

1. __ne__(self: pyrosetta.rosetta.core.enzymes.ConsensusSequenceType, arg0: pyrosetta.rosetta.core.enzymes.ConsensusSequenceType) -> bool
2. __ne__(self: pyrosetta.rosetta.core.enzymes.ConsensusSequenceType, arg0: int) -> bool

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__(self: pyrosetta.rosetta.core.enzymes.ConsensusSequenceType) → str

__setattr__

Implement setattr(self, name, value).

__setstate__(self: pyrosetta.rosetta.core.enzymes.ConsensusSequenceType, arg0: tuple) → None

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

class pyrosetta.rosetta.core.enzymes.EnzymeData

Bases: pybind11_builtins.pybind11_object

A structure for storing reaction information for specific virtual enzymes.

__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.core.enzymes.EnzymeData) -> None
2. __init__(self: pyrosetta.rosetta.core.enzymes.EnzymeData, arg0: pyrosetta.rosetta.core.enzymes.EnzymeData) -> None

__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.core.enzymes.EnzymeData, : pyrosetta.rosetta.core.enzymes.EnzymeData) → pyrosetta.rosetta.core.enzymes.EnzymeData

C++: core::enzymes::EnzymeData::operator=(const struct core::enzymes::EnzymeData &) –> struct core::enzymes::EnzymeData &

class pyrosetta.rosetta.core.enzymes.EnzymeManager

Bases: pyrosetta.rosetta.utility.SingletonBase_core_enzymes_EnzymeManager_t

This class is a singleton and manages enzyme data that should only be read from the database one time as needed and shared among all instances of EnzymeMovers.

__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__

Initialize self. See help(type(self)) for accurate signature.

__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).

get_consensus_residues(family: str, species: str, enzyme: str) → pyrosetta.rosetta.utility.vector1_utility_vector1_std_string_std_allocator_std_string_t

Return the identifiers (such as 3-letter codes) of the residues of the consensus sequence.

C++: core::enzymes::EnzymeManager::get_consensus_residues(const class std::basic_string<char> &, const class std::basic_string<char> &, const class std::basic_string<char> &) –> const class utility::vector1<class utility::vector1<std::string, class std::allocator<std::string > >, class std::allocator<class utility::vector1<std::string, class std::allocator<std::string > > > > &

get_consensus_sequence(family: str, species: str, enzyme: str) → str

Return the consensus sequence of the requested enzyme.

C++: core::enzymes::EnzymeManager::get_consensus_sequence(const class std::basic_string<char> &, const class std::basic_string<char> &, const class std::basic_string<char> &) –> const std::string &

get_consensus_sequence_type(family: str, species: str, enzyme: str) → pyrosetta.rosetta.core.enzymes.ConsensusSequenceType

Return the consensus sequence type of the requested enzyme.

C++: core::enzymes::EnzymeManager::get_consensus_sequence_type(const class std::basic_string<char> &, const class std::basic_string<char> &, const class std::basic_string<char> &) –> enum core::enzymes::ConsensusSequenceType

get_efficiency(family: str, species: str, enzyme: str) → float

Return the efficiency of the requested enzyme.

C++: core::enzymes::EnzymeManager::get_efficiency(const class std::basic_string<char> &, const class std::basic_string<char> &, const class std::basic_string<char> &) –> double

get_instance() → core::enzymes::EnzymeManager

C++: utility::SingletonBase<core::enzymes::EnzymeManager>::get_instance() –> class core::enzymes::EnzymeManager *

get_reactive_atom(family: str, species: str, enzyme: str) → str

Return the name of the reactive site atom.

C++: core::enzymes::EnzymeManager::get_reactive_atom(const class std::basic_string<char> &, const class std::basic_string<char> &, const class std::basic_string<char> &) –> const std::string &

get_reactive_residue_consensus_sequence_position(family: str, species: str, enzyme: str) → int

Return the position in the consensus sequence of the reactive residue.

C++: core::enzymes::EnzymeManager::get_reactive_residue_consensus_sequence_position(const class std::basic_string<char> &, const class std::basic_string<char> &, const class std::basic_string<char> &) –> unsigned long

get_second_substrates_or_byproducts(family: str, species: str, enzyme: str) → pyrosetta.rosetta.utility.vector1_std_string

Return the second substrates or byproducts of the requested enzyme.

C++: core::enzymes::EnzymeManager::get_second_substrates_or_byproducts(const class std::basic_string<char> &, const class std::basic_string<char> &, const class std::basic_string<char> &) –> const class utility::vector1<std::string, class std::allocator<std::string > > &

pyrosetta.rosetta.core.enzymes.get_3_letter_codes_from_peptide_consensus_sequence(sequence: str) → pyrosetta.rosetta.utility.vector1_utility_vector1_std_string_std_allocator_std_string_t

Parse a peptide consensus sequence and return a list of AA residue 3-letter codes.

C++: core::enzymes::get_3_letter_codes_from_peptide_consensus_sequence(const class std::basic_string<char> &) –> class utility::vector1<class utility::vector1<std::string, class std::allocator<std::string > >, class std::allocator<class utility::vector1<std::string, class std::allocator<std::string > > > >

pyrosetta.rosetta.core.enzymes.get_codes_from_NA_consensus_sequence(sequence: str) → pyrosetta.rosetta.utility.vector1_utility_vector1_std_string_std_allocator_std_string_t

Parse a nucleic acid consensus sequence and return a list of NA residue codes.

C++: core::enzymes::get_codes_from_NA_consensus_sequence(const class std::basic_string<char> &) –> class utility::vector1<class utility::vector1<std::string, class std::allocator<std::string > >, class std::allocator<class utility::vector1<std::string, class std::allocator<std::string > > > >

pyrosetta.rosetta.core.enzymes.get_codes_from_saccharide_consensus_sequence(sequence: str) → pyrosetta.rosetta.utility.vector1_utility_vector1_std_string_std_allocator_std_string_t

Parse a saccharide consensus sequence and return a list of monosaccharide residue codes.

C++: core::enzymes::get_codes_from_saccharide_consensus_sequence(const class std::basic_string<char> &) –> class utility::vector1<class utility::vector1<std::string, class std::allocator<std::string > >, class std::allocator<class utility::vector1<std::string, class std::allocator<std::string > > > >

pyrosetta.rosetta.core.enzymes.read_enzyme_data_from_file(filename: str) → pyrosetta.rosetta.core.enzymes.EnzymeData

C++: core::enzymes::read_enzyme_data_from_file(const class std::basic_string<char> &) –> struct core::enzymes::EnzymeData