enzymes

Bindings for core::enzymes namespace

class pyrosetta.rosetta.core.enzymes.ConsensusSequenceType

Bases: pybind11_object

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

Members:

AA

NA

SACCHARIDE

AA = <ConsensusSequenceType.AA: 1>

NA = <ConsensusSequenceType.NA: 2>

SACCHARIDE = <ConsensusSequenceType.SACCHARIDE: 3>

property name

property value

class pyrosetta.rosetta.core.enzymes.EnzymeData

Bases: pybind11_object

A structure for storing reaction information for specific virtual enzymes.

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 &

property atom_to_modify

property consensus_residues

property consensus_sequence

property cs_resnum

property cs_type

property efficiency

property second_substrates_or_byproducts

class pyrosetta.rosetta.core.enzymes.EnzymeManager

Bases: 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.

static 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 std::string &, const std::string &, const std::string &) –> 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 > > > > &

static 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 std::string &, const std::string &, const std::string &) –> const std::string &

static 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 std::string &, const std::string &, const std::string &) –> enum core::enzymes::ConsensusSequenceType

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

Return the efficiency of the requested enzyme.

C++: core::enzymes::EnzymeManager::get_efficiency(const std::string &, const std::string &, const std::string &) –> double

static get_instance() → core::enzymes::EnzymeManager

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

static 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 std::string &, const std::string &, const std::string &) –> const std::string &

static 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 std::string &, const std::string &, const std::string &) –> unsigned long

static 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 std::string &, const std::string &, const std::string &) –> const class utility::vector1<std::string, class std::allocator<std::string > > &

pyrosetta.rosetta.core.enzymes.get_3_letter_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 3-letter codes.

C++: core::enzymes::get_3_letter_codes_from_NA_consensus_sequence(const std::string &) –> 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_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 std::string &) –> 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 std::string &) –> 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 std::string &) –> struct core::enzymes::EnzymeData