io

Bindings for utility::io namespace

class pyrosetta.rosetta.utility.io.FileContentsMap

Bases: pybind11_builtins.pybind11_object

The %FileContentsMap is a class that will minimize the number of times files are accessed from disk. The first time the contents of a file are requested, it will cache the contents the file in memory as a strings. All subsequent requests for the contents of that file will then be delivered without having to go to disk. WARNING: The %FileContentsMap will not update the contents that it holds for a file after the first time it loads it, so if the contents change on disk, the %FileContentsMap will be out of date.

The %FileContentsMap offers two settings that are both off by default.

1) You can set whether it should delete files when they reach a “read limit,” which in turn requires that you first define a read limit for the file. This can prevent the %FileContentsMap from loading too much into memory as long as the utility of a file is expected to be short (i.e. it’s read several times in a short period and then never again). Setting a file’s read limit to zero signals that the contents of the file should never be deleted from memory i.e. that it has an infinite read limit. If the contents of a file is requested before read limit has been set, then the read limit is set to zero (i.e. infinity).

2) You can set whether it should refuse to load unexpected files. Before you request the contents of a file, you must provide a read limit (zero is an acceptible value here; see above) for that file, or the %FileContentsMap will throw an exception when you request that file.

assign(self: pyrosetta.rosetta.utility.io.FileContentsMap, : pyrosetta.rosetta.utility.io.FileContentsMap) pyrosetta.rosetta.utility.io.FileContentsMap

C++: utility::io::FileContentsMap::operator=(const class utility::io::FileContentsMap &) –> class utility::io::FileContentsMap &

clear(self: pyrosetta.rosetta.utility.io.FileContentsMap) None

Delete the contents of all files and file-read counts from memory

C++: utility::io::FileContentsMap::clear() –> void

delete_contents_at_nread_limit(*args, **kwargs)

Overloaded function.

  1. delete_contents_at_nread_limit(self: pyrosetta.rosetta.utility.io.FileContentsMap, setting: bool) -> None

Enable or disable the behavior that the %FileContentsMap will delete

the contents of files from memory after they have been read as many times as they were expected to be read (their read limit).

C++: utility::io::FileContentsMap::delete_contents_at_nread_limit(bool) –> void

  1. delete_contents_at_nread_limit(self: pyrosetta.rosetta.utility.io.FileContentsMap) -> bool

Return the boolean value describing whether the %FileContentsMap will

delete the contents of files from memory after they have reached their read limit.

C++: utility::io::FileContentsMap::delete_contents_at_nread_limit() const –> bool

delete_file_contents(self: pyrosetta.rosetta.utility.io.FileContentsMap, fname: str) None

Delete the contents of a particular file from memory

C++: utility::io::FileContentsMap::delete_file_contents(const std::string &) –> void

get_file_contents(self: pyrosetta.rosetta.utility.io.FileContentsMap, fname: str) str
Return the string contents of a file, possibly loading the contents of that file

into memory for the first time, always updating internal data, and possibly deleting the contents of a file if it is expected to no longer be needed.

C++: utility::io::FileContentsMap::get_file_contents(const std::string &) –> std::string

get_file_contents_ref(self: pyrosetta.rosetta.utility.io.FileContentsMap, fname: str) str
Return a reference to the string contents of a file, possibly loading the contents

of that file into memory for the first time, but not deleting the contents of that file.

C++: utility::io::FileContentsMap::get_file_contents_ref(const std::string &) –> const std::string &

has_file_contents(self: pyrosetta.rosetta.utility.io.FileContentsMap, fname: str) bool

Return whether or not the %FileContentsMap has the contents of a file in memory

C++: utility::io::FileContentsMap::has_file_contents(const std::string &) const –> bool

has_read_limit_for_file(self: pyrosetta.rosetta.utility.io.FileContentsMap, fname: str) bool

Return whether a read limit (even one of zero) has been set for a file

C++: utility::io::FileContentsMap::has_read_limit_for_file(const std::string &) const –> bool

increment_nread_limit(self: pyrosetta.rosetta.utility.io.FileContentsMap, fname: str) None

Increment the internal nread limit for a file

C++: utility::io::FileContentsMap::increment_nread_limit(const std::string &) –> void

nread_limit_for_file(self: pyrosetta.rosetta.utility.io.FileContentsMap, fname: str) int
Return the read limit that has been set for this file; this will return

a value of zero even if the file has not had a read limit set. Use has_read_limit to determine if a read limit has been set for a particular file.

C++: utility::io::FileContentsMap::nread_limit_for_file(const std::string &) const –> unsigned long

nreads_for_file(self: pyrosetta.rosetta.utility.io.FileContentsMap, fname: str) int

Return the number of times a particular file has been read

C++: utility::io::FileContentsMap::nreads_for_file(const std::string &) const –> unsigned long

refuse_unexpected_files(*args, **kwargs)

Overloaded function.

  1. refuse_unexpected_files(self: pyrosetta.rosetta.utility.io.FileContentsMap, setting: bool) -> None

Enable or disable the behavior that the FCM will refuse to load a file if

a non-zero expected number of reads for that file has not been previously provided.

C++: utility::io::FileContentsMap::refuse_unexpected_files(bool) –> void

  1. refuse_unexpected_files(self: pyrosetta.rosetta.utility.io.FileContentsMap) -> bool

Return the boolean value describing whether the %FileContentsMap will refuse

to load files that it does not expect to load.

C++: utility::io::FileContentsMap::refuse_unexpected_files() const –> bool

set_file_contents(self: pyrosetta.rosetta.utility.io.FileContentsMap, fname: str, contents: str) None
Set the contents of a file from an input string thereby avoiding a read from

disk.

C++: utility::io::FileContentsMap::set_file_contents(const std::string &, const std::string &) –> void

set_nread_limit_for_file(self: pyrosetta.rosetta.utility.io.FileContentsMap, fname: str, limit: int) None
Set the maximum number of reads for a file; if this is zero, then that

file can be read an indefinite number of times.

C++: utility::io::FileContentsMap::set_nread_limit_for_file(const std::string &, unsigned long) –> void

class pyrosetta.rosetta.utility.io.GeneralFileContents

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.utility.io.GeneralFileContents, : pyrosetta.rosetta.utility.io.GeneralFileContents) pyrosetta.rosetta.utility.io.GeneralFileContents

C++: utility::io::GeneralFileContents::operator=(const class utility::io::GeneralFileContents &) –> class utility::io::GeneralFileContents &

clone(self: pyrosetta.rosetta.utility.io.GeneralFileContents) pyrosetta.rosetta.utility.io.GeneralFileContents

Clone function: make a copy of this object and return an owning pointer to the copy.

C++: utility::io::GeneralFileContents::clone() const –> class std::shared_ptr<class utility::io::GeneralFileContents>

get_file_contents(self: pyrosetta.rosetta.utility.io.GeneralFileContents) str

C++: utility::io::GeneralFileContents::get_file_contents() const –> const std::string &

class pyrosetta.rosetta.utility.io.GeneralFileContentsVector

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.utility.io.GeneralFileContentsVector, : pyrosetta.rosetta.utility.io.GeneralFileContentsVector) pyrosetta.rosetta.utility.io.GeneralFileContentsVector

C++: utility::io::GeneralFileContentsVector::operator=(const class utility::io::GeneralFileContentsVector &) –> class utility::io::GeneralFileContentsVector &

clone(self: pyrosetta.rosetta.utility.io.GeneralFileContentsVector) pyrosetta.rosetta.utility.io.GeneralFileContentsVector

Clone function: make a copy of this object and return an owning pointer to the copy.

C++: utility::io::GeneralFileContentsVector::clone() const –> class std::shared_ptr<class utility::io::GeneralFileContentsVector>

get_file_contents(self: pyrosetta.rosetta.utility.io.GeneralFileContentsVector) pyrosetta.rosetta.utility.vector1_std_string

C++: utility::io::GeneralFileContentsVector::get_file_contents() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

class pyrosetta.rosetta.utility.io.GeneralFileManager

Bases: pyrosetta.rosetta.utility.SingletonBase_utility_io_GeneralFileManager_t

get_file_contents(self: pyrosetta.rosetta.utility.io.GeneralFileManager, filename: str) str

Get a weights file. Load it from disk if it has not already been loaded.

Threadsafe and lazily loaded.

C++: utility::io::GeneralFileManager::get_file_contents(const std::string &) const –> const std::string &

static get_instance() utility::io::GeneralFileManager

C++: utility::SingletonBase<utility::io::GeneralFileManager>::get_instance() –> class utility::io::GeneralFileManager *

class pyrosetta.rosetta.utility.io.GeneralFileManagerVector

Bases: pyrosetta.rosetta.utility.SingletonBase_utility_io_GeneralFileManagerVector_t

get_file_contents(self: pyrosetta.rosetta.utility.io.GeneralFileManagerVector, filename: str) pyrosetta.rosetta.utility.vector1_std_string

Get a vector of file contents. Load it from disk if it has not already been loaded.

Threadsafe and lazily loaded.

C++: utility::io::GeneralFileManagerVector::get_file_contents(const std::string &) const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

static get_instance() utility::io::GeneralFileManagerVector

C++: utility::SingletonBase<utility::io::GeneralFileManagerVector>::get_instance() –> class utility::io::GeneralFileManagerVector *

pyrosetta.rosetta.utility.io.base64_decode(s: str) str

C++: utility::io::base64_decode(const std::string &) –> std::string

pyrosetta.rosetta.utility.io.base64_encode(: int, len: int) str

C++: utility::io::base64_encode(const unsigned char *, unsigned int) –> std::string

pyrosetta.rosetta.utility.io.get_lines_from_file_data(filename: str) pyrosetta.rosetta.utility.vector1_std_string

General method that opens a file and returns its data as a list of lines after checking for errors.

C++: utility::io::get_lines_from_file_data(const std::string &) –> class utility::vector1<std::string, class std::allocator<std::string > >

pyrosetta.rosetta.utility.io.getline(*args, **kwargs)

Overloaded function.

  1. getline(stream: pyrosetta.rosetta.utility.io.izstream, line: str) -> pyrosetta.rosetta.utility.io.izstream

std::getline( std::istream, std::string ) wrapper

C++: utility::io::getline(class utility::io::izstream &, std::string &) –> class utility::io::izstream &

  1. getline(stream: pyrosetta.rosetta.utility.io.izstream, line: str, delim: str) -> pyrosetta.rosetta.utility.io.izstream

std::getline( std::istream, std::string, char ) wrapper

C++: utility::io::getline(class utility::io::izstream &, std::string &, const char) –> class utility::io::izstream &

class pyrosetta.rosetta.utility.io.icstream

Bases: pyrosetta.rosetta.utility.io.irstream

icstream: Input channel stream wrapper class

bad(self: pyrosetta.rosetta.utility.io.icstream) bool

Bad?

C++: utility::io::icstream::bad() const –> bool

clear(self: pyrosetta.rosetta.utility.io.icstream) None

Clear the stream

C++: utility::io::icstream::clear() –> void

compressed(self: pyrosetta.rosetta.utility.io.icstream) bool

Compressed?

C++: utility::io::icstream::compressed() const –> bool

eof(self: pyrosetta.rosetta.utility.io.icstream) bool

End of file?

C++: utility::io::icstream::eof() const –> bool

fail(self: pyrosetta.rosetta.utility.io.icstream) bool

Fail?

C++: utility::io::icstream::fail() const –> bool

get(*args, **kwargs)

Overloaded function.

  1. get(self: pyrosetta.rosetta.utility.io.icstream) -> int

Get the next character

C++: utility::io::icstream::get() –> int

  1. get(self: pyrosetta.rosetta.utility.io.icstream, c: str) -> pyrosetta.rosetta.utility.io.icstream

Get the next character

C++: utility::io::icstream::get(char &) –> class utility::io::icstream &

  1. get(self: pyrosetta.rosetta.utility.io.icstream, str: str, count: int) -> pyrosetta.rosetta.utility.io.icstream

Get the next specified number of characters

C++: utility::io::icstream::get(char *, const long) –> class utility::io::icstream &

  1. get(self: pyrosetta.rosetta.utility.io.icstream, str: str, count: int, delim: str) -> pyrosetta.rosetta.utility.io.icstream

Get the next specified number of characters

C++: utility::io::icstream::get(char *, const long, const char) –> class utility::io::icstream &

  1. get(self: pyrosetta.rosetta.utility.io.icstream, str: str, count: int) -> pyrosetta.rosetta.utility.io.icstream

Get the next specified number of characters

C++: utility::io::icstream::get(std::string &, const long) –> class utility::io::icstream &

  1. get(self: pyrosetta.rosetta.utility.io.icstream, str: str, count: int, delim: str) -> pyrosetta.rosetta.utility.io.icstream

Get the next specified number of characters

C++: utility::io::icstream::get(std::string &, const long, const char) –> class utility::io::icstream &

getline(*args, **kwargs)

Overloaded function.

  1. getline(self: pyrosetta.rosetta.utility.io.icstream, line: str, count: int) -> pyrosetta.rosetta.utility.io.icstream

Get the rest of the line

C++: utility::io::icstream::getline(char *, const long) –> class utility::io::icstream &

  1. getline(self: pyrosetta.rosetta.utility.io.icstream, line: str, count: int, delim: str) -> pyrosetta.rosetta.utility.io.icstream

Get the rest of the line

C++: utility::io::icstream::getline(char *, const long, const char) –> class utility::io::icstream &

  1. getline(self: pyrosetta.rosetta.utility.io.icstream, line: str) -> pyrosetta.rosetta.utility.io.icstream

Get the rest of the line

C++: utility::io::icstream::getline(std::string &) –> class utility::io::icstream &

  1. getline(self: pyrosetta.rosetta.utility.io.icstream, line: str, delim: str) -> pyrosetta.rosetta.utility.io.icstream

Get the rest of the line

C++: utility::io::icstream::getline(std::string &, const char) –> class utility::io::icstream &

good(self: pyrosetta.rosetta.utility.io.icstream) bool

Good?

C++: utility::io::icstream::good() const –> bool

gzipped(self: pyrosetta.rosetta.utility.io.icstream) bool

gzipped?

C++: utility::io::icstream::gzipped() const –> bool

ignore(*args, **kwargs)

Overloaded function.

  1. ignore(self: pyrosetta.rosetta.utility.io.icstream) -> pyrosetta.rosetta.utility.io.icstream

Skip over the next character

C++: utility::io::icstream::ignore() –> class utility::io::icstream &

  1. ignore(self: pyrosetta.rosetta.utility.io.icstream, count: int) -> pyrosetta.rosetta.utility.io.icstream

Skip over the next specified number of characters

C++: utility::io::icstream::ignore(const long) –> class utility::io::icstream &

  1. ignore(self: pyrosetta.rosetta.utility.io.icstream, count: int, delim: str) -> pyrosetta.rosetta.utility.io.icstream

Skip over the next specified number of characters

C++: utility::io::icstream::ignore(const long, const char) –> class utility::io::icstream &

peek(self: pyrosetta.rosetta.utility.io.icstream) int

Returns the next character without extracting it

C++: utility::io::icstream::peek() –> int

putback(self: pyrosetta.rosetta.utility.io.icstream, c: str) pyrosetta.rosetta.utility.io.icstream

Put the last character read back into the stream and check that passed character is correct

C++: utility::io::icstream::putback(char) –> class utility::io::icstream &

rdbuf(self: pyrosetta.rosetta.utility.io.icstream) pyrosetta.rosetta.std.streambuf

Pointer to the stream buffer

C++: utility::io::icstream::rdbuf() const –> class std::basic_streambuf<char> *

read(*args, **kwargs)

Overloaded function.

  1. read(self: pyrosetta.rosetta.utility.io.icstream, str: str, count: int) -> pyrosetta.rosetta.utility.io.icstream

Read the next specified number of characters

C++: utility::io::icstream::read(char *, const long) –> class utility::io::icstream &

  1. read(self: pyrosetta.rosetta.utility.io.icstream, str: str, count: int) -> pyrosetta.rosetta.utility.io.icstream

Read the next specified number of characters

C++: utility::io::icstream::read(std::string &, const long) –> class utility::io::icstream &

readsome(*args, **kwargs)

Overloaded function.

  1. readsome(self: pyrosetta.rosetta.utility.io.icstream, str: str, count: int) -> int

Read the next available specified number of characters

C++: utility::io::icstream::readsome(char *, const long) –> long

  1. readsome(self: pyrosetta.rosetta.utility.io.icstream, str: str, count: int) -> int

Read the next available specified number of characters

C++: utility::io::icstream::readsome(std::string &, const long) –> long

seek_beg(self: pyrosetta.rosetta.utility.io.icstream) None

Seek to the beginning

C++: utility::io::icstream::seek_beg() –> void

stream(self: pyrosetta.rosetta.utility.io.icstream) pyrosetta.rosetta.std.istream

Stream access

C++: utility::io::icstream::stream() –> std::istream &

uncompressed(self: pyrosetta.rosetta.utility.io.icstream) bool

Uncompressed?

C++: utility::io::icstream::uncompressed() const –> bool

unget(self: pyrosetta.rosetta.utility.io.icstream) pyrosetta.rosetta.utility.io.icstream

Put the last character read back into the stream

C++: utility::io::icstream::unget() –> class utility::io::icstream &

class pyrosetta.rosetta.utility.io.irstream

Bases: pybind11_builtins.pybind11_object

orstream: Input stream wrapper abstract base class

bad(self: pyrosetta.rosetta.utility.io.irstream) bool

Bad?

C++: utility::io::irstream::bad() const –> bool

clear(self: pyrosetta.rosetta.utility.io.irstream) None

Clear the stream

C++: utility::io::irstream::clear() –> void

compressed(self: pyrosetta.rosetta.utility.io.irstream) bool

Compressed?

C++: utility::io::irstream::compressed() const –> bool

eof(self: pyrosetta.rosetta.utility.io.irstream) bool

End of file?

C++: utility::io::irstream::eof() const –> bool

fail(self: pyrosetta.rosetta.utility.io.irstream) bool

Fail?

C++: utility::io::irstream::fail() const –> bool

get(*args, **kwargs)

Overloaded function.

  1. get(self: pyrosetta.rosetta.utility.io.irstream) -> int

Get the next character

C++: utility::io::irstream::get() –> int

  1. get(self: pyrosetta.rosetta.utility.io.irstream, c: str) -> pyrosetta.rosetta.utility.io.irstream

Get the next character

C++: utility::io::irstream::get(char &) –> class utility::io::irstream &

  1. get(self: pyrosetta.rosetta.utility.io.irstream, str: str, count: int) -> pyrosetta.rosetta.utility.io.irstream

Get the next specified number of characters

C++: utility::io::irstream::get(char *, const long) –> class utility::io::irstream &

  1. get(self: pyrosetta.rosetta.utility.io.irstream, str: str, count: int, delim: str) -> pyrosetta.rosetta.utility.io.irstream

Get the next specified number of characters

C++: utility::io::irstream::get(char *, const long, const char) –> class utility::io::irstream &

  1. get(self: pyrosetta.rosetta.utility.io.irstream, str: str, count: int) -> pyrosetta.rosetta.utility.io.irstream

Get the next specified number of characters

C++: utility::io::irstream::get(std::string &, const long) –> class utility::io::irstream &

  1. get(self: pyrosetta.rosetta.utility.io.irstream, str: str, count: int, delim: str) -> pyrosetta.rosetta.utility.io.irstream

Get the next specified number of characters

C++: utility::io::irstream::get(std::string &, const long, const char) –> class utility::io::irstream &

getline(*args, **kwargs)

Overloaded function.

  1. getline(self: pyrosetta.rosetta.utility.io.irstream, line: str, count: int) -> pyrosetta.rosetta.utility.io.irstream

Get the rest of the line

C++: utility::io::irstream::getline(char *, const long) –> class utility::io::irstream &

  1. getline(self: pyrosetta.rosetta.utility.io.irstream, line: str, count: int, delim: str) -> pyrosetta.rosetta.utility.io.irstream

Get the rest of the line

C++: utility::io::irstream::getline(char *, const long, const char) –> class utility::io::irstream &

  1. getline(self: pyrosetta.rosetta.utility.io.irstream, line: str) -> pyrosetta.rosetta.utility.io.irstream

Get the rest of the line

C++: utility::io::irstream::getline(std::string &) –> class utility::io::irstream &

  1. getline(self: pyrosetta.rosetta.utility.io.irstream, line: str, delim: str) -> pyrosetta.rosetta.utility.io.irstream

Get the rest of the line

C++: utility::io::irstream::getline(std::string &, const char) –> class utility::io::irstream &

good(self: pyrosetta.rosetta.utility.io.irstream) bool

Good?

C++: utility::io::irstream::good() const –> bool

gzipped(self: pyrosetta.rosetta.utility.io.irstream) bool

gzipped?

C++: utility::io::irstream::gzipped() const –> bool

ignore(*args, **kwargs)

Overloaded function.

  1. ignore(self: pyrosetta.rosetta.utility.io.irstream) -> pyrosetta.rosetta.utility.io.irstream

Skip over the next character

C++: utility::io::irstream::ignore() –> class utility::io::irstream &

  1. ignore(self: pyrosetta.rosetta.utility.io.irstream, count: int) -> pyrosetta.rosetta.utility.io.irstream

Skip over the next specified number of characters

C++: utility::io::irstream::ignore(const long) –> class utility::io::irstream &

  1. ignore(self: pyrosetta.rosetta.utility.io.irstream, count: int, delim: str) -> pyrosetta.rosetta.utility.io.irstream

Skip over the next specified number of characters

C++: utility::io::irstream::ignore(const long, const char) –> class utility::io::irstream &

peek(self: pyrosetta.rosetta.utility.io.irstream) int

Returns the next character without extracting it

C++: utility::io::irstream::peek() –> int

putback(self: pyrosetta.rosetta.utility.io.irstream, c: str) pyrosetta.rosetta.utility.io.irstream

Put the last character read back into the stream and check that passed character is correct

C++: utility::io::irstream::putback(char) –> class utility::io::irstream &

rdbuf(self: pyrosetta.rosetta.utility.io.irstream) pyrosetta.rosetta.std.streambuf

Pointer to the stream buffer

C++: utility::io::irstream::rdbuf() const –> class std::basic_streambuf<char> *

read(*args, **kwargs)

Overloaded function.

  1. read(self: pyrosetta.rosetta.utility.io.irstream, str: str, count: int) -> pyrosetta.rosetta.utility.io.irstream

Read the next specified number of characters

C++: utility::io::irstream::read(char *, const long) –> class utility::io::irstream &

  1. read(self: pyrosetta.rosetta.utility.io.irstream, str: str, count: int) -> pyrosetta.rosetta.utility.io.irstream

Read the next specified number of characters

C++: utility::io::irstream::read(std::string &, const long) –> class utility::io::irstream &

readsome(*args, **kwargs)

Overloaded function.

  1. readsome(self: pyrosetta.rosetta.utility.io.irstream, str: str, count: int) -> int

Read the next available specified number of characters

C++: utility::io::irstream::readsome(char *, const long) –> long

  1. readsome(self: pyrosetta.rosetta.utility.io.irstream, str: str, count: int) -> int

Read the next available specified number of characters

C++: utility::io::irstream::readsome(std::string &, const long) –> long

seek_beg(self: pyrosetta.rosetta.utility.io.irstream) None

Seek to the beginning

C++: utility::io::irstream::seek_beg() –> void

stream(self: pyrosetta.rosetta.utility.io.irstream) pyrosetta.rosetta.std.istream

Stream access

C++: utility::io::irstream::stream() –> std::istream &

uncompressed(self: pyrosetta.rosetta.utility.io.irstream) bool

Uncompressed?

C++: utility::io::irstream::uncompressed() const –> bool

unget(self: pyrosetta.rosetta.utility.io.irstream) pyrosetta.rosetta.utility.io.irstream

Put the last character read back into the stream

C++: utility::io::irstream::unget() –> class utility::io::irstream &

class pyrosetta.rosetta.utility.io.izstream

Bases: pyrosetta.rosetta.utility.io.irstream

izstream: Input file stream wrapper for uncompressed and compressed files

bad(self: pyrosetta.rosetta.utility.io.izstream) bool

Bad?

C++: utility::io::izstream::bad() const –> bool

clear(self: pyrosetta.rosetta.utility.io.izstream) None

Clear the stream(s)

C++: utility::io::izstream::clear() –> void

close(self: pyrosetta.rosetta.utility.io.izstream) None

Close the ifstream and reset the state

C++: utility::io::izstream::close() –> void

compressed(self: pyrosetta.rosetta.utility.io.izstream) bool

Compressed?

C++: utility::io::izstream::compressed() const –> bool

eof(self: pyrosetta.rosetta.utility.io.izstream) bool

End of file?

C++: utility::io::izstream::eof() const –> bool

fail(self: pyrosetta.rosetta.utility.io.izstream) bool

Fail?

C++: utility::io::izstream::fail() const –> bool

filename(self: pyrosetta.rosetta.utility.io.izstream) str

File name

C++: utility::io::izstream::filename() const –> const std::string &

gcount(self: pyrosetta.rosetta.utility.io.izstream) int

Get the number of characters read by the last unformatted read

C++: utility::io::izstream::gcount() const –> long

get(*args, **kwargs)

Overloaded function.

  1. get(self: pyrosetta.rosetta.utility.io.izstream) -> int

Get the next character

C++: utility::io::izstream::get() –> int

  1. get(self: pyrosetta.rosetta.utility.io.izstream, c: str) -> pyrosetta.rosetta.utility.io.izstream

Get the next character

C++: utility::io::izstream::get(char &) –> class utility::io::izstream &

  1. get(self: pyrosetta.rosetta.utility.io.izstream, str: str, count: int) -> pyrosetta.rosetta.utility.io.izstream

Get the next specified number of characters

C++: utility::io::izstream::get(char *, const long) –> class utility::io::izstream &

  1. get(self: pyrosetta.rosetta.utility.io.izstream, str: str, count: int, delim: str) -> pyrosetta.rosetta.utility.io.izstream

Get the next specified number of characters

C++: utility::io::izstream::get(char *, const long, const char) –> class utility::io::izstream &

  1. get(self: pyrosetta.rosetta.utility.io.izstream, str: str, count: int) -> pyrosetta.rosetta.utility.io.izstream

Get the next specified number of characters

C++: utility::io::izstream::get(std::string &, const long) –> class utility::io::izstream &

  1. get(self: pyrosetta.rosetta.utility.io.izstream, str: str, count: int, delim: str) -> pyrosetta.rosetta.utility.io.izstream

Get the next specified number of characters

C++: utility::io::izstream::get(std::string &, const long, const char) –> class utility::io::izstream &

static get_alternative_search_paths() pyrosetta.rosetta.utility.vector1_std_string

C++: utility::io::izstream::get_alternative_search_paths() –> class utility::vector1<std::string, class std::allocator<std::string > >

getline(*args, **kwargs)

Overloaded function.

  1. getline(self: pyrosetta.rosetta.utility.io.izstream, line: str, count: int) -> pyrosetta.rosetta.utility.io.izstream

Get the rest of the line

C++: utility::io::izstream::getline(char *, const long) –> class utility::io::izstream &

  1. getline(self: pyrosetta.rosetta.utility.io.izstream, line: str, count: int, delim: str) -> pyrosetta.rosetta.utility.io.izstream

Get the rest of the line

C++: utility::io::izstream::getline(char *, const long, const char) –> class utility::io::izstream &

  1. getline(self: pyrosetta.rosetta.utility.io.izstream, line: str) -> pyrosetta.rosetta.utility.io.izstream

Get the rest of the line

C++: utility::io::izstream::getline(std::string &) –> class utility::io::izstream &

  1. getline(self: pyrosetta.rosetta.utility.io.izstream, line: str, delim: str) -> pyrosetta.rosetta.utility.io.izstream

Get the rest of the line

C++: utility::io::izstream::getline(std::string &, const char) –> class utility::io::izstream &

good(self: pyrosetta.rosetta.utility.io.izstream) bool

Good?

C++: utility::io::izstream::good() const –> bool

gzipped(self: pyrosetta.rosetta.utility.io.izstream) bool

gzipped?

C++: utility::io::izstream::gzipped() const –> bool

ignore(*args, **kwargs)

Overloaded function.

  1. ignore(self: pyrosetta.rosetta.utility.io.izstream) -> pyrosetta.rosetta.utility.io.izstream

Skip over the next character

C++: utility::io::izstream::ignore() –> class utility::io::izstream &

  1. ignore(self: pyrosetta.rosetta.utility.io.izstream, count: int) -> pyrosetta.rosetta.utility.io.izstream

Skip over the next specified number of characters

C++: utility::io::izstream::ignore(const long) –> class utility::io::izstream &

  1. ignore(self: pyrosetta.rosetta.utility.io.izstream, count: int, delim: str) -> pyrosetta.rosetta.utility.io.izstream

Skip over the next specified number of characters

C++: utility::io::izstream::ignore(const long, const char) –> class utility::io::izstream &

open(*args, **kwargs)

Overloaded function.

  1. open(self: pyrosetta.rosetta.utility.io.izstream, filename_a: str) -> None

  2. open(self: pyrosetta.rosetta.utility.io.izstream, filename_a: str, open_mode: pyrosetta.rosetta.std._Ios_Openmode) -> None

Open a file

C++: utility::io::izstream::open(const std::string &, enum std::_Ios_Openmode) –> void

peek(self: pyrosetta.rosetta.utility.io.izstream) int

Returns the next character without extracting it

C++: utility::io::izstream::peek() –> int

putback(self: pyrosetta.rosetta.utility.io.izstream, c: str) pyrosetta.rosetta.utility.io.izstream
Put the last character read back into the stream and check

that passed character is correct

C++: utility::io::izstream::putback(char) –> class utility::io::izstream &

rdbuf(self: pyrosetta.rosetta.utility.io.izstream) pyrosetta.rosetta.std.streambuf

Pointer to the stream buffer

C++: utility::io::izstream::rdbuf() const –> class std::basic_streambuf<char> *

read(*args, **kwargs)

Overloaded function.

  1. read(self: pyrosetta.rosetta.utility.io.izstream, str: str, count: int) -> pyrosetta.rosetta.utility.io.izstream

Read the next specified number of characters

C++: utility::io::izstream::read(char *, const long) –> class utility::io::izstream &

  1. read(self: pyrosetta.rosetta.utility.io.izstream, str: str, count: int) -> pyrosetta.rosetta.utility.io.izstream

Read the next specified number of characters

C++: utility::io::izstream::read(std::string &, const long) –> class utility::io::izstream &

readsome(*args, **kwargs)

Overloaded function.

  1. readsome(self: pyrosetta.rosetta.utility.io.izstream, str: str, count: int) -> int

Read the next available specified number of characters

C++: utility::io::izstream::readsome(char *, const long) –> long

  1. readsome(self: pyrosetta.rosetta.utility.io.izstream, str: str, count: int) -> int

Read the next available specified number of characters

C++: utility::io::izstream::readsome(std::string &, const long) –> long

seek_beg(self: pyrosetta.rosetta.utility.io.izstream) None

Seek to the beginning

C++: utility::io::izstream::seek_beg() –> void

static set_alternative_search_paths(alternative_search_paths: pyrosetta.rosetta.utility.vector1_std_string) None

C++: utility::io::izstream::set_alternative_search_paths(class utility::vector1<std::string, class std::allocator<std::string > >) –> void

stream(self: pyrosetta.rosetta.utility.io.izstream) pyrosetta.rosetta.std.istream

Stream access

C++: utility::io::izstream::stream() –> std::istream &

uncompressed(self: pyrosetta.rosetta.utility.io.izstream) bool

Uncompressed?

C++: utility::io::izstream::uncompressed() const –> bool

unget(self: pyrosetta.rosetta.utility.io.izstream) pyrosetta.rosetta.utility.io.izstream

Put the last character read back into the stream

C++: utility::io::izstream::unget() –> class utility::io::izstream &

class pyrosetta.rosetta.utility.io.ocstream

Bases: pyrosetta.rosetta.utility.io.orstream

ocstream: Output channel stream wrapper class

bad(self: pyrosetta.rosetta.utility.io.ocstream) bool

Bad?

C++: utility::io::ocstream::bad() const –> bool

clear(self: pyrosetta.rosetta.utility.io.ocstream) None

Clear the stream

C++: utility::io::ocstream::clear() –> void

compressed(self: pyrosetta.rosetta.utility.io.ocstream) bool

Compressed?

C++: utility::io::ocstream::compressed() const –> bool

eof(self: pyrosetta.rosetta.utility.io.ocstream) bool

End of file?

C++: utility::io::ocstream::eof() const –> bool

fail(self: pyrosetta.rosetta.utility.io.ocstream) bool

Fail?

C++: utility::io::ocstream::fail() const –> bool

flush(self: pyrosetta.rosetta.utility.io.ocstream) pyrosetta.rosetta.utility.io.ocstream

Flush the stream

C++: utility::io::ocstream::flush() –> class utility::io::ocstream &

good(self: pyrosetta.rosetta.utility.io.ocstream) bool

Good?

C++: utility::io::ocstream::good() const –> bool

gzipped(self: pyrosetta.rosetta.utility.io.ocstream) bool

gzipped?

C++: utility::io::ocstream::gzipped() const –> bool

put(self: pyrosetta.rosetta.utility.io.ocstream, c: str) pyrosetta.rosetta.utility.io.ocstream

Write a char

C++: utility::io::ocstream::put(const char) –> class utility::io::ocstream &

rdbuf(self: pyrosetta.rosetta.utility.io.ocstream) pyrosetta.rosetta.std.streambuf

Pointer to the stream buffer

C++: utility::io::ocstream::rdbuf() const –> class std::basic_streambuf<char> *

stream(self: pyrosetta.rosetta.utility.io.ocstream) pyrosetta.rosetta.std.ostream

Stream access

C++: utility::io::ocstream::stream() –> std::ostream &

uncompressed(self: pyrosetta.rosetta.utility.io.ocstream) bool

Uncompressed?

C++: utility::io::ocstream::uncompressed() const –> bool

write(*args, **kwargs)

Overloaded function.

  1. write(self: pyrosetta.rosetta.utility.io.ocstream, str: str, count: int) -> pyrosetta.rosetta.utility.io.ocstream

Write a string

C++: utility::io::ocstream::write(const char *, const long) –> class utility::io::ocstream &

  1. write(self: pyrosetta.rosetta.utility.io.ocstream, str: str, count: int) -> pyrosetta.rosetta.utility.io.ocstream

Write a string

C++: utility::io::ocstream::write(const std::string &, const long) –> class utility::io::ocstream &

class pyrosetta.rosetta.utility.io.orstream

Bases: pybind11_builtins.pybind11_object

orstream: Output stream wrapper base class

bad(self: pyrosetta.rosetta.utility.io.orstream) bool

Bad?

C++: utility::io::orstream::bad() const –> bool

clear(self: pyrosetta.rosetta.utility.io.orstream) None

Clear the stream

C++: utility::io::orstream::clear() –> void

compressed(self: pyrosetta.rosetta.utility.io.orstream) bool

Compressed?

C++: utility::io::orstream::compressed() const –> bool

eof(self: pyrosetta.rosetta.utility.io.orstream) bool

End of file?

C++: utility::io::orstream::eof() const –> bool

fail(self: pyrosetta.rosetta.utility.io.orstream) bool

Fail?

C++: utility::io::orstream::fail() const –> bool

flush(self: pyrosetta.rosetta.utility.io.orstream) pyrosetta.rosetta.utility.io.orstream

Flush the stream

C++: utility::io::orstream::flush() –> class utility::io::orstream &

good(self: pyrosetta.rosetta.utility.io.orstream) bool

Good?

C++: utility::io::orstream::good() const –> bool

gzipped(self: pyrosetta.rosetta.utility.io.orstream) bool

gzipped?

C++: utility::io::orstream::gzipped() const –> bool

put(self: pyrosetta.rosetta.utility.io.orstream, c: str) pyrosetta.rosetta.utility.io.orstream

Write a char

C++: utility::io::orstream::put(const char) –> class utility::io::orstream &

rdbuf(self: pyrosetta.rosetta.utility.io.orstream) pyrosetta.rosetta.std.streambuf

Pointer to the stream buffer

C++: utility::io::orstream::rdbuf() const –> class std::basic_streambuf<char> *

stream(self: pyrosetta.rosetta.utility.io.orstream) pyrosetta.rosetta.std.ostream

Stream access

C++: utility::io::orstream::stream() –> std::ostream &

uncompressed(self: pyrosetta.rosetta.utility.io.orstream) bool

Uncompressed?

C++: utility::io::orstream::uncompressed() const –> bool

write(*args, **kwargs)

Overloaded function.

  1. write(self: pyrosetta.rosetta.utility.io.orstream, str: str, count: int) -> pyrosetta.rosetta.utility.io.orstream

Write a string

C++: utility::io::orstream::write(const char *, const long) –> class utility::io::orstream &

  1. write(self: pyrosetta.rosetta.utility.io.orstream, str: str, count: int) -> pyrosetta.rosetta.utility.io.orstream

Write a string

C++: utility::io::orstream::write(const std::string &, const long) –> class utility::io::orstream &

class pyrosetta.rosetta.utility.io.ozstream

Bases: pyrosetta.rosetta.utility.io.orstream

ozstream: Output file stream wrapper for uncompressed and compressed files

static MPI_reroute_rank() int

C++: utility::io::ozstream::MPI_reroute_rank() –> int

bad(self: pyrosetta.rosetta.utility.io.ozstream) bool

Bad?

C++: utility::io::ozstream::bad() const –> bool

buffer_size(*args, **kwargs)

Overloaded function.

  1. buffer_size(self: pyrosetta.rosetta.utility.io.ozstream) -> int

get buffer size (bytes)

In uncompressed mode this is the size of the character buffer.

In compressed mode this is the size of the zip buffer.

C++: utility::io::ozstream::buffer_size() const –> long

  1. buffer_size(self: pyrosetta.rosetta.utility.io.ozstream, buf_size: int) -> None

set buffer size (bytes)

In uncompressed mode this is the size of the character buffer.

In compressed mode this is the size of the zip buffer. Lower bound of 4KB is enforced due to zipstream requirements. Operation is skipped if the file is currently open, as the buffer is considered locked.

C++: utility::io::ozstream::buffer_size(const long &) –> void

clear(self: pyrosetta.rosetta.utility.io.ozstream) None

Clear the stream

C++: utility::io::ozstream::clear() –> void

close(self: pyrosetta.rosetta.utility.io.ozstream) None

Close the ofstream and reset the state

C++: utility::io::ozstream::close() –> void

compressed(self: pyrosetta.rosetta.utility.io.ozstream) bool

Compressed?

C++: utility::io::ozstream::compressed() const –> bool

static enable_MPI_reroute(min_client_rank: int, master_rank: int) None

C++: utility::io::ozstream::enable_MPI_reroute(int, int) –> void

eof(self: pyrosetta.rosetta.utility.io.ozstream) bool

End of file?

C++: utility::io::ozstream::eof() const –> bool

fail(self: pyrosetta.rosetta.utility.io.ozstream) bool

Fail?

C++: utility::io::ozstream::fail() const –> bool

filename(self: pyrosetta.rosetta.utility.io.ozstream) str

File name

C++: utility::io::ozstream::filename() const –> const std::string &

flush(self: pyrosetta.rosetta.utility.io.ozstream) pyrosetta.rosetta.utility.io.ozstream

Flush the stream – currently alias to flush_finalize()

Instead doing a regular flush, we currently force a

completion of the zip stream. We do this to pre-empt against several things: (1) the expensive operation of closing and re-opening a stream (2) confusion and inconvenience that may result from users calling flushes and ending upon with broken or corrupted files if a job is somehow interrupted (e.g. on a cluster). Please note that calling flush_finalize() too often can seriously degrade compression. zlib documentation appears to imply that every 1MB or so is a reasonable rule of thumb.

C++: utility::io::ozstream::flush() –> class utility::io::ozstream &

flush_finalize(self: pyrosetta.rosetta.utility.io.ozstream) pyrosetta.rosetta.utility.io.ozstream

Flush the streams and finalize the zip stream

Calling this will complete the zip stream.

Upon the next write, a new zip stream will be started. Please note that calling flush_finalize() too often can seriously degrade compression. zlib documentation appears to imply that every 1MB or so is a reasonable rule of thumb.

C++: utility::io::ozstream::flush_finalize() –> class utility::io::ozstream &

good(self: pyrosetta.rosetta.utility.io.ozstream) bool

Good?

C++: utility::io::ozstream::good() const –> bool

gzipped(self: pyrosetta.rosetta.utility.io.ozstream) bool

gzipped?

C++: utility::io::ozstream::gzipped() const –> bool

open(*args, **kwargs)

Overloaded function.

  1. open(self: pyrosetta.rosetta.utility.io.ozstream, filename_a: str) -> None

  2. open(self: pyrosetta.rosetta.utility.io.ozstream, filename_a: str, open_mode: pyrosetta.rosetta.std._Ios_Openmode) -> None

Open a file

C++: utility::io::ozstream::open(const std::string &, enum std::_Ios_Openmode) –> void

open_append(self: pyrosetta.rosetta.utility.io.ozstream, filename_a: str) None

Open a text file for appending

C++: utility::io::ozstream::open_append(const std::string &) –> void

open_append_if_existed(self: pyrosetta.rosetta.utility.io.ozstream, filename_a: str, preprinted_header: pyrosetta.rosetta.std.stringstream) None

open file as append if it exists, return true if file existed before, false if it is new.

C++: utility::io::ozstream::open_append_if_existed(const std::string &, class std::basic_stringstream<char> &) –> void

put(self: pyrosetta.rosetta.utility.io.ozstream, c: str) pyrosetta.rosetta.utility.io.ozstream

Write a char

C++: utility::io::ozstream::put(const char) –> class utility::io::ozstream &

rdbuf(self: pyrosetta.rosetta.utility.io.ozstream) pyrosetta.rosetta.std.streambuf

Pointer to the stream buffer

C++: utility::io::ozstream::rdbuf() const –> class std::basic_streambuf<char> *

stream(self: pyrosetta.rosetta.utility.io.ozstream) pyrosetta.rosetta.std.ostream

Stream access

C++: utility::io::ozstream::stream() –> std::ostream &

uncompressed(self: pyrosetta.rosetta.utility.io.ozstream) bool

Uncompressed?

C++: utility::io::ozstream::uncompressed() const –> bool

write(*args, **kwargs)

Overloaded function.

  1. write(self: pyrosetta.rosetta.utility.io.ozstream, str: str, count: int) -> pyrosetta.rosetta.utility.io.ozstream

Write a string

C++: utility::io::ozstream::write(const char *, const long) –> class utility::io::ozstream &

  1. write(self: pyrosetta.rosetta.utility.io.ozstream, str: str, count: int) -> pyrosetta.rosetta.utility.io.ozstream

Write a string

C++: utility::io::ozstream::write(const std::string &, const long) –> class utility::io::ozstream &

zflush(self: pyrosetta.rosetta.utility.io.ozstream) None

Flush the zip_ostream

this will flush but not finalize the zip stream

C++: utility::io::ozstream::zflush() –> void

zflush_finalize(self: pyrosetta.rosetta.utility.io.ozstream) None

Flush and finalize the zip_stream

Calling this will complete the zip stream.

Upon the next write, a new zip stream will be started Please note that calling zflush_finalize() too often can seriously degrade compression. zlib documentation appears to imply that every 1MB or so is a reasonable rule of thumb.

C++: utility::io::ozstream::zflush_finalize() –> void

pyrosetta.rosetta.utility.io.remove_inline_comments(line: str) None

General method for removing comments from a line read from a database file.

C++: utility::io::remove_inline_comments(std::string &) –> void

pyrosetta.rosetta.utility.io.skip(*args, **kwargs)

Overloaded function.

  1. skip(stream: pyrosetta.rosetta.utility.io.izstream) -> pyrosetta.rosetta.std.istream

Skip rest of line and line terminator (manipulator)

C++: utility::io::skip(class utility::io::izstream &) –> std::istream &

  1. skip(stream: pyrosetta.rosetta.std.istream) -> pyrosetta.rosetta.std.istream

Skip rest of line and line terminator (manipulator)

C++: utility::io::skip(std::istream &) –> std::istream &