basic¶

Bindings for ::basic namespace

class pyrosetta.rosetta.basic.Emitter¶

Bases: pybind11_builtins.pybind11_object

Lightweight class to ease writting YAML documents (http://yaml.org)

YAML is a structured data format, a more human-readable

alternative to XML.

I use the terms “map” and “list” here, but you may also see “mapping” and “sequence”. The former is a series of key : value pairs, while the latter is a simple series of items. This class is not entirely able to enforce the generation of valid YAML – you can still e.g. write a key : value pair in the middle of a list. It will print a warning message but will otherwise try to continue on.

YAML documents have optional explicit start/end markers; if the emitter supports them, they will be auto-generated when the class is initialized and when you’re finished and you call end().

Whitespace is YAML documents is semi-significant. By default, this class will try to pretty-print, showing the depth of nesting through indentation. When starting a new list or map, you can request that it not be indented (i.e., be printed all on one line), but all lists and maps nested inside it will also be printed without linebreaks, regardless of the requested indentation. YAML refers to these two styles as “block” and “flow”, respectively.

__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.basic.Emitter, out: pyrosetta.rosetta.std.ostream) → 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).

depth(self: pyrosetta.rosetta.basic.Emitter) → int¶

Number of closing brackets/braces required to end document (non-negative)

C++: basic::Emitter::depth() const –> int

end(*args, **kwargs)¶

Overloaded function.

end(self: pyrosetta.rosetta.basic.Emitter) -> None
end(self: pyrosetta.rosetta.basic.Emitter, desired_depth: int) -> None

By default, closes all open maps/lists, ending the document.

C++: basic::Emitter::end(unsigned long) –> void

end_list(self: pyrosetta.rosetta.basic.Emitter) → None¶

Counterpart to start_list() – writes closing bracket.

C++: basic::Emitter::end_list() –> void

end_map(self: pyrosetta.rosetta.basic.Emitter) → None¶

Counterpart to start_map() – writes closing brace.

C++: basic::Emitter::end_map() –> void

flush(self: pyrosetta.rosetta.basic.Emitter) → None¶

Flush the underlying output stream.

C++: basic::Emitter::flush() –> void

set_indent(self: pyrosetta.rosetta.basic.Emitter, num_spaces: int) → None¶

Number of spaces used for indenting. Default is one.

C++: basic::Emitter::set_indent(int) –> void

start_doc(self: pyrosetta.rosetta.basic.Emitter) → None¶

Start a new document, ending the previous one first if necessary.: A no-op for some types of output (e.g. JSON) that don’t allow multiple documents.

C++: basic::Emitter::start_doc() –> void

start_list(*args, **kwargs)¶

Overloaded function.

start_list(self: pyrosetta.rosetta.basic.Emitter) -> None
start_list(self: pyrosetta.rosetta.basic.Emitter, indent: bool) -> None

Write method for use inside lists / arrays

C++: basic::Emitter::start_list(bool) –> void

start_list(self: pyrosetta.rosetta.basic.Emitter, label: str) -> None
start_list(self: pyrosetta.rosetta.basic.Emitter, label: str, indent: bool) -> None

Write method for use inside maps / dicts / objects

C++: basic::Emitter::start_list(const class std::basic_string<char> &, bool) –> void

start_list(self: pyrosetta.rosetta.basic.Emitter, label: str) -> None
start_list(self: pyrosetta.rosetta.basic.Emitter, label: str, indent: bool) -> None

Write method for use inside maps / dicts / objects

C++: basic::Emitter::start_list(const char *, bool) –> void

start_map(*args, **kwargs)¶

Overloaded function.

start_map(self: pyrosetta.rosetta.basic.Emitter) -> None
start_map(self: pyrosetta.rosetta.basic.Emitter, indent: bool) -> None

Write method for use inside lists / arrays

C++: basic::Emitter::start_map(bool) –> void

start_map(self: pyrosetta.rosetta.basic.Emitter, label: str) -> None
start_map(self: pyrosetta.rosetta.basic.Emitter, label: str, indent: bool) -> None

Write method for use inside maps / dicts / objects

C++: basic::Emitter::start_map(const class std::basic_string<char> &, bool) –> void

start_map(self: pyrosetta.rosetta.basic.Emitter, label: str) -> None
start_map(self: pyrosetta.rosetta.basic.Emitter, label: str, indent: bool) -> None

Write method for use inside maps / dicts / objects

C++: basic::Emitter::start_map(const char *, bool) –> void

pyrosetta.rosetta.basic.Error(*args, **kwargs)¶

Overloaded function.

Error() -> pyrosetta.rosetta.basic.Tracer
Error(priority: pyrosetta.rosetta.basic.TracerPriority) -> pyrosetta.rosetta.basic.Tracer

Predefined Error tracer.

C++: basic::Error(enum basic::TracerPriority) –> class basic::Tracer &

class pyrosetta.rosetta.basic.ExecutionResult¶

Bases: pybind11_builtins.pybind11_object

Struct that hold result code + output of external process

__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.basic.ExecutionResult) -> None
__init__(self: pyrosetta.rosetta.basic.ExecutionResult, arg0: pyrosetta.rosetta.basic.ExecutionResult) -> 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.basic.ExecutionResult, : pyrosetta.rosetta.basic.ExecutionResult) → pyrosetta.rosetta.basic.ExecutionResult¶: C++: basic::ExecutionResult::operator=(const struct basic::ExecutionResult &) –> struct basic::ExecutionResult &

class pyrosetta.rosetta.basic.JsonEmitter¶

Bases: pyrosetta.rosetta.basic.Emitter

Lightweight class to ease writting JSON documents, a subset of YAML (http://json.org)

Using this class is not recommended – use YamlEmitter instead.

JSON is JavaScript Object Notation, the format for object and array literals in the JavaScript language. It also looks a great deal like nested Python dicts and lists, except for the special JSON values true, false, and null. (Python uses True, False, and None instead. Otherwise, JSON can be embedded directly into Python scripts.)

JSON is legal subset of YAML, but leaves out much of YAML’s complexity and advanced features. At the present time, there appears to be more library support for JSON than for YAML, especially for reading and parsing. (Both are fairly easy to write, as demonstrated here.)

The topmost level of every valid JSON document consists of exactly one map, which is automatically started for you when the class is initialized. When you’re finished you should call end(), and then probably flush().

Whitespace is JSON documents is not significant. By default, this class will try to pretty-print, showing the depth of nesting through indentation. When starting a new list or map, you can request that it not be indented (i.e., be printed all on one line), but all lists and maps nested inside it will also be printed without linebreaks, regardless of the requested indentation.

__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.basic.JsonEmitter, out: pyrosetta.rosetta.std.ostream) → 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).

depth(self: pyrosetta.rosetta.basic.Emitter) → int¶

Number of closing brackets/braces required to end document (non-negative)

C++: basic::Emitter::depth() const –> int

end(*args, **kwargs)¶

Overloaded function.

end(self: pyrosetta.rosetta.basic.Emitter) -> None
end(self: pyrosetta.rosetta.basic.Emitter, desired_depth: int) -> None

By default, closes all open maps/lists, ending the document.

C++: basic::Emitter::end(unsigned long) –> void

end_list(self: pyrosetta.rosetta.basic.Emitter) → None¶

Counterpart to start_list() – writes closing bracket.

C++: basic::Emitter::end_list() –> void

end_map(self: pyrosetta.rosetta.basic.Emitter) → None¶

Counterpart to start_map() – writes closing brace.

C++: basic::Emitter::end_map() –> void

flush(self: pyrosetta.rosetta.basic.Emitter) → None¶

Flush the underlying output stream.

C++: basic::Emitter::flush() –> void

set_indent(self: pyrosetta.rosetta.basic.Emitter, num_spaces: int) → None¶

Number of spaces used for indenting. Default is one.

C++: basic::Emitter::set_indent(int) –> void

start_doc(self: pyrosetta.rosetta.basic.JsonEmitter) → None¶

JSON doesn’t support multiple documents, so this just calls end(1): to return you to the top (least-nested) level.

C++: basic::JsonEmitter::start_doc() –> void

start_list(*args, **kwargs)¶

Overloaded function.

start_list(self: pyrosetta.rosetta.basic.Emitter) -> None
start_list(self: pyrosetta.rosetta.basic.Emitter, indent: bool) -> None

Write method for use inside lists / arrays

C++: basic::Emitter::start_list(bool) –> void

start_list(self: pyrosetta.rosetta.basic.Emitter, label: str) -> None
start_list(self: pyrosetta.rosetta.basic.Emitter, label: str, indent: bool) -> None

Write method for use inside maps / dicts / objects

C++: basic::Emitter::start_list(const class std::basic_string<char> &, bool) –> void

start_list(self: pyrosetta.rosetta.basic.Emitter, label: str) -> None
start_list(self: pyrosetta.rosetta.basic.Emitter, label: str, indent: bool) -> None

Write method for use inside maps / dicts / objects

C++: basic::Emitter::start_list(const char *, bool) –> void

start_map(*args, **kwargs)¶

Overloaded function.

start_map(self: pyrosetta.rosetta.basic.Emitter) -> None
start_map(self: pyrosetta.rosetta.basic.Emitter, indent: bool) -> None

Write method for use inside lists / arrays

C++: basic::Emitter::start_map(bool) –> void

start_map(self: pyrosetta.rosetta.basic.Emitter, label: str) -> None
start_map(self: pyrosetta.rosetta.basic.Emitter, label: str, indent: bool) -> None

Write method for use inside maps / dicts / objects

C++: basic::Emitter::start_map(const class std::basic_string<char> &, bool) –> void

start_map(self: pyrosetta.rosetta.basic.Emitter, label: str) -> None
start_map(self: pyrosetta.rosetta.basic.Emitter, label: str, indent: bool) -> None

Write method for use inside maps / dicts / objects

C++: basic::Emitter::start_map(const char *, bool) –> void

class pyrosetta.rosetta.basic.PyTracer¶

Bases: pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t

Special PyRosetta friendly Tracer like buffer. Use it to capture Tracer output with set_ios_hook

_M_write(self: pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t, __s: str, __n: int) → None¶: C++: std::basic_ostream<char, std::char_traits<char> >::_M_write(const char *, long) –> 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__(self: pyrosetta.rosetta.basic.PyTracer) → 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).

buf(*args, **kwargs)¶

Overloaded function.

buf(self: pyrosetta.rosetta.basic.PyTracer) -> str

C++: basic::PyTracer::buf() –> std::string

buf(self: pyrosetta.rosetta.basic.PyTracer, b: str) -> None

C++: basic::PyTracer::buf(class std::basic_string<char>) –> void

flush(self: pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t) → pyrosetta.rosetta.std.ostream¶: C++: std::basic_ostream<char, std::char_traits<char> >::flush() –> std::ostream &

is_flushed(self: pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t) → bool¶: C++: basic::basic_otstream<char, std::char_traits<char> >::is_flushed() const –> bool

output_callback(self: pyrosetta.rosetta.basic.PyTracer, : str) → None¶: C++: basic::PyTracer::output_callback(class std::basic_string<char>) –> void

put(self: pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t, __c: str) → pyrosetta.rosetta.std.ostream¶: C++: std::basic_ostream<char, std::char_traits<char> >::put(char) –> std::ostream &

seekp(self: pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t, : int, : pyrosetta.rosetta.std._Ios_Seekdir) → pyrosetta.rosetta.std.ostream¶: C++: std::basic_ostream<char, std::char_traits<char> >::seekp(long, enum std::_Ios_Seekdir) –> std::ostream &

write(self: pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t, __s: str, __n: int) → pyrosetta.rosetta.std.ostream¶: C++: std::basic_ostream<char, std::char_traits<char> >::write(const char *, long) –> std::ostream &

class pyrosetta.rosetta.basic.Report¶

Bases: pybind11_builtins.pybind11_object

Data class to hold Report information. Use Reporter class for write 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.

__init__(self: pyrosetta.rosetta.basic.Report, file_name: str) -> None
__init__(self: pyrosetta.rosetta.basic.Report, arg0: pyrosetta.rosetta.basic.Report) -> 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.basic.Report, : pyrosetta.rosetta.basic.Report) → pyrosetta.rosetta.basic.Report¶: C++: basic::Report::operator=(const class basic::Report &) –> class basic::Report &

write(self: pyrosetta.rosetta.basic.Report) → None¶: C++: basic::Report::write() –> void

class pyrosetta.rosetta.basic.Reporter¶

Bases: pybind11_builtins.pybind11_object

Proxy class to access Reporter class though OP. Allow null OP on init (all reporter function in this case do nothing)

__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.basic.Reporter) -> None

doc

__init__(self: pyrosetta.rosetta.basic.Reporter, report: pyrosetta.rosetta.basic.Report) -> None
__init__(self: pyrosetta.rosetta.basic.Reporter, arg0: pyrosetta.rosetta.basic.Reporter) -> 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.basic.Reporter, : pyrosetta.rosetta.basic.Reporter) → pyrosetta.rosetta.basic.Reporter¶: C++: basic::Reporter::operator=(const class basic::Reporter &) –> class basic::Reporter &

pyrosetta.rosetta.basic.T(: str, : pyrosetta.rosetta.basic.TracerPriority) → pyrosetta.rosetta.basic.Tracer¶

T is special function for assign tracer property on the static object.

C++: basic::T(const class std::basic_string<char> &, enum basic::TracerPriority) –> class basic::Tracer &

class pyrosetta.rosetta.basic.Tracer¶

Bases: pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t

Class for handling user debug/warnings/errors. Use instance of this class instead of ‘std::cout’ for all your regular io. Channel argument must be related to the location of the source file. For example if you create Tracer object in src/basic/scoring/myfile.cc,

then channel must be something like ‘src.basic.scoring.myfile’

_M_write(self: pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t, __s: str, __n: int) → None¶: C++: std::basic_ostream<char, std::char_traits<char> >::_M_write(const char *, long) –> void

__call__(self: pyrosetta.rosetta.basic.Tracer, priority: int) → pyrosetta.rosetta.basic.Tracer¶: C++: basic::Tracer::operator()(int) –> class basic::Tracer &

__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.basic.Tracer) -> None

doc

__init__(self: pyrosetta.rosetta.basic.Tracer, arg0: str) -> None

doc

__init__(self: pyrosetta.rosetta.basic.Tracer, arg0: str, arg1: pyrosetta.rosetta.basic.TracerPriority) -> None

doc

__init__(self: pyrosetta.rosetta.basic.Tracer, channel: str, priority: pyrosetta.rosetta.basic.TracerPriority, muted_by_default: bool) -> None
__init__(self: pyrosetta.rosetta.basic.Tracer, arg0: str, arg1: pyrosetta.rosetta.utility.CSI_Sequence) -> None

doc

__init__(self: pyrosetta.rosetta.basic.Tracer, arg0: str, arg1: pyrosetta.rosetta.utility.CSI_Sequence, arg2: pyrosetta.rosetta.utility.CSI_Sequence) -> None

doc

__init__(self: pyrosetta.rosetta.basic.Tracer, arg0: str, arg1: pyrosetta.rosetta.utility.CSI_Sequence, arg2: pyrosetta.rosetta.utility.CSI_Sequence, arg3: pyrosetta.rosetta.basic.TracerPriority) -> None

doc

__init__(self: pyrosetta.rosetta.basic.Tracer, channel: str, channel_color: pyrosetta.rosetta.utility.CSI_Sequence, channel_name_color: pyrosetta.rosetta.utility.CSI_Sequence, priority: pyrosetta.rosetta.basic.TracerPriority, muted_by_default: bool) -> 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).

calculate_tracer_visibilities() → None¶

This function should be invoked after the options system has been: initialized, so that the visibility for all tracers that have so far been constructed and have been waiting for the options system to be initialized can now have their visibility calculated. After this function completes, all newly-constructed Tracers will calculate their visibility in their constructors. Visibility is no longer be calculated on a just-in-time basis and stored in mutable data members.

C++: basic::Tracer::calculate_tracer_visibilities() –> void

channel(self: pyrosetta.rosetta.basic.Tracer) → str¶: C++: basic::Tracer::channel() const –> const std::string &

channel_color(*args, **kwargs)¶

Overloaded function.

channel_color(self: pyrosetta.rosetta.basic.Tracer) -> pyrosetta.rosetta.utility.CSI_Sequence

Get the channel color.

C++: basic::Tracer::channel_color() –> const class utility::CSI_Sequence &

channel_color(self: pyrosetta.rosetta.basic.Tracer, color: pyrosetta.rosetta.utility.CSI_Sequence) -> None

Set the channel color.

This can be done in a stream like this:

TR << TR.bgWhite << TR.Black << “Example” << TR.Reset << std::endl;

C++: basic::Tracer::channel_color(const class utility::CSI_Sequence &) –> void

channel_name_color(*args, **kwargs)¶

Overloaded function.

channel_name_color(self: pyrosetta.rosetta.basic.Tracer) -> pyrosetta.rosetta.utility.CSI_Sequence

C++: basic::Tracer::channel_name_color() –> const class utility::CSI_Sequence &

channel_name_color(self: pyrosetta.rosetta.basic.Tracer, color: pyrosetta.rosetta.utility.CSI_Sequence) -> None

C++: basic::Tracer::channel_name_color(const class utility::CSI_Sequence &) –> void

final_stream() → pyrosetta.rosetta.std.ostream¶

set ios hook for final tracer stream (deafult is std::cout).

C++: basic::Tracer::final_stream() –> std::ostream *&

flush(self: pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t) → pyrosetta.rosetta.std.ostream¶: C++: std::basic_ostream<char, std::char_traits<char> >::flush() –> std::ostream &

flush_all_channels(self: pyrosetta.rosetta.basic.Tracer) → None¶

flush tracer buffer and flush buffers of all: sub-channels ie: Fatal, Error, Warning, Info, Debug, Trace

C++: basic::Tracer::flush_all_channels() –> void

flush_all_tracers() → None¶: C++: basic::Tracer::flush_all_tracers() –> void

get_all_channels_string() → str¶: C++: basic::Tracer::get_all_channels_string() –> const std::string &

init(self: pyrosetta.rosetta.basic.Tracer, tr: pyrosetta.rosetta.basic.Tracer) → None¶

re-init using data from another tracer object.

C++: basic::Tracer::init(const class basic::Tracer &) –> void

is_flushed(self: pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t) → bool¶: C++: basic::basic_otstream<char, std::char_traits<char> >::is_flushed() const –> bool

output_prefix(*args, **kwargs)¶

Overloaded function.

output_prefix(: str) -> None

set/get globale string-prefix for all Tracer output strings

C++: basic::Tracer::output_prefix(const class std::basic_string<char> &) –> void

output_prefix() -> str

C++: basic::Tracer::output_prefix() –> std::string

priority(*args, **kwargs)¶

Overloaded function.

priority(self: pyrosetta.rosetta.basic.Tracer) -> int

get/set tracer priority level.

C++: basic::Tracer::priority() const –> int

priority(self: pyrosetta.rosetta.basic.Tracer, priority: int) -> None

C++: basic::Tracer::priority(int) –> void

put(self: pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t, __c: str) → pyrosetta.rosetta.std.ostream¶: C++: std::basic_ostream<char, std::char_traits<char> >::put(char) –> std::ostream &

seekp(self: pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t, : int, : pyrosetta.rosetta.std._Ios_Seekdir) → pyrosetta.rosetta.std.ostream¶: C++: std::basic_ostream<char, std::char_traits<char> >::seekp(long, enum std::_Ios_Seekdir) –> std::ostream &

set_default_final_stream() → None¶: C++: basic::Tracer::set_default_final_stream() –> void

set_ios_hook(*args, **kwargs)¶

Overloaded function.

set_ios_hook(tr: pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t, monitoring_channels_list: str) -> None
set_ios_hook(tr: pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t, monitoring_channels_list: str, raw: bool) -> None

C++: basic::Tracer::set_ios_hook(class std::shared_ptr<class basic::basic_otstream<char, struct std::char_traits<char> > >, const class std::basic_string<char> &, bool) –> void

set_new_final_stream(new_final_stream: pyrosetta.rosetta.std.ostream) → None¶: C++: basic::Tracer::set_new_final_stream(class std::basic_ostream<char> *) –> void

super_mute(*args, **kwargs)¶

Overloaded function.

super_mute() -> bool

global super mute flag that allow to mute all io no matter what.

C++: basic::Tracer::super_mute() –> bool

super_mute(f: bool) -> None

C++: basic::Tracer::super_mute(bool) –> void

tracer_options() → pyrosetta.rosetta.basic.TracerOptions¶

get/set tracer options - global options for Tracer IO.

C++: basic::Tracer::tracer_options() –> struct basic::TracerOptions &

visible(*args, **kwargs)¶

Overloaded function.

visible(self: pyrosetta.rosetta.basic.Tracer) -> bool

Is this tracer currently visible?.

C++: basic::Tracer::visible() const –> bool

visible(self: pyrosetta.rosetta.basic.Tracer, priority: int) -> bool

is this tracer visible, if it used the given priority value?

C++: basic::Tracer::visible(int) const –> bool

write(self: pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t, __s: str, __n: int) → pyrosetta.rosetta.std.ostream¶: C++: std::basic_ostream<char, std::char_traits<char> >::write(const char *, long) –> std::ostream &

class pyrosetta.rosetta.basic.TracerManager¶

Bases: pyrosetta.rosetta.utility.SingletonBase_basic_TracerManager_t

Simple singleton class to hold the all_tracers_ array, which otherwise suffers from funky double-construction problems when declared as a static data member of Tracer.

__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).

all_tracers(self: pyrosetta.rosetta.basic.TracerManager) → pyrosetta.rosetta.std.vector_basic_Tracer_*¶: C++: basic::TracerManager::all_tracers() –> class std::vector<class basic::Tracer *, class std::allocator<class basic::Tracer *> > &

get_instance() → basic::TracerManager¶: C++: utility::SingletonBase<basic::TracerManager>::get_instance() –> class basic::TracerManager *

class pyrosetta.rosetta.basic.TracerOptions¶

Bases: pybind11_builtins.pybind11_object

data structure to store all system level options for Tracer system.

__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.basic.TracerOptions) → 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).

class pyrosetta.rosetta.basic.TracerPriority¶

Bases: pybind11_builtins.pybind11_object

Priority levels for T() and Tracer object, modeled on the log4j project and its offspring. Priorities in Tracer are still ints so users can pass other arbitrary integer values (for now).

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__(*args, **kwargs)¶

Overloaded function.

__eq__(self: pyrosetta.rosetta.basic.TracerPriority, arg0: pyrosetta.rosetta.basic.TracerPriority) -> bool
__eq__(self: pyrosetta.rosetta.basic.TracerPriority, arg0: int) -> bool

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__getstate__(self: pyrosetta.rosetta.basic.TracerPriority) → tuple¶

__gt__¶: Return self>value.

__hash__(self: pyrosetta.rosetta.basic.TracerPriority) → int¶

__init__(self: pyrosetta.rosetta.basic.TracerPriority, 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.basic.TracerPriority) → int¶

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__(*args, **kwargs)¶

Overloaded function.

__ne__(self: pyrosetta.rosetta.basic.TracerPriority, arg0: pyrosetta.rosetta.basic.TracerPriority) -> bool
__ne__(self: pyrosetta.rosetta.basic.TracerPriority, 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.basic.TracerPriority) → str¶

__setattr__¶: Implement setattr(self, name, value).

__setstate__(self: pyrosetta.rosetta.basic.TracerPriority, 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).

pyrosetta.rosetta.basic.Warning(*args, **kwargs)¶

Overloaded function.

Warning() -> pyrosetta.rosetta.basic.Tracer
Warning(priority: pyrosetta.rosetta.basic.TracerPriority) -> pyrosetta.rosetta.basic.Tracer

Predefined Warning tracer.

C++: basic::Warning(enum basic::TracerPriority) –> class basic::Tracer &

class pyrosetta.rosetta.basic.YamlEmitter¶

Bases: pyrosetta.rosetta.basic.Emitter

Emitter for more classically formatted YAML

__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.basic.YamlEmitter, out: pyrosetta.rosetta.std.ostream) → 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).

depth(self: pyrosetta.rosetta.basic.Emitter) → int¶

Number of closing brackets/braces required to end document (non-negative)

C++: basic::Emitter::depth() const –> int

end(*args, **kwargs)¶

Overloaded function.

end(self: pyrosetta.rosetta.basic.Emitter) -> None
end(self: pyrosetta.rosetta.basic.Emitter, desired_depth: int) -> None

By default, closes all open maps/lists, ending the document.

C++: basic::Emitter::end(unsigned long) –> void

end_list(self: pyrosetta.rosetta.basic.Emitter) → None¶

Counterpart to start_list() – writes closing bracket.

C++: basic::Emitter::end_list() –> void

end_map(self: pyrosetta.rosetta.basic.Emitter) → None¶

Counterpart to start_map() – writes closing brace.

C++: basic::Emitter::end_map() –> void

flush(self: pyrosetta.rosetta.basic.Emitter) → None¶

Flush the underlying output stream.

C++: basic::Emitter::flush() –> void

set_indent(self: pyrosetta.rosetta.basic.Emitter, num_spaces: int) → None¶

Number of spaces used for indenting. Default is one.

C++: basic::Emitter::set_indent(int) –> void

start_doc(self: pyrosetta.rosetta.basic.YamlEmitter) → None¶

Start a new YAML document, ending the previous one first if necessary

C++: basic::YamlEmitter::start_doc() –> void

start_list(*args, **kwargs)¶

Overloaded function.

start_list(self: pyrosetta.rosetta.basic.Emitter) -> None
start_list(self: pyrosetta.rosetta.basic.Emitter, indent: bool) -> None

Write method for use inside lists / arrays

C++: basic::Emitter::start_list(bool) –> void

start_list(self: pyrosetta.rosetta.basic.Emitter, label: str) -> None
start_list(self: pyrosetta.rosetta.basic.Emitter, label: str, indent: bool) -> None

Write method for use inside maps / dicts / objects

C++: basic::Emitter::start_list(const class std::basic_string<char> &, bool) –> void

start_list(self: pyrosetta.rosetta.basic.Emitter, label: str) -> None
start_list(self: pyrosetta.rosetta.basic.Emitter, label: str, indent: bool) -> None

Write method for use inside maps / dicts / objects

C++: basic::Emitter::start_list(const char *, bool) –> void

start_map(*args, **kwargs)¶

Overloaded function.

start_map(self: pyrosetta.rosetta.basic.Emitter) -> None
start_map(self: pyrosetta.rosetta.basic.Emitter, indent: bool) -> None

Write method for use inside lists / arrays

C++: basic::Emitter::start_map(bool) –> void

start_map(self: pyrosetta.rosetta.basic.Emitter, label: str) -> None
start_map(self: pyrosetta.rosetta.basic.Emitter, label: str, indent: bool) -> None

Write method for use inside maps / dicts / objects

C++: basic::Emitter::start_map(const class std::basic_string<char> &, bool) –> void

start_map(self: pyrosetta.rosetta.basic.Emitter, label: str) -> None
start_map(self: pyrosetta.rosetta.basic.Emitter, label: str, indent: bool) -> None

Write method for use inside maps / dicts / objects

C++: basic::Emitter::start_map(const char *, bool) –> void

pyrosetta.rosetta.basic.angle_in_range(ang: float) → None¶

taken from wobble.cc

C++: basic::angle_in_range(double &) –> void

pyrosetta.rosetta.basic.calc_quadratic(a: float, b: float, c: float, n1: float, n2: float) → None¶: C++: basic::calc_quadratic(double, double, double, double &, double &) –> void

pyrosetta.rosetta.basic.execute(*args, **kwargs)¶

Overloaded function.

execute(message: str, command_line: str) -> pyrosetta.rosetta.basic.ExecutionResult
execute(message: str, command_line: str, terminate_on_failure: bool) -> pyrosetta.rosetta.basic.ExecutionResult
execute(message: str, command_line: str, terminate_on_failure: bool, silent: bool) -> pyrosetta.rosetta.basic.ExecutionResult

excute provided command_line though shell and return exit_code and output

C++: basic::execute(const class std::basic_string<char> &, const class std::basic_string<char> &, bool, bool) –> struct basic::ExecutionResult

pyrosetta.rosetta.basic.get_pymol_chain(i: int) → str¶: C++: basic::get_pymol_chain(unsigned long) –> char

pyrosetta.rosetta.basic.get_pymol_chain_index_1(c: str) → int¶: C++: basic::get_pymol_chain_index_1(char) –> unsigned long

pyrosetta.rosetta.basic.get_pymol_num_unique_ids() → int¶: C++: basic::get_pymol_num_unique_ids() –> unsigned long

pyrosetta.rosetta.basic.get_usage_from_procfilesystem(mem_report: pyrosetta.rosetta.std.ostream) → None¶: C++: basic::get_usage_from_procfilesystem(class std::basic_ostream<char> &) –> void

pyrosetta.rosetta.basic.handles_metric_value(metric_value: pyrosetta.rosetta.basic.MetricValueBase) → bool¶

check whether a MetricValue can be written to or read from a stream

C++: basic::handles_metric_value(const class basic::MetricValueBase &) –> bool

pyrosetta.rosetta.basic.init() → None¶

set global ‘init_was_called’ to true

C++: basic::init() –> void

pyrosetta.rosetta.basic.interpolate_2d_func_of_angles(x: float, y: float, xy_func: ObjexxFCL::FArray2A<double>, val: float, dval_dx: float, dval_dy: float) → None¶: C++: basic::interpolate_2d_func_of_angles(const double, const double, class ObjexxFCL::FArray2A<double>, double &, double &, double &) –> void

pyrosetta.rosetta.basic.interpolate_bilinear(xbin: int, xbin_next: int, xd: float, ybin: int, ybin_next: int, yd: float, xy_func: ObjexxFCL::FArray2A<double>, xbin_count: int, ybin_count: int, binrange: float, angles: bool, val: float, dval_dx: float, dval_dy: float) → None¶: C++: basic::interpolate_bilinear(const int, const int, const double, const int, const int, const double, class ObjexxFCL::FArray2A<double>, const int, const int, const double, const bool, double &, double &, double &) –> void

pyrosetta.rosetta.basic.interpolate_bilinear_by_value(x0y0: float, x1y0: float, x0y1: float, x1y1: float, xd: float, yd: float, binrange: float, angles: bool, val: float, dval_dx: float, dval_dy: float) → None¶: C++: basic::interpolate_bilinear_by_value(const double, const double, const double, const double, const double, const double, const double, const bool, double &, double &, double &) –> void

pyrosetta.rosetta.basic.interpolate_get_angle_bins(x: float, binrange: float, xbin: int, xbin_next: int, xd: float) → None¶: C++: basic::interpolate_get_angle_bins(const double, const double, int &, int &, double &) –> void

pyrosetta.rosetta.basic.interpolate_trilinear(xbin: int, xbin_next: int, xd: float, ybin: int, ybin_next: int, yd: float, zbin: int, zbin_next: int, zd: float, xyz_func: ObjexxFCL::FArray3A<double>, xbin_count: int, ybin_count: int, zbin_count: int, binrange: float, angles: bool, val: float, dval_dx: float, dval_dy: float, dval_dz: float) → None¶: C++: basic::interpolate_trilinear(const int, const int, const double, const int, const int, const double, const int, const int, const double, class ObjexxFCL::FArray3A<double>, const int, const int, const int, const double, const bool, double &, double &, double &, double &) –> void

pyrosetta.rosetta.basic.interpolate_trilinear_by_value(x0y0z0: float, x1y0z0: float, x0y1z0: float, x1y1z0: float, x0y0z1: float, x1y0z1: float, x0y1z1: float, x1y1z1: float, xd: float, yd: float, zd: float, binrange: float, angles: bool, val: float, dval_dx: float, dval_dy: float, dval_dz: float) → None¶: C++: basic::interpolate_trilinear_by_value(const double, const double, const double, const double, const double, const double, const double, const double, const double, const double, const double, const double, const bool, double &, double &, double &, double &) –> void

pyrosetta.rosetta.basic.periodic_range(a: float, x: float) → float¶: C++: basic::periodic_range(double, double) –> double

pyrosetta.rosetta.basic.prof_reset() → None¶: C++: basic::prof_reset() –> void

pyrosetta.rosetta.basic.prof_show() → None¶: C++: basic::prof_show() –> void

pyrosetta.rosetta.basic.prof_start_function_body(tag: pyrosetta.rosetta.basic.ProfTag) → None¶: C++: basic::prof_start_function_body(const enum basic::ProfTag) –> void

pyrosetta.rosetta.basic.prof_stop_function_body(tag: pyrosetta.rosetta.basic.ProfTag) → None¶: C++: basic::prof_stop_function_body(const enum basic::ProfTag) –> void

pyrosetta.rosetta.basic.read_metric_value(*args, **kwargs)¶

Overloaded function.

read_metric_value(is: pyrosetta.rosetta.std.istream, metric_value: pyrosetta.rosetta.basic.MetricValueBase) -> bool

read a MetricValue from a stream, returns true if successful

C++: basic::read_metric_value(class std::basic_istream<char> &, class basic::MetricValueBase &) –> bool

read_metric_value(is: pyrosetta.rosetta.std.istream) -> pyrosetta.rosetta.basic.MetricValueBase

read a MetricValue from a stream, returns NULL if unsuccessful

C++: basic::read_metric_value(class std::basic_istream<char> &) –> class std::shared_ptr<class basic::MetricValueBase>

pyrosetta.rosetta.basic.show_time(tr: pyrosetta.rosetta.basic.Tracer, msg: str) → None¶: C++: basic::show_time(class basic::Tracer &, const class std::basic_string<char> &) –> void

pyrosetta.rosetta.basic.subtract_degree_angles(a: float, b: float) → float¶: C++: basic::subtract_degree_angles(double, double) –> double

pyrosetta.rosetta.basic.subtract_radian_angles(a: float, b: float) → float¶: C++: basic::subtract_radian_angles(double, double) –> double

pyrosetta.rosetta.basic.unsigned_periodic_range(a: float, x: float) → float¶

a is restricted to [0.,x), assuming that a=a+n*x,, n=any integer

C++: basic::unsigned_periodic_range(double, double) –> double

pyrosetta.rosetta.basic.was_init_called() → bool¶

return true if core::init was already called and false otherwise

C++: basic::was_init_called() –> bool

pyrosetta.rosetta.basic.write_metric_value(os: pyrosetta.rosetta.std.ostream, metric_value: pyrosetta.rosetta.basic.MetricValueBase) → bool¶

write a MetricValue to a stream, returns true if successful

This function currently supports some of the most often used MetricValues. The type is always encoded in the output so that an object of the same class can be generated during reading. The supported types and their formats is as follows:

double double <num> int Int <num> std::size_t std::size_t <num> bool Bool <0 or 1> utility::vector1<double> Real[ <num1> <num2> … ] utility::vector1<int> Int[ <num1> <num2> … ] utility::vector1<size_t> size_t[ <num1> <num2> … ] utility::vector1<bool> Bool[ <bool1> <bool2> … ]

C++: basic::write_metric_value(class std::basic_ostream<char> &, const class basic::MetricValueBase &) –> bool