sequence_comparation¶

Bindings for core::io::sequence_comparation namespace

class pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast¶

Bases: pybind11_builtins.pybind11_object

DesignContrast contains information for comparing the native protein sequence to designed protein sequence. And output the compare resultes to a special formated file which can be used for statistics calculations

__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.

__init__(self: pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast) -> None
__init__(self: pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast, arg0: pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast) -> 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.io.sequence_comparation.DesignContrast, : pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast) → pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast¶: C++: core::io::sequence_comparation::DesignContrast::operator=(const class core::io::sequence_comparation::DesignContrast &) –> class core::io::sequence_comparation::DesignContrast &

clear(self: pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast) → None¶

clear function to clear all datas in this class.

C++: core::io::sequence_comparation::DesignContrast::clear() –> void

getListNames(self: pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast) → pyrosetta.rosetta.utility.vector1_utility_file_FileName¶: C++: core::io::sequence_comparation::DesignContrast::getListNames() –> class utility::vector1<class utility::file::FileName, class std::allocator<class utility::file::FileName> > &

getNeighbors(self: pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast) → pyrosetta.rosetta.utility.vector1_int¶

Get number of neighbors for all residues in pose

C++: core::io::sequence_comparation::DesignContrast::getNeighbors() –> class utility::vector1<int, class std::allocator<int> > &

getPdbCodes(self: pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast) → pyrosetta.rosetta.utility.vector1_std_string¶: C++: core::io::sequence_comparation::DesignContrast::getPdbCodes() –> class utility::vector1<std::string, class std::allocator<std::string > > &

getPdbNames(self: pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast) → pyrosetta.rosetta.utility.vector1_utility_file_FileName¶: C++: core::io::sequence_comparation::DesignContrast::getPdbNames() –> class utility::vector1<class utility::file::FileName, class std::allocator<class utility::file::FileName> > &

getSecStruct(self: pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast) → pyrosetta.rosetta.utility.vector1_std_string¶

Get secondary structure for all residues in pose

C++: core::io::sequence_comparation::DesignContrast::getSecStruct() –> class utility::vector1<std::string, class std::allocator<std::string > > &

output_sqc_file(self: pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast, native_pose: pyrosetta.rosetta.core.pose.Pose, decoy_pose: pyrosetta.rosetta.core.pose.Pose, single_code: str, sqc: pyrosetta.rosetta.std.ofstream) → None¶

this function will output the sequence comparing result between native pose and designed pose

C++: core::io::sequence_comparation::DesignContrast::output_sqc_file(class core::pose::Pose &, class core::pose::Pose &, const class std::basic_string<char> &, class std::basic_ofstream<char> &) –> void

setNames(self: pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast) → None¶

Get pdb file names from the pdb list files.

C++: core::io::sequence_comparation::DesignContrast::setNames() –> void

setNeighbors(self: pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Set number of neighbors for all residues in pose

C++: core::io::sequence_comparation::DesignContrast::setNeighbors(class core::pose::Pose &) –> void

setPdbCodes(self: pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast) → None¶: C++: core::io::sequence_comparation::DesignContrast::setPdbCodes() –> void

setSecStruct(self: pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Set secondary structure for all residues in pose

C++: core::io::sequence_comparation::DesignContrast::setSecStruct(class core::pose::Pose &) –> void