basic

Bindings for ::basic namespace

class pyrosetta.rosetta.basic.ComparingTracer

Bases: pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t

_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

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

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(*args, **kwargs)

Overloaded function.

  1. seekp(self: pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t, : pyrosetta.rosetta.std.fpos___mbstate_t_t) -> pyrosetta.rosetta.std.ostream

C++: std::basic_ostream<char, std::char_traits<char> >::seekp(class std::fpos<__mbstate_t>) –> std::ostream &

  1. 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 &

class sentry

Bases: pybind11_builtins.pybind11_object

tellp(self: pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t) pyrosetta.rosetta.std.fpos___mbstate_t_t

C++: std::basic_ostream<char, std::char_traits<char> >::tellp() –> class std::fpos<__mbstate_t>

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.DynamicProfileThis

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.basic.DynamicProfileThis, : pyrosetta.rosetta.basic.DynamicProfileThis) pyrosetta.rosetta.basic.DynamicProfileThis

C++: basic::DynamicProfileThis::operator=(const class basic::DynamicProfileThis &) –> class basic::DynamicProfileThis &

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.

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.

  1. end(self: pyrosetta.rosetta.basic.Emitter) -> None

  2. 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.

  1. start_list(self: pyrosetta.rosetta.basic.Emitter) -> None

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

Write method for use inside lists / arrays

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

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

  2. 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 std::string &, bool) –> void

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

  2. 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.

  1. start_map(self: pyrosetta.rosetta.basic.Emitter) -> None

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

Write method for use inside lists / arrays

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

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

  2. 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 std::string &, bool) –> void

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

  2. 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() basic::Tracer

Predefined Error-level tracer, for use in headers

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

class pyrosetta.rosetta.basic.ExecutionResult

Bases: pybind11_builtins.pybind11_object

Struct that hold result code + output of external process

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 &

property output
property result
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.

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.

  1. end(self: pyrosetta.rosetta.basic.Emitter) -> None

  2. 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.

  1. start_list(self: pyrosetta.rosetta.basic.Emitter) -> None

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

Write method for use inside lists / arrays

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

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

  2. 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 std::string &, bool) –> void

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

  2. 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.

  1. start_map(self: pyrosetta.rosetta.basic.Emitter) -> None

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

Write method for use inside lists / arrays

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

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

  2. 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 std::string &, bool) –> void

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

  2. 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.MemTracer

Bases: pyrosetta.rosetta.basic.Tracer

class TracerProxy

Bases: pybind11_builtins.pybind11_object

/ The priority proxy objects

flush(self: pyrosetta.rosetta.basic.Tracer.TracerProxy) None

C++: basic::Tracer::TracerProxy::flush() –> void

visible(self: pyrosetta.rosetta.basic.Tracer.TracerProxy) bool

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

channel(self: pyrosetta.rosetta.basic.Tracer) str

C++: basic::Tracer::channel() –> const std::string &

flags(*args, **kwargs)

Overloaded function.

  1. flags(self: pyrosetta.rosetta.basic.Tracer) -> pyrosetta.rosetta.std._Ios_Fmtflags

C++: basic::Tracer::flags() –> enum std::_Ios_Fmtflags

  1. flags(self: pyrosetta.rosetta.basic.Tracer, fmtfl: pyrosetta.rosetta.std._Ios_Fmtflags) -> pyrosetta.rosetta.std._Ios_Fmtflags

C++: basic::Tracer::flags(enum std::_Ios_Fmtflags) –> enum std::_Ios_Fmtflags

flush(self: pyrosetta.rosetta.basic.Tracer) None

C++: basic::Tracer::flush() –> void

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

static get_all_channels_string() str

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

get_local_print_channel_name(self: pyrosetta.rosetta.basic.Tracer) bool

Get whether we’re printing the channel name.

This looks at the local setting, but does not check the global setting.

In practice, if the local setting is true then the global setting is used. If the local setting is false, it overrides the global setting.

Vikram K. Mulligan (vmulligan.org)

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

precision(*args, **kwargs)

Overloaded function.

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

C++: basic::Tracer::precision() –> long

  1. precision(self: pyrosetta.rosetta.basic.Tracer, prec: int) -> int

C++: basic::Tracer::precision(long) –> long

static set_ios_hook(*args, **kwargs)

Overloaded function.

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

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

TODO: See if we can kill any usage of this, except for the esoteric

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

set_local_print_channel_name(self: pyrosetta.rosetta.basic.Tracer, setting: bool) None

Set whether we’re printing the channel name.

This overrides the local setting, but does not alter the global setting.

In practice, if the local setting is true then the global setting is used. If the local setting is false, it overrides the global setting.

Vikram K. Mulligan (vmulligan.org)

C++: basic::Tracer::set_local_print_channel_name(const bool) –> void

static super_mute(*args, **kwargs)

Overloaded function.

  1. super_mute() -> bool

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

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

  1. super_mute(f: bool) -> None

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

visible(*args, **kwargs)

Overloaded function.

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

C++: basic::Tracer::visible() –> bool

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

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

width(*args, **kwargs)

Overloaded function.

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

/ The IOS manipulators

C++: basic::Tracer::width() –> long

  1. width(self: pyrosetta.rosetta.basic.Tracer, wide: int) -> int

C++: basic::Tracer::width(long) –> long

class pyrosetta.rosetta.basic.MemTracerImpl

Bases: pyrosetta.rosetta.basic.TracerImpl

class TracerProxyImpl

Bases: pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t

Inner Classes

Small inner class acting as a proxy to an object that hold it.

_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

calculate_visibility(self: pyrosetta.rosetta.basic.TracerImpl.TracerProxyImpl) None

determine the visibility of the proxy.

C++: basic::TracerImpl::TracerProxyImpl::calculate_visibility() –> 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

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(*args, **kwargs)

Overloaded function.

  1. seekp(self: pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t, : pyrosetta.rosetta.std.fpos___mbstate_t_t) -> pyrosetta.rosetta.std.ostream

C++: std::basic_ostream<char, std::char_traits<char> >::seekp(class std::fpos<__mbstate_t>) –> std::ostream &

  1. 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 &

class sentry

Bases: pybind11_builtins.pybind11_object

tellp(self: pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t) pyrosetta.rosetta.std.fpos___mbstate_t_t

C++: std::basic_ostream<char, std::char_traits<char> >::tellp() –> class std::fpos<__mbstate_t>

visible(self: pyrosetta.rosetta.basic.TracerImpl.TracerProxyImpl) bool

Is the output from this TracerProxy visible?

C++: basic::TracerImpl::TracerProxyImpl::visible() –> 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 &

_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

channel(self: pyrosetta.rosetta.basic.TracerImpl) str

C++: basic::TracerImpl::channel() const –> const std::string &

channel_color(*args, **kwargs)

Overloaded function.

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

Get the channel color.

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

  1. channel_color(self: pyrosetta.rosetta.basic.TracerImpl, 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::TracerImpl::channel_color(const class utility::CSI_Sequence &) –> void

channel_name_color(*args, **kwargs)

Overloaded function.

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

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

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

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

flush_all_channels(self: pyrosetta.rosetta.basic.TracerImpl) None
flush tracer buffer and flush buffers of all

sub-channels ie: Fatal, Error, Warning, Info, Debug, Trace

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

static get_all_channels_string() str

C++: basic::TracerImpl::get_all_channels_string() –> const std::string &

get_local_print_channel_name(self: pyrosetta.rosetta.basic.TracerImpl) bool

Get whether we’re printing the channel name.

This gets the local setting, but does not look at the global setting. (In practice, if the local setting is true then the global setting is used.)

Vikram K. Mulligan (vmulligan.org)

C++: basic::TracerImpl::get_local_print_channel_name() const –> bool

get_proxy_by_priority(self: pyrosetta.rosetta.basic.TracerImpl, priority: pyrosetta.rosetta.basic.TracerPriority) basic::TracerImpl::TracerProxyImpl

C++: basic::TracerImpl::get_proxy_by_priority(enum basic::TracerPriority) –> class basic::TracerImpl::TracerProxyImpl &

init(self: pyrosetta.rosetta.basic.TracerImpl, tr: pyrosetta.rosetta.basic.TracerImpl) None

re-init using data from another tracer object.

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

static output_prefix(*args, **kwargs)

Overloaded function.

  1. output_prefix(: str) -> None

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

C++: basic::TracerImpl::output_prefix(const std::string &) –> void

  1. output_prefix() -> str

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

priority(*args, **kwargs)

Overloaded function.

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

get/set tracer priority level.

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

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

C++: basic::TracerImpl::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(*args, **kwargs)

Overloaded function.

  1. seekp(self: pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t, : pyrosetta.rosetta.std.fpos___mbstate_t_t) -> pyrosetta.rosetta.std.ostream

C++: std::basic_ostream<char, std::char_traits<char> >::seekp(class std::fpos<__mbstate_t>) –> std::ostream &

  1. 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 &

class sentry

Bases: pybind11_builtins.pybind11_object

static set_default_final_stream() None

C++: basic::TracerImpl::set_default_final_stream() –> void

static set_ios_hook(*args, **kwargs)

Overloaded function.

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

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

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

set_local_print_channel_name(self: pyrosetta.rosetta.basic.TracerImpl, setting: bool) None

Set whether we’re printing the channel name.

This overrides the local setting, but does not alter the global setting.

Vikram K. Mulligan (vmulligan.org)

C++: basic::TracerImpl::set_local_print_channel_name(const bool) –> void

static set_new_final_stream(new_final_stream: pyrosetta.rosetta.std.ostream) None

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

C++: basic::TracerImpl::set_new_final_stream(std::ostream *) –> void

static set_tracer_options(to: pyrosetta.rosetta.basic.TracerOptions) None

set tracer options - global options for Tracer IO.

C++: basic::TracerImpl::set_tracer_options(const struct basic::TracerOptions &) –> void

static super_mute(*args, **kwargs)

Overloaded function.

  1. super_mute() -> bool

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

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

  1. super_mute(f: bool) -> None

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

tellp(self: pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t) pyrosetta.rosetta.std.fpos___mbstate_t_t

C++: std::basic_ostream<char, std::char_traits<char> >::tellp() –> class std::fpos<__mbstate_t>

visible(*args, **kwargs)

Overloaded function.

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

Is this tracer currently visible?.

C++: basic::TracerImpl::visible() –> bool

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

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

C++: basic::TracerImpl::visible(int) –> 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.MetricValueBase

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.basic.MetricValueBase, : pyrosetta.rosetta.basic.MetricValueBase) pyrosetta.rosetta.basic.MetricValueBase

C++: basic::MetricValueBase::operator=(const class basic::MetricValueBase &) –> class basic::MetricValueBase &

clone(self: pyrosetta.rosetta.basic.MetricValueBase) pyrosetta.rosetta.basic.MetricValueBase

C++: basic::MetricValueBase::clone() const –> class std::shared_ptr<class basic::MetricValueBase>

class pyrosetta.rosetta.basic.ProfTag

Bases: pybind11_builtins.pybind11_object

Members:

TEST1

TEST2

TEST3

TEST4

TEST5

ATOM_TREE_UPDATE_INTERNAL_COORDS

ATOM_TREE_UPDATE_XYZ_COORDS

UPDATE_RESIDUE_TORSIONS

UPDATE_RESIDUE_COORDINATES

ROTAMER_TRIALS

PACK_ROTAMERS

UPDATE_RESIDUE_NEIGHBORS

SETUP_NBLIST

CONSTRAINT_SCORE

CONSTRAINT_SET_COPY

SCORE

SCORE_SETUP

SCORE_FINALIZE

SCORE_ONEBODY_ENERGIES

SCORE_NEIGHBOR_ENERGIES

SCORE_LONG_RANGE_ENERGIES

SCORE_DOT

SCORE_END_NOTIFY

SCORE_BEGIN_NOTIFY

VDW_ENERGY

ENERGY_ENVPAIR_POTENTIAL

SECONDARY_STRUCTURE_ENERGY

SECONDARY_STRUCTURE_SSPAIR_ENERGY

SECONDARY_STRUCTURE_HSPAIR_ENERGY

SECONDARY_STRUCTURE_SHEETS_FROM_DIMERS_ENERGY

POSE_COPY

ENERGY_GRAPH_COPY

ENERGIES_COPY

CONFORMATION_DETECT_DISULF

CONFORMATION_FIX_DISULF

CONFORMATION_COPY

CHEMICAL_MAKE_POSE

CCD_CLOSE

FUNC

DFUNC

GET_ENERGIES

SIMANNEALING

INSERT_FRAGS

MC_ACCEPT

GB_SETUP_FOR_PACKING

GB_GET_ALL_BORN_RADII

GEN_BORN_ROTAMER_PAIR_ENERGIES

GEN_BORN_ROTAMER_BACKGROUND_ENERGIES

MULTIPOLE_SETUP

MULTIPOLE_ENERGIES

FACTS_SETUP_FOR_PACKING

FACTS_GET_ALL_BORN_RADII

FACTS_ROTAMER_PAIR_ENERGIES

FACTS_ROTAMER_BACKGROUND_ENERGIES

ABINITIO

STAGE1

STAGE2

STAGE3

STAGE4

STAGE5

FRAGMENT_MOVER

MINMOVER_APPLY

BACKRUB_MOVER

FIND_SUGAR_AND_SUITE_FRAGS_I

FIND_SUGAR_AND_SUITE_FRAGS_II

MAKE_BASE_PAIR_MOVE

MAKE_BASE_STEP_MOVE

RG

RG_LOCAL

SEQUENCE_COMPARISON

KDTREE_CONSTRUCT

KDTREE_SEARCH

CONSTRUCT_DISTANCE_MATRIX

DALPHABALL

DALPHABALL_DERIV

MPI_FILE_BUF

JD2

JD2_OUTPUT

JD2_SILENT_OUTPUTTER

JD2_INIT_MOVER

ARCHIVE_SYNC_BATCHES

ARCHIVE_JOBSCOMPLETE

ARCHIVE_BLOCK_FILE

SAVE_ARCHIVE

ARCHIVE_CRITICAL_JOBSCOMPLETE

ARCHIVE_GEN_BATCH

ARCHIVE_READ_DECOYS

ARCHIVE_EVAL_DECOYS

ARCHIVE_FILL_POSE

ARCHIVE_SCORE_POSE

ARCHIVE_EVALUATORS

MPI_JD2_WAITS_FOR_ARCHIVE

MPI_NOTIFY_ARCHIVE

SILENT_READ_TAG_TEST

CA_RMSD_EVALUATION

CA_DME_EVALUATION

TRUNCATED_SCORE_EVALUATOR

SAXS

FRAGMENTPICKING_CS_SCORE

FRAGMENTPICKING_PROFILE_SCORE

FRAGMENTPICKING_PROFILE_CAHING

FRAGMENTPICKING_SECONDARY_SCORE

FRAGMENTPICKING_READ_VALL

FRAGMENTPICKING

FRAGMENTPICKING_CANDIDATES_COLLECTING

FRAGMENTPICKING_ATOMPAIR_SCORE

FRAGMENTPICKING_PHIPSI_SCORE

FRAGMENTPICKING_DIHEDRALCONSTR_SCORE

MPICANONICALSAMPLING

MPIPOOLCOMMUNICATION

MPICOMMCREATION

MPIBARRIER

MPIBARRIER_BEGIN

MPIBARRIER_END

MPI_GATHER_BARRIER

FARRAY_MANIPULATION

MPI_SLAVE_REPORT_NEW_COORDS

MPI_SLAVE_REPORT_SIZES

MPI_SEND_UPDATE

MPI_SYNC_POOL_DIFF

MPI_SEND_ACCEPTED

POOL_RMSD_ADD_STRUCTURE

POOL_RMSD_EVALUATE

POOL_RMSD_MASTER_EVALUATE

MPI_MASTER_BCAST_COORDS

MPI_MASTER_BCAST_WINNING_RANKS

MPI_MASTER_BCAST_WINNING_STRUCTURES

MPI_MASTER_BCAST_NEW_COMM_SIZE

MPI_MASTER_BCAST_NEW_POOL_RANKS

MPI_MASTER_BCAST_NUM_STRUCTURES_TO_ADD

MPI_POOL_MASTER_THINKS

MPI_POOL_SLAVE_THINKS

SIDECHAINMCMOVER

SIMPLEINTGRAPH

SIDECHAINMOVER

INITIALIZE

COMM_REDUCE_SIZE

CANONICALMOVER_WRITE_TO_FILE

WRITE_TO_FILE

CHECK_COMM_SIZE

APPLY_MOVE

DATA_STORAGE

MASTER_PROCESS_NEW_STRUCTURES

COPY_COORDS

APPLY_SC_MOVE

APPLY_BB_MOVE

HIERARCHICAL_EVALUATE

HIERARCHICAL_ADD

LOAD_HIERARCHY

HIERARCHY_SEND_COORDS

HIERARCHY_RECV_COORDS

INITIALIZE_HIERARCHY

HIERARCHY_SETUP_TO_RECV

WRITE_DECOYS_TO_HIERARCHY

HIERARCHY_GET_NEXT_CANDIDATE

HIERARCHY_FIND_ADDRESS

MPIH_EVAL_CHECK_PROGRESS

MPIH_EVAL_COMMUNICATE_NEW

MPIH_EVAL_AGAINST_NBR

MPIH_PREPARE_WRITE_STRUCTURES

MPIH_UPDATE_EVAL

MPIH_ADD_FIRST_STRUCTURE

MPIH_WRITE_STRUCT

FINALIZE

SORT_POOL

HIERARCHICAL_FIND

HIERARCHICAL_FIND_ADDRESS

HIERARCHICAL_SORT_ADDRESSES

HIERARCHICAL_ROUND

HIERARCHICAL_POOL_SIZE

HIERARCHICAL_ADD_ELEM_TO_CACHE

LIB_FULL_PATH

NOESY_ASSIGN_TOTAL

NOESY_ASSIGN_INITIAL

NOESY_ASSIGN_DIAGONAL

NOESY_ASSIGN_CHEMSHIFT

NOESY_ASSIGN_SYMMETRY

NOESY_ASSIGN_DISTANCE

NOESY_ASSIGN_DECOY_COMP

NOESY_ASSIGN_NETWORK_TOTAL

NOESY_ASSIGN_NETWORK

NOESY_ASSIGN_NETWORK_FIND_RAW_ASSIGN

NOESY_ASSIGN_NETWORK_FILL_COV_GAMMA

NOESY_ASSIGN_NETWORK_RETRIEVE_ASSIGN

NOESY_ASSIGN_NETWORK_COMPUTE_NK

NOESY_ASSIGN_NETWORK_PEAK_COUNT

NOESY_ASSIGN_NETWORK_PEAK_COUNT_EVAL

NOESY_ASSIGN_NETWORK_INVALIDATE_SEQ_NOE

NOESY_ASSIGN_UPDATE_PEAK_VOL

NOESY_ASSIGN_CALIBRATE

NOESY_ASSIGN_ELIMINATE

NOESY_ASSIGN_GEN_CST

NOESY_ASSIGN_WRITE_CST

NOESY_ASSIGN_MAP2CB

NOESY_ASSIGN_CP_GEN_CST

NOESY_ASSIGN_PA_GEN_CST

NOESY_ASSIGN_NMR_STRING

NOESY_ASSIGN_REQUIRES_CB_MAPPING

NOESY_ASSIGN_MAP2CB_NEW

NOESY_ASSIGN_WRITE_ASSIGNMENTS

NOESY_ASSIGN_READ_INPUT

NOESY_ASSIGN_DIST_INIT

NOESY_ASSIGN_DIST_PREP_SCORE

NOESY_ASSIGN_DIST_SET_COMPABILITY_SCORE

NOESY_ASSIGN_DIST_APPLY

NOESY_ASSIGN_DIST_MAKE_POSE

NOESY_ASSIGN_DIST_CST_EVAL

NOESY_ASSIGN_DIST_CST_CAST

SILENT_FILL_POSE

SILENT_SET_POSE_COORDS

SILENT_FILL_STRUCT

MEAN_FIELD

TOTAL

n_prof_tags

ABINITIO = <ProfTag.ABINITIO: 55>
APPLY_BB_MOVE = <ProfTag.APPLY_BB_MOVE: 146>
APPLY_MOVE = <ProfTag.APPLY_MOVE: 141>
APPLY_SC_MOVE = <ProfTag.APPLY_SC_MOVE: 145>
ARCHIVE_BLOCK_FILE = <ProfTag.ARCHIVE_BLOCK_FILE: 83>
ARCHIVE_CRITICAL_JOBSCOMPLETE = <ProfTag.ARCHIVE_CRITICAL_JOBSCOMPLETE: 85>
ARCHIVE_EVALUATORS = <ProfTag.ARCHIVE_EVALUATORS: 91>
ARCHIVE_EVAL_DECOYS = <ProfTag.ARCHIVE_EVAL_DECOYS: 88>
ARCHIVE_FILL_POSE = <ProfTag.ARCHIVE_FILL_POSE: 89>
ARCHIVE_GEN_BATCH = <ProfTag.ARCHIVE_GEN_BATCH: 86>
ARCHIVE_JOBSCOMPLETE = <ProfTag.ARCHIVE_JOBSCOMPLETE: 82>
ARCHIVE_READ_DECOYS = <ProfTag.ARCHIVE_READ_DECOYS: 87>
ARCHIVE_SCORE_POSE = <ProfTag.ARCHIVE_SCORE_POSE: 90>
ARCHIVE_SYNC_BATCHES = <ProfTag.ARCHIVE_SYNC_BATCHES: 81>
ATOM_TREE_UPDATE_INTERNAL_COORDS = <ProfTag.ATOM_TREE_UPDATE_INTERNAL_COORDS: 6>
ATOM_TREE_UPDATE_XYZ_COORDS = <ProfTag.ATOM_TREE_UPDATE_XYZ_COORDS: 7>
BACKRUB_MOVER = <ProfTag.BACKRUB_MOVER: 63>
CANONICALMOVER_WRITE_TO_FILE = <ProfTag.CANONICALMOVER_WRITE_TO_FILE: 138>
CA_DME_EVALUATION = <ProfTag.CA_DME_EVALUATION: 96>
CA_RMSD_EVALUATION = <ProfTag.CA_RMSD_EVALUATION: 95>
CCD_CLOSE = <ProfTag.CCD_CLOSE: 38>
CHECK_COMM_SIZE = <ProfTag.CHECK_COMM_SIZE: 140>
CHEMICAL_MAKE_POSE = <ProfTag.CHEMICAL_MAKE_POSE: 37>
COMM_REDUCE_SIZE = <ProfTag.COMM_REDUCE_SIZE: 137>
CONFORMATION_COPY = <ProfTag.CONFORMATION_COPY: 36>
CONFORMATION_DETECT_DISULF = <ProfTag.CONFORMATION_DETECT_DISULF: 34>
CONFORMATION_FIX_DISULF = <ProfTag.CONFORMATION_FIX_DISULF: 35>
CONSTRAINT_SCORE = <ProfTag.CONSTRAINT_SCORE: 14>
CONSTRAINT_SET_COPY = <ProfTag.CONSTRAINT_SET_COPY: 15>
CONSTRUCT_DISTANCE_MATRIX = <ProfTag.CONSTRUCT_DISTANCE_MATRIX: 73>
COPY_COORDS = <ProfTag.COPY_COORDS: 144>
DALPHABALL = <ProfTag.DALPHABALL: 74>
DALPHABALL_DERIV = <ProfTag.DALPHABALL_DERIV: 75>
DATA_STORAGE = <ProfTag.DATA_STORAGE: 142>
DFUNC = <ProfTag.DFUNC: 40>
ENERGIES_COPY = <ProfTag.ENERGIES_COPY: 33>
ENERGY_ENVPAIR_POTENTIAL = <ProfTag.ENERGY_ENVPAIR_POTENTIAL: 26>
ENERGY_GRAPH_COPY = <ProfTag.ENERGY_GRAPH_COPY: 32>
FACTS_GET_ALL_BORN_RADII = <ProfTag.FACTS_GET_ALL_BORN_RADII: 52>
FACTS_ROTAMER_BACKGROUND_ENERGIES = <ProfTag.FACTS_ROTAMER_BACKGROUND_ENERGIES: 54>
FACTS_ROTAMER_PAIR_ENERGIES = <ProfTag.FACTS_ROTAMER_PAIR_ENERGIES: 53>
FACTS_SETUP_FOR_PACKING = <ProfTag.FACTS_SETUP_FOR_PACKING: 51>
FARRAY_MANIPULATION = <ProfTag.FARRAY_MANIPULATION: 116>
FINALIZE = <ProfTag.FINALIZE: 164>
FIND_SUGAR_AND_SUITE_FRAGS_I = <ProfTag.FIND_SUGAR_AND_SUITE_FRAGS_I: 64>
FIND_SUGAR_AND_SUITE_FRAGS_II = <ProfTag.FIND_SUGAR_AND_SUITE_FRAGS_II: 65>
FRAGMENTPICKING = <ProfTag.FRAGMENTPICKING: 104>
FRAGMENTPICKING_ATOMPAIR_SCORE = <ProfTag.FRAGMENTPICKING_ATOMPAIR_SCORE: 106>
FRAGMENTPICKING_CANDIDATES_COLLECTING = <ProfTag.FRAGMENTPICKING_CANDIDATES_COLLECTING: 105>
FRAGMENTPICKING_CS_SCORE = <ProfTag.FRAGMENTPICKING_CS_SCORE: 99>
FRAGMENTPICKING_DIHEDRALCONSTR_SCORE = <ProfTag.FRAGMENTPICKING_DIHEDRALCONSTR_SCORE: 108>
FRAGMENTPICKING_PHIPSI_SCORE = <ProfTag.FRAGMENTPICKING_PHIPSI_SCORE: 107>
FRAGMENTPICKING_PROFILE_CAHING = <ProfTag.FRAGMENTPICKING_PROFILE_CAHING: 101>
FRAGMENTPICKING_PROFILE_SCORE = <ProfTag.FRAGMENTPICKING_PROFILE_SCORE: 100>
FRAGMENTPICKING_READ_VALL = <ProfTag.FRAGMENTPICKING_READ_VALL: 103>
FRAGMENTPICKING_SECONDARY_SCORE = <ProfTag.FRAGMENTPICKING_SECONDARY_SCORE: 102>
FRAGMENT_MOVER = <ProfTag.FRAGMENT_MOVER: 61>
FUNC = <ProfTag.FUNC: 39>
GB_GET_ALL_BORN_RADII = <ProfTag.GB_GET_ALL_BORN_RADII: 46>
GB_SETUP_FOR_PACKING = <ProfTag.GB_SETUP_FOR_PACKING: 45>
GEN_BORN_ROTAMER_BACKGROUND_ENERGIES = <ProfTag.GEN_BORN_ROTAMER_BACKGROUND_ENERGIES: 48>
GEN_BORN_ROTAMER_PAIR_ENERGIES = <ProfTag.GEN_BORN_ROTAMER_PAIR_ENERGIES: 47>
GET_ENERGIES = <ProfTag.GET_ENERGIES: 41>
HIERARCHICAL_ADD = <ProfTag.HIERARCHICAL_ADD: 148>
HIERARCHICAL_ADD_ELEM_TO_CACHE = <ProfTag.HIERARCHICAL_ADD_ELEM_TO_CACHE: 171>
HIERARCHICAL_EVALUATE = <ProfTag.HIERARCHICAL_EVALUATE: 147>
HIERARCHICAL_FIND = <ProfTag.HIERARCHICAL_FIND: 166>
HIERARCHICAL_FIND_ADDRESS = <ProfTag.HIERARCHICAL_FIND_ADDRESS: 167>
HIERARCHICAL_POOL_SIZE = <ProfTag.HIERARCHICAL_POOL_SIZE: 170>
HIERARCHICAL_ROUND = <ProfTag.HIERARCHICAL_ROUND: 169>
HIERARCHICAL_SORT_ADDRESSES = <ProfTag.HIERARCHICAL_SORT_ADDRESSES: 168>
HIERARCHY_FIND_ADDRESS = <ProfTag.HIERARCHY_FIND_ADDRESS: 156>
HIERARCHY_GET_NEXT_CANDIDATE = <ProfTag.HIERARCHY_GET_NEXT_CANDIDATE: 155>
HIERARCHY_RECV_COORDS = <ProfTag.HIERARCHY_RECV_COORDS: 151>
HIERARCHY_SEND_COORDS = <ProfTag.HIERARCHY_SEND_COORDS: 150>
HIERARCHY_SETUP_TO_RECV = <ProfTag.HIERARCHY_SETUP_TO_RECV: 153>
INITIALIZE = <ProfTag.INITIALIZE: 136>
INITIALIZE_HIERARCHY = <ProfTag.INITIALIZE_HIERARCHY: 152>
INSERT_FRAGS = <ProfTag.INSERT_FRAGS: 43>
JD2 = <ProfTag.JD2: 77>
JD2_INIT_MOVER = <ProfTag.JD2_INIT_MOVER: 80>
JD2_OUTPUT = <ProfTag.JD2_OUTPUT: 78>
JD2_SILENT_OUTPUTTER = <ProfTag.JD2_SILENT_OUTPUTTER: 79>
KDTREE_CONSTRUCT = <ProfTag.KDTREE_CONSTRUCT: 71>
LIB_FULL_PATH = <ProfTag.LIB_FULL_PATH: 172>
LOAD_HIERARCHY = <ProfTag.LOAD_HIERARCHY: 149>
MAKE_BASE_PAIR_MOVE = <ProfTag.MAKE_BASE_PAIR_MOVE: 66>
MAKE_BASE_STEP_MOVE = <ProfTag.MAKE_BASE_STEP_MOVE: 67>
MASTER_PROCESS_NEW_STRUCTURES = <ProfTag.MASTER_PROCESS_NEW_STRUCTURES: 143>
MC_ACCEPT = <ProfTag.MC_ACCEPT: 44>
MEAN_FIELD = <ProfTag.MEAN_FIELD: 212>
MINMOVER_APPLY = <ProfTag.MINMOVER_APPLY: 62>
MPIBARRIER = <ProfTag.MPIBARRIER: 112>
MPIBARRIER_BEGIN = <ProfTag.MPIBARRIER_BEGIN: 113>
MPIBARRIER_END = <ProfTag.MPIBARRIER_END: 114>
MPICANONICALSAMPLING = <ProfTag.MPICANONICALSAMPLING: 109>
MPICOMMCREATION = <ProfTag.MPICOMMCREATION: 111>
MPIH_ADD_FIRST_STRUCTURE = <ProfTag.MPIH_ADD_FIRST_STRUCTURE: 162>
MPIH_EVAL_AGAINST_NBR = <ProfTag.MPIH_EVAL_AGAINST_NBR: 159>
MPIH_EVAL_CHECK_PROGRESS = <ProfTag.MPIH_EVAL_CHECK_PROGRESS: 157>
MPIH_EVAL_COMMUNICATE_NEW = <ProfTag.MPIH_EVAL_COMMUNICATE_NEW: 158>
MPIH_PREPARE_WRITE_STRUCTURES = <ProfTag.MPIH_PREPARE_WRITE_STRUCTURES: 160>
MPIH_UPDATE_EVAL = <ProfTag.MPIH_UPDATE_EVAL: 161>
MPIH_WRITE_STRUCT = <ProfTag.MPIH_WRITE_STRUCT: 163>
MPIPOOLCOMMUNICATION = <ProfTag.MPIPOOLCOMMUNICATION: 110>
MPI_FILE_BUF = <ProfTag.MPI_FILE_BUF: 76>
MPI_GATHER_BARRIER = <ProfTag.MPI_GATHER_BARRIER: 115>
MPI_JD2_WAITS_FOR_ARCHIVE = <ProfTag.MPI_JD2_WAITS_FOR_ARCHIVE: 92>
MPI_MASTER_BCAST_COORDS = <ProfTag.MPI_MASTER_BCAST_COORDS: 125>
MPI_MASTER_BCAST_NEW_COMM_SIZE = <ProfTag.MPI_MASTER_BCAST_NEW_COMM_SIZE: 128>
MPI_MASTER_BCAST_NEW_POOL_RANKS = <ProfTag.MPI_MASTER_BCAST_NEW_POOL_RANKS: 129>
MPI_MASTER_BCAST_NUM_STRUCTURES_TO_ADD = <ProfTag.MPI_MASTER_BCAST_NUM_STRUCTURES_TO_ADD: 130>
MPI_MASTER_BCAST_WINNING_RANKS = <ProfTag.MPI_MASTER_BCAST_WINNING_RANKS: 126>
MPI_MASTER_BCAST_WINNING_STRUCTURES = <ProfTag.MPI_MASTER_BCAST_WINNING_STRUCTURES: 127>
MPI_NOTIFY_ARCHIVE = <ProfTag.MPI_NOTIFY_ARCHIVE: 93>
MPI_POOL_MASTER_THINKS = <ProfTag.MPI_POOL_MASTER_THINKS: 131>
MPI_POOL_SLAVE_THINKS = <ProfTag.MPI_POOL_SLAVE_THINKS: 132>
MPI_SEND_ACCEPTED = <ProfTag.MPI_SEND_ACCEPTED: 121>
MPI_SEND_UPDATE = <ProfTag.MPI_SEND_UPDATE: 119>
MPI_SLAVE_REPORT_NEW_COORDS = <ProfTag.MPI_SLAVE_REPORT_NEW_COORDS: 117>
MPI_SLAVE_REPORT_SIZES = <ProfTag.MPI_SLAVE_REPORT_SIZES: 118>
MPI_SYNC_POOL_DIFF = <ProfTag.MPI_SYNC_POOL_DIFF: 120>
MULTIPOLE_ENERGIES = <ProfTag.MULTIPOLE_ENERGIES: 50>
MULTIPOLE_SETUP = <ProfTag.MULTIPOLE_SETUP: 49>
NOESY_ASSIGN_CALIBRATE = <ProfTag.NOESY_ASSIGN_CALIBRATE: 190>
NOESY_ASSIGN_CHEMSHIFT = <ProfTag.NOESY_ASSIGN_CHEMSHIFT: 176>
NOESY_ASSIGN_CP_GEN_CST = <ProfTag.NOESY_ASSIGN_CP_GEN_CST: 195>
NOESY_ASSIGN_DECOY_COMP = <ProfTag.NOESY_ASSIGN_DECOY_COMP: 179>
NOESY_ASSIGN_DIAGONAL = <ProfTag.NOESY_ASSIGN_DIAGONAL: 175>
NOESY_ASSIGN_DISTANCE = <ProfTag.NOESY_ASSIGN_DISTANCE: 178>
NOESY_ASSIGN_DIST_APPLY = <ProfTag.NOESY_ASSIGN_DIST_APPLY: 205>
NOESY_ASSIGN_DIST_CST_CAST = <ProfTag.NOESY_ASSIGN_DIST_CST_CAST: 208>
NOESY_ASSIGN_DIST_CST_EVAL = <ProfTag.NOESY_ASSIGN_DIST_CST_EVAL: 207>
NOESY_ASSIGN_DIST_INIT = <ProfTag.NOESY_ASSIGN_DIST_INIT: 202>
NOESY_ASSIGN_DIST_MAKE_POSE = <ProfTag.NOESY_ASSIGN_DIST_MAKE_POSE: 206>
NOESY_ASSIGN_DIST_PREP_SCORE = <ProfTag.NOESY_ASSIGN_DIST_PREP_SCORE: 203>
NOESY_ASSIGN_DIST_SET_COMPABILITY_SCORE = <ProfTag.NOESY_ASSIGN_DIST_SET_COMPABILITY_SCORE: 204>
NOESY_ASSIGN_ELIMINATE = <ProfTag.NOESY_ASSIGN_ELIMINATE: 191>
NOESY_ASSIGN_GEN_CST = <ProfTag.NOESY_ASSIGN_GEN_CST: 192>
NOESY_ASSIGN_INITIAL = <ProfTag.NOESY_ASSIGN_INITIAL: 174>
NOESY_ASSIGN_MAP2CB = <ProfTag.NOESY_ASSIGN_MAP2CB: 194>
NOESY_ASSIGN_MAP2CB_NEW = <ProfTag.NOESY_ASSIGN_MAP2CB_NEW: 199>
NOESY_ASSIGN_NETWORK = <ProfTag.NOESY_ASSIGN_NETWORK: 181>
NOESY_ASSIGN_NETWORK_COMPUTE_NK = <ProfTag.NOESY_ASSIGN_NETWORK_COMPUTE_NK: 185>
NOESY_ASSIGN_NETWORK_FILL_COV_GAMMA = <ProfTag.NOESY_ASSIGN_NETWORK_FILL_COV_GAMMA: 183>
NOESY_ASSIGN_NETWORK_FIND_RAW_ASSIGN = <ProfTag.NOESY_ASSIGN_NETWORK_FIND_RAW_ASSIGN: 182>
NOESY_ASSIGN_NETWORK_INVALIDATE_SEQ_NOE = <ProfTag.NOESY_ASSIGN_NETWORK_INVALIDATE_SEQ_NOE: 188>
NOESY_ASSIGN_NETWORK_PEAK_COUNT = <ProfTag.NOESY_ASSIGN_NETWORK_PEAK_COUNT: 186>
NOESY_ASSIGN_NETWORK_PEAK_COUNT_EVAL = <ProfTag.NOESY_ASSIGN_NETWORK_PEAK_COUNT_EVAL: 187>
NOESY_ASSIGN_NETWORK_RETRIEVE_ASSIGN = <ProfTag.NOESY_ASSIGN_NETWORK_RETRIEVE_ASSIGN: 184>
NOESY_ASSIGN_NETWORK_TOTAL = <ProfTag.NOESY_ASSIGN_NETWORK_TOTAL: 180>
NOESY_ASSIGN_NMR_STRING = <ProfTag.NOESY_ASSIGN_NMR_STRING: 197>
NOESY_ASSIGN_PA_GEN_CST = <ProfTag.NOESY_ASSIGN_PA_GEN_CST: 196>
NOESY_ASSIGN_READ_INPUT = <ProfTag.NOESY_ASSIGN_READ_INPUT: 201>
NOESY_ASSIGN_REQUIRES_CB_MAPPING = <ProfTag.NOESY_ASSIGN_REQUIRES_CB_MAPPING: 198>
NOESY_ASSIGN_SYMMETRY = <ProfTag.NOESY_ASSIGN_SYMMETRY: 177>
NOESY_ASSIGN_TOTAL = <ProfTag.NOESY_ASSIGN_TOTAL: 173>
NOESY_ASSIGN_UPDATE_PEAK_VOL = <ProfTag.NOESY_ASSIGN_UPDATE_PEAK_VOL: 189>
NOESY_ASSIGN_WRITE_ASSIGNMENTS = <ProfTag.NOESY_ASSIGN_WRITE_ASSIGNMENTS: 200>
NOESY_ASSIGN_WRITE_CST = <ProfTag.NOESY_ASSIGN_WRITE_CST: 193>
PACK_ROTAMERS = <ProfTag.PACK_ROTAMERS: 11>
POOL_RMSD_ADD_STRUCTURE = <ProfTag.POOL_RMSD_ADD_STRUCTURE: 122>
POOL_RMSD_EVALUATE = <ProfTag.POOL_RMSD_EVALUATE: 123>
POOL_RMSD_MASTER_EVALUATE = <ProfTag.POOL_RMSD_MASTER_EVALUATE: 124>
POSE_COPY = <ProfTag.POSE_COPY: 31>
RG = <ProfTag.RG: 68>
RG_LOCAL = <ProfTag.RG_LOCAL: 69>
ROTAMER_TRIALS = <ProfTag.ROTAMER_TRIALS: 10>
SAVE_ARCHIVE = <ProfTag.SAVE_ARCHIVE: 84>
SAXS = <ProfTag.SAXS: 98>
SCORE = <ProfTag.SCORE: 16>
SCORE_BEGIN_NOTIFY = <ProfTag.SCORE_BEGIN_NOTIFY: 24>
SCORE_DOT = <ProfTag.SCORE_DOT: 22>
SCORE_END_NOTIFY = <ProfTag.SCORE_END_NOTIFY: 23>
SCORE_FINALIZE = <ProfTag.SCORE_FINALIZE: 18>
SCORE_LONG_RANGE_ENERGIES = <ProfTag.SCORE_LONG_RANGE_ENERGIES: 21>
SCORE_NEIGHBOR_ENERGIES = <ProfTag.SCORE_NEIGHBOR_ENERGIES: 20>
SCORE_ONEBODY_ENERGIES = <ProfTag.SCORE_ONEBODY_ENERGIES: 19>
SCORE_SETUP = <ProfTag.SCORE_SETUP: 17>
SECONDARY_STRUCTURE_ENERGY = <ProfTag.SECONDARY_STRUCTURE_ENERGY: 27>
SECONDARY_STRUCTURE_HSPAIR_ENERGY = <ProfTag.SECONDARY_STRUCTURE_HSPAIR_ENERGY: 29>
SECONDARY_STRUCTURE_SHEETS_FROM_DIMERS_ENERGY = <ProfTag.SECONDARY_STRUCTURE_SHEETS_FROM_DIMERS_ENERGY: 30>
SECONDARY_STRUCTURE_SSPAIR_ENERGY = <ProfTag.SECONDARY_STRUCTURE_SSPAIR_ENERGY: 28>
SEQUENCE_COMPARISON = <ProfTag.SEQUENCE_COMPARISON: 70>
SETUP_NBLIST = <ProfTag.SETUP_NBLIST: 13>
SIDECHAINMCMOVER = <ProfTag.SIDECHAINMCMOVER: 133>
SIDECHAINMOVER = <ProfTag.SIDECHAINMOVER: 135>
SILENT_FILL_POSE = <ProfTag.SILENT_FILL_POSE: 209>
SILENT_FILL_STRUCT = <ProfTag.SILENT_FILL_STRUCT: 211>
SILENT_READ_TAG_TEST = <ProfTag.SILENT_READ_TAG_TEST: 94>
SILENT_SET_POSE_COORDS = <ProfTag.SILENT_SET_POSE_COORDS: 210>
SIMANNEALING = <ProfTag.SIMANNEALING: 42>
SIMPLEINTGRAPH = <ProfTag.SIMPLEINTGRAPH: 134>
SORT_POOL = <ProfTag.SORT_POOL: 165>
STAGE1 = <ProfTag.STAGE1: 56>
STAGE2 = <ProfTag.STAGE2: 57>
STAGE3 = <ProfTag.STAGE3: 58>
STAGE4 = <ProfTag.STAGE4: 59>
STAGE5 = <ProfTag.STAGE5: 60>
TEST1 = <ProfTag.TEST1: 1>
TEST2 = <ProfTag.TEST2: 2>
TEST3 = <ProfTag.TEST3: 3>
TEST4 = <ProfTag.TEST4: 4>
TEST5 = <ProfTag.TEST5: 5>
TOTAL = <ProfTag.TOTAL: 213>
TRUNCATED_SCORE_EVALUATOR = <ProfTag.TRUNCATED_SCORE_EVALUATOR: 97>
UPDATE_RESIDUE_COORDINATES = <ProfTag.UPDATE_RESIDUE_COORDINATES: 9>
UPDATE_RESIDUE_NEIGHBORS = <ProfTag.UPDATE_RESIDUE_NEIGHBORS: 12>
UPDATE_RESIDUE_TORSIONS = <ProfTag.UPDATE_RESIDUE_TORSIONS: 8>
VDW_ENERGY = <ProfTag.VDW_ENERGY: 25>
WRITE_DECOYS_TO_HIERARCHY = <ProfTag.WRITE_DECOYS_TO_HIERARCHY: 154>
WRITE_TO_FILE = <ProfTag.WRITE_TO_FILE: 139>
n_prof_tags = <ProfTag.TOTAL: 213>
property name
class pyrosetta.rosetta.basic.ProfileThis

Bases: pybind11_builtins.pybind11_object

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

buf(*args, **kwargs)

Overloaded function.

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

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

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

C++: basic::PyTracer::buf(std::string) –> 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(std::string) –> 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(*args, **kwargs)

Overloaded function.

  1. seekp(self: pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t, : pyrosetta.rosetta.std.fpos___mbstate_t_t) -> pyrosetta.rosetta.std.ostream

C++: std::basic_ostream<char, std::char_traits<char> >::seekp(class std::fpos<__mbstate_t>) –> std::ostream &

  1. 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 &

class sentry

Bases: pybind11_builtins.pybind11_object

tellp(self: pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t) pyrosetta.rosetta.std.fpos___mbstate_t_t

C++: std::basic_ostream<char, std::char_traits<char> >::tellp() –> class std::fpos<__mbstate_t>

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

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)

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 &

class pyrosetta.rosetta.basic.Tracer

Bases: pybind11_builtins.pybind11_object

The funky indirection to TracerImpl here is so that the heavy-weight TracerImpl object is only constructed on first use, and isn’t static or thread_local

class TracerProxy

Bases: pybind11_builtins.pybind11_object

/ The priority proxy objects

flush(self: pyrosetta.rosetta.basic.Tracer.TracerProxy) None

C++: basic::Tracer::TracerProxy::flush() –> void

visible(self: pyrosetta.rosetta.basic.Tracer.TracerProxy) bool

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

channel(self: pyrosetta.rosetta.basic.Tracer) str

C++: basic::Tracer::channel() –> const std::string &

flags(*args, **kwargs)

Overloaded function.

  1. flags(self: pyrosetta.rosetta.basic.Tracer) -> pyrosetta.rosetta.std._Ios_Fmtflags

C++: basic::Tracer::flags() –> enum std::_Ios_Fmtflags

  1. flags(self: pyrosetta.rosetta.basic.Tracer, fmtfl: pyrosetta.rosetta.std._Ios_Fmtflags) -> pyrosetta.rosetta.std._Ios_Fmtflags

C++: basic::Tracer::flags(enum std::_Ios_Fmtflags) –> enum std::_Ios_Fmtflags

flush(self: pyrosetta.rosetta.basic.Tracer) None

C++: basic::Tracer::flush() –> void

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

static get_all_channels_string() str

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

get_local_print_channel_name(self: pyrosetta.rosetta.basic.Tracer) bool

Get whether we’re printing the channel name.

This looks at the local setting, but does not check the global setting.

In practice, if the local setting is true then the global setting is used. If the local setting is false, it overrides the global setting.

Vikram K. Mulligan (vmulligan.org)

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

precision(*args, **kwargs)

Overloaded function.

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

C++: basic::Tracer::precision() –> long

  1. precision(self: pyrosetta.rosetta.basic.Tracer, prec: int) -> int

C++: basic::Tracer::precision(long) –> long

static set_ios_hook(*args, **kwargs)

Overloaded function.

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

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

TODO: See if we can kill any usage of this, except for the esoteric

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

set_local_print_channel_name(self: pyrosetta.rosetta.basic.Tracer, setting: bool) None

Set whether we’re printing the channel name.

This overrides the local setting, but does not alter the global setting.

In practice, if the local setting is true then the global setting is used. If the local setting is false, it overrides the global setting.

Vikram K. Mulligan (vmulligan.org)

C++: basic::Tracer::set_local_print_channel_name(const bool) –> void

static super_mute(*args, **kwargs)

Overloaded function.

  1. super_mute() -> bool

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

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

  1. super_mute(f: bool) -> None

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

visible(*args, **kwargs)

Overloaded function.

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

C++: basic::Tracer::visible() –> bool

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

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

width(*args, **kwargs)

Overloaded function.

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

/ The IOS manipulators

C++: basic::Tracer::width() –> long

  1. width(self: pyrosetta.rosetta.basic.Tracer, wide: int) -> int

C++: basic::Tracer::width(long) –> long

class pyrosetta.rosetta.basic.TracerImpl

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’

class TracerProxyImpl

Bases: pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t

Inner Classes

Small inner class acting as a proxy to an object that hold it.

_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

calculate_visibility(self: pyrosetta.rosetta.basic.TracerImpl.TracerProxyImpl) None

determine the visibility of the proxy.

C++: basic::TracerImpl::TracerProxyImpl::calculate_visibility() –> 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

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(*args, **kwargs)

Overloaded function.

  1. seekp(self: pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t, : pyrosetta.rosetta.std.fpos___mbstate_t_t) -> pyrosetta.rosetta.std.ostream

C++: std::basic_ostream<char, std::char_traits<char> >::seekp(class std::fpos<__mbstate_t>) –> std::ostream &

  1. 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 &

class sentry

Bases: pybind11_builtins.pybind11_object

tellp(self: pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t) pyrosetta.rosetta.std.fpos___mbstate_t_t

C++: std::basic_ostream<char, std::char_traits<char> >::tellp() –> class std::fpos<__mbstate_t>

visible(self: pyrosetta.rosetta.basic.TracerImpl.TracerProxyImpl) bool

Is the output from this TracerProxy visible?

C++: basic::TracerImpl::TracerProxyImpl::visible() –> 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 &

_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

channel(self: pyrosetta.rosetta.basic.TracerImpl) str

C++: basic::TracerImpl::channel() const –> const std::string &

channel_color(*args, **kwargs)

Overloaded function.

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

Get the channel color.

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

  1. channel_color(self: pyrosetta.rosetta.basic.TracerImpl, 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::TracerImpl::channel_color(const class utility::CSI_Sequence &) –> void

channel_name_color(*args, **kwargs)

Overloaded function.

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

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

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

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

flush_all_channels(self: pyrosetta.rosetta.basic.TracerImpl) None
flush tracer buffer and flush buffers of all

sub-channels ie: Fatal, Error, Warning, Info, Debug, Trace

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

static get_all_channels_string() str

C++: basic::TracerImpl::get_all_channels_string() –> const std::string &

get_local_print_channel_name(self: pyrosetta.rosetta.basic.TracerImpl) bool

Get whether we’re printing the channel name.

This gets the local setting, but does not look at the global setting. (In practice, if the local setting is true then the global setting is used.)

Vikram K. Mulligan (vmulligan.org)

C++: basic::TracerImpl::get_local_print_channel_name() const –> bool

get_proxy_by_priority(self: pyrosetta.rosetta.basic.TracerImpl, priority: pyrosetta.rosetta.basic.TracerPriority) basic::TracerImpl::TracerProxyImpl

C++: basic::TracerImpl::get_proxy_by_priority(enum basic::TracerPriority) –> class basic::TracerImpl::TracerProxyImpl &

init(self: pyrosetta.rosetta.basic.TracerImpl, tr: pyrosetta.rosetta.basic.TracerImpl) None

re-init using data from another tracer object.

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

static output_prefix(*args, **kwargs)

Overloaded function.

  1. output_prefix(: str) -> None

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

C++: basic::TracerImpl::output_prefix(const std::string &) –> void

  1. output_prefix() -> str

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

priority(*args, **kwargs)

Overloaded function.

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

get/set tracer priority level.

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

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

C++: basic::TracerImpl::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(*args, **kwargs)

Overloaded function.

  1. seekp(self: pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t, : pyrosetta.rosetta.std.fpos___mbstate_t_t) -> pyrosetta.rosetta.std.ostream

C++: std::basic_ostream<char, std::char_traits<char> >::seekp(class std::fpos<__mbstate_t>) –> std::ostream &

  1. 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 &

class sentry

Bases: pybind11_builtins.pybind11_object

static set_default_final_stream() None

C++: basic::TracerImpl::set_default_final_stream() –> void

static set_ios_hook(*args, **kwargs)

Overloaded function.

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

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

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

set_local_print_channel_name(self: pyrosetta.rosetta.basic.TracerImpl, setting: bool) None

Set whether we’re printing the channel name.

This overrides the local setting, but does not alter the global setting.

Vikram K. Mulligan (vmulligan.org)

C++: basic::TracerImpl::set_local_print_channel_name(const bool) –> void

static set_new_final_stream(new_final_stream: pyrosetta.rosetta.std.ostream) None

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

C++: basic::TracerImpl::set_new_final_stream(std::ostream *) –> void

static set_tracer_options(to: pyrosetta.rosetta.basic.TracerOptions) None

set tracer options - global options for Tracer IO.

C++: basic::TracerImpl::set_tracer_options(const struct basic::TracerOptions &) –> void

static super_mute(*args, **kwargs)

Overloaded function.

  1. super_mute() -> bool

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

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

  1. super_mute(f: bool) -> None

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

tellp(self: pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t) pyrosetta.rosetta.std.fpos___mbstate_t_t

C++: std::basic_ostream<char, std::char_traits<char> >::tellp() –> class std::fpos<__mbstate_t>

visible(*args, **kwargs)

Overloaded function.

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

Is this tracer currently visible?.

C++: basic::TracerImpl::visible() –> bool

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

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

C++: basic::TracerImpl::visible(int) –> 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.TracerOptions

Bases: pybind11_builtins.pybind11_object

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

property level
property levels
property muted
property print_channel_name
property timestamp
property unmuted
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).

Members:

t_fatal

t_error

t_warning

t_info

t_debug

t_trace

property name
t_debug = <TracerPriority.t_debug: 400>
t_error = <TracerPriority.t_error: 100>
t_fatal = <TracerPriority.t_fatal: 0>
t_info = <TracerPriority.t_info: 300>
t_trace = <TracerPriority.t_trace: 500>
t_warning = <TracerPriority.t_warning: 200>
class pyrosetta.rosetta.basic.TracerToFile

Bases: pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t

_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

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

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(*args, **kwargs)

Overloaded function.

  1. seekp(self: pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t, : pyrosetta.rosetta.std.fpos___mbstate_t_t) -> pyrosetta.rosetta.std.ostream

C++: std::basic_ostream<char, std::char_traits<char> >::seekp(class std::fpos<__mbstate_t>) –> std::ostream &

  1. 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 &

class sentry

Bases: pybind11_builtins.pybind11_object

tellp(self: pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t) pyrosetta.rosetta.std.fpos___mbstate_t_t

C++: std::basic_ostream<char, std::char_traits<char> >::tellp() –> class std::fpos<__mbstate_t>

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 &

pyrosetta.rosetta.basic.Warning() basic::Tracer

Predefined Warning tracer, for use in headers.

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

class pyrosetta.rosetta.basic.YamlEmitter

Bases: pyrosetta.rosetta.basic.Emitter

Emitter for more classically formatted YAML

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.

  1. end(self: pyrosetta.rosetta.basic.Emitter) -> None

  2. 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.

  1. start_list(self: pyrosetta.rosetta.basic.Emitter) -> None

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

Write method for use inside lists / arrays

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

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

  2. 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 std::string &, bool) –> void

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

  2. 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.

  1. start_map(self: pyrosetta.rosetta.basic.Emitter) -> None

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

Write method for use inside lists / arrays

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

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

  2. 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 std::string &, bool) –> void

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

  2. 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

class pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t

Bases: pyrosetta.rosetta.std.ostream

_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

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

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(*args, **kwargs)

Overloaded function.

  1. seekp(self: pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t, : pyrosetta.rosetta.std.fpos___mbstate_t_t) -> pyrosetta.rosetta.std.ostream

C++: std::basic_ostream<char, std::char_traits<char> >::seekp(class std::fpos<__mbstate_t>) –> std::ostream &

  1. 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 &

class sentry

Bases: pybind11_builtins.pybind11_object

tellp(self: pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t) pyrosetta.rosetta.std.fpos___mbstate_t_t

C++: std::basic_ostream<char, std::char_traits<char> >::tellp() –> class std::fpos<__mbstate_t>

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 &

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.

  1. execute(message: str, command: str, args: pyrosetta.rosetta.std.vector_std_string) -> pyrosetta.rosetta.basic.ExecutionResult

  2. execute(message: str, command: str, args: pyrosetta.rosetta.std.vector_std_string, terminate_on_failure: bool) -> pyrosetta.rosetta.basic.ExecutionResult

  3. execute(message: str, command: str, args: pyrosetta.rosetta.std.vector_std_string, 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 std::string &, const std::string &, const class std::vector<std::string, class std::allocator<std::string > > &, 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(std::ostream &) –> 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: pyrosetta.rosetta.ObjexxFCL.FArray2A_double_t, 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: pyrosetta.rosetta.ObjexxFCL.FArray2A_double_t, 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: pyrosetta.rosetta.ObjexxFCL.FArray3A_double_t, 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.

  1. 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(std::istream &, class basic::MetricValueBase &) –> bool

  1. 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(std::istream &) –> 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 std::string &) –> 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(std::ostream &, const class basic::MetricValueBase &) –> bool