utility

• excn
• factory
• file
• graph
• has_insertion_operator_implementation
• io
• json_spirit
• keys
• libsvm
• options
• py
• signals
• sql_database
• tag
• tools
• xsd_util

Bindings for ::utility namespace

pyrosetta.rosetta.utility.CSI_Black() → pyrosetta.rosetta.utility.CSI_Sequence

C++: utility::CSI_Black() –> class utility::CSI_Sequence

pyrosetta.rosetta.utility.CSI_Blue() → pyrosetta.rosetta.utility.CSI_Sequence

C++: utility::CSI_Blue() –> class utility::CSI_Sequence

pyrosetta.rosetta.utility.CSI_Bold() → pyrosetta.rosetta.utility.CSI_Sequence

C++: utility::CSI_Bold() –> class utility::CSI_Sequence

pyrosetta.rosetta.utility.CSI_Cyan() → pyrosetta.rosetta.utility.CSI_Sequence

C++: utility::CSI_Cyan() –> class utility::CSI_Sequence

pyrosetta.rosetta.utility.CSI_Default() → pyrosetta.rosetta.utility.CSI_Sequence

C++: utility::CSI_Default() –> class utility::CSI_Sequence

pyrosetta.rosetta.utility.CSI_Green() → pyrosetta.rosetta.utility.CSI_Sequence

C++: utility::CSI_Green() –> class utility::CSI_Sequence

pyrosetta.rosetta.utility.CSI_Magenta() → pyrosetta.rosetta.utility.CSI_Sequence

C++: utility::CSI_Magenta() –> class utility::CSI_Sequence

pyrosetta.rosetta.utility.CSI_Nothing() → pyrosetta.rosetta.utility.CSI_Sequence

Functions to return CSI_Seqeunce objects.

These are not static constants, due to the static initilization order fiasco. Codes below is all Hogwarts-approved magic numbers, so do not modify them. For reference see: http://en.wikipedia.org/wiki/ANSI_escape_code#CSI_codes

C++: utility::CSI_Nothing() –> class utility::CSI_Sequence

pyrosetta.rosetta.utility.CSI_Red() → pyrosetta.rosetta.utility.CSI_Sequence

C++: utility::CSI_Red() –> class utility::CSI_Sequence

pyrosetta.rosetta.utility.CSI_Reset() → pyrosetta.rosetta.utility.CSI_Sequence

C++: utility::CSI_Reset() –> class utility::CSI_Sequence

class pyrosetta.rosetta.utility.CSI_Sequence

Bases: pybind11_builtins.pybind11_object

Class to hold all Terminal ASCII codes as static data for CSI_Sequence. Note: that on non-tty terminals the codes will not print to avoid polution of Rosetta logs.

__add__(self: pyrosetta.rosetta.utility.CSI_Sequence, right: pyrosetta.rosetta.utility.CSI_Sequence) → pyrosetta.rosetta.utility.CSI_Sequence

C++: utility::CSI_Sequence::operator+(const class utility::CSI_Sequence &) const –> class utility::CSI_Sequence

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.utility.CSI_Sequence) -> None

doc

2. __init__(self: pyrosetta.rosetta.utility.CSI_Sequence, sequence: str) -> None
3. __init__(self: pyrosetta.rosetta.utility.CSI_Sequence, arg0: pyrosetta.rosetta.utility.CSI_Sequence) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.utility.CSI_Sequence) → str

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

assign(self: pyrosetta.rosetta.utility.CSI_Sequence, : pyrosetta.rosetta.utility.CSI_Sequence) → pyrosetta.rosetta.utility.CSI_Sequence

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

suppress_CSI_codes() → None

If called, suppress all future printing of CSI codes

C++: utility::CSI_Sequence::suppress_CSI_codes() –> void

pyrosetta.rosetta.utility.CSI_Underline() → pyrosetta.rosetta.utility.CSI_Sequence

C++: utility::CSI_Underline() –> class utility::CSI_Sequence

pyrosetta.rosetta.utility.CSI_White() → pyrosetta.rosetta.utility.CSI_Sequence

C++: utility::CSI_White() –> class utility::CSI_Sequence

pyrosetta.rosetta.utility.CSI_Yellow() → pyrosetta.rosetta.utility.CSI_Sequence

C++: utility::CSI_Yellow() –> class utility::CSI_Sequence

pyrosetta.rosetta.utility.CSI_bgBlack() → pyrosetta.rosetta.utility.CSI_Sequence

C++: utility::CSI_bgBlack() –> class utility::CSI_Sequence

pyrosetta.rosetta.utility.CSI_bgBlue() → pyrosetta.rosetta.utility.CSI_Sequence

C++: utility::CSI_bgBlue() –> class utility::CSI_Sequence

pyrosetta.rosetta.utility.CSI_bgCyan() → pyrosetta.rosetta.utility.CSI_Sequence

C++: utility::CSI_bgCyan() –> class utility::CSI_Sequence

pyrosetta.rosetta.utility.CSI_bgDefault() → pyrosetta.rosetta.utility.CSI_Sequence

C++: utility::CSI_bgDefault() –> class utility::CSI_Sequence

pyrosetta.rosetta.utility.CSI_bgGreen() → pyrosetta.rosetta.utility.CSI_Sequence

C++: utility::CSI_bgGreen() –> class utility::CSI_Sequence

pyrosetta.rosetta.utility.CSI_bgMagenta() → pyrosetta.rosetta.utility.CSI_Sequence

C++: utility::CSI_bgMagenta() –> class utility::CSI_Sequence

pyrosetta.rosetta.utility.CSI_bgRed() → pyrosetta.rosetta.utility.CSI_Sequence

C++: utility::CSI_bgRed() –> class utility::CSI_Sequence

pyrosetta.rosetta.utility.CSI_bgWhite() → pyrosetta.rosetta.utility.CSI_Sequence

C++: utility::CSI_bgWhite() –> class utility::CSI_Sequence

pyrosetta.rosetta.utility.CSI_bgYellow() → pyrosetta.rosetta.utility.CSI_Sequence

C++: utility::CSI_bgYellow() –> class utility::CSI_Sequence

pyrosetta.rosetta.utility.Real2string(: float, decimal_places: int) → str

convert a Real to string at a number of decimal places, optionally pad left.

C++: utility::Real2string(double, const unsigned long) –> std::string

class pyrosetta.rosetta.utility.SimulateMPI

Bases: pybind11_builtins.pybind11_object

singleton class storing simulated MPI state

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__

Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

initialize_simulation(nprocs: int) → None

C++: utility::SimulateMPI::initialize_simulation(int) –> void

mpi_nprocs() → int

C++: utility::SimulateMPI::mpi_nprocs() –> int

mpi_rank() → int

C++: utility::SimulateMPI::mpi_rank() –> int

receive_char_from_node(source: int) → str

C++: utility::SimulateMPI::receive_char_from_node(int) –> char

receive_double_from_node(source: int) → float

C++: utility::SimulateMPI::receive_double_from_node(int) –> double

receive_doubles_from_node(source: int) → pyrosetta.rosetta.utility.vector1_double

C++: utility::SimulateMPI::receive_doubles_from_node(int) –> class utility::vector1<double, class std::allocator<double> >

receive_integer_from_anyone() → int

C++: utility::SimulateMPI::receive_integer_from_anyone() –> int

receive_integer_from_node(source: int) → int

C++: utility::SimulateMPI::receive_integer_from_node(int) –> int

receive_integers_from_node(source: int) → pyrosetta.rosetta.utility.vector1_int

C++: utility::SimulateMPI::receive_integers_from_node(int) –> class utility::vector1<int, class std::allocator<int> >

receive_size_from_node(source: int) → int

C++: utility::SimulateMPI::receive_size_from_node(int) –> unsigned long

receive_sizes_from_node(source: int) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: utility::SimulateMPI::receive_sizes_from_node(int) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

receive_string_from_node(source: int) → str

C++: utility::SimulateMPI::receive_string_from_node(int) –> std::string

send_char_to_node(destination: int, message: str) → None

C++: utility::SimulateMPI::send_char_to_node(int, char) –> void

send_double_to_node(destination: int, message: float) → None

C++: utility::SimulateMPI::send_double_to_node(int, double) –> void

send_doubles_to_node(destination: int, message: pyrosetta.rosetta.utility.vector1_double) → None

C++: utility::SimulateMPI::send_doubles_to_node(int, const class utility::vector1<double, class std::allocator<double> > &) –> void

send_integer_to_node(destination: int, message: int) → None

C++: utility::SimulateMPI::send_integer_to_node(int, int) –> void

send_integers_to_node(destination: int, message: pyrosetta.rosetta.utility.vector1_int) → None

C++: utility::SimulateMPI::send_integers_to_node(int, const class utility::vector1<int, class std::allocator<int> > &) –> void

send_size_to_node(destination: int, message: int) → None

C++: utility::SimulateMPI::send_size_to_node(int, unsigned long) –> void

send_sizes_to_node(destination: int, message: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: utility::SimulateMPI::send_sizes_to_node(int, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

send_string_to_node(destination: int, message: str) → None

C++: utility::SimulateMPI::send_string_to_node(int, const class std::basic_string<char> &) –> void

set_mpi_rank(value: int) → None

C++: utility::SimulateMPI::set_mpi_rank(int) –> void

simulate_mpi() → bool

C++: utility::SimulateMPI::simulate_mpi() –> bool

pyrosetta.rosetta.utility.__dummy__() → pyrosetta.rosetta.utility.vector0_core_io_AtomInformation

C++: utility::__dummy__() –> class utility::vector0<struct core::io::AtomInformation, class std::allocator<struct core::io::AtomInformation> >

pyrosetta.rosetta.utility.arg_min(input: pyrosetta.rosetta.utility.vector1_double) → int

C++: utility::arg_min(const class utility::vector1<double, class std::allocator<double> > &) –> unsigned long

pyrosetta.rosetta.utility.code_from_6bit(_8bit: int) → int

C++: utility::code_from_6bit(unsigned char) –> unsigned char

pyrosetta.rosetta.utility.code_to_6bit(_6bit: int) → int

uuencode

C++: utility::code_to_6bit(unsigned char) –> unsigned char

pyrosetta.rosetta.utility.cond_exit(*args, **kwargs)

Overloaded function.

1. cond_exit(condition: bool, file: str, line: int, message: str) -> int
2. cond_exit(condition: bool, file: str, line: int, message: str, status: int) -> int

Conditional Exit with file + line + message + optional status. WIll exit if the condition is not met!

C++: utility::cond_exit(bool, const class std::basic_string<char> &, const int, const class std::basic_string<char> &, const int) –> int

pyrosetta.rosetta.utility.copysign(x: float, y: float) → float

C++: utility::copysign(const double &, const double &) –> double

pyrosetta.rosetta.utility.decode6bit(memory: int, jar: str) → int

C++: utility::decode6bit(unsigned char *, const class std::basic_string<char> &) –> int

pyrosetta.rosetta.utility.decode_32_to_24(i0: int, i1: int, i2: int, i3: int, o0: int, o1: int, o2: int) → None

C++: utility::decode_32_to_24(unsigned char, unsigned char, unsigned char, unsigned char, unsigned char &, unsigned char &, unsigned char &) –> void

pyrosetta.rosetta.utility.down_cast(*args, **kwargs)

Overloaded function.

1. down_cast(s: utility::options::OptionKey) -> utility::options::BooleanOptionKey

C++: utility::down_cast(const class utility::options::OptionKey &) –> const class utility::options::BooleanOptionKey &

2. down_cast(s: utility::options::OptionKey) -> utility::options::IntegerOptionKey

C++: utility::down_cast(const class utility::options::OptionKey &) –> const class utility::options::IntegerOptionKey &

3. down_cast(s: utility::options::OptionKey) -> utility::options::RealOptionKey

C++: utility::down_cast(const class utility::options::OptionKey &) –> const class utility::options::RealOptionKey &

4. down_cast(s: utility::options::OptionKey) -> utility::options::StringOptionKey

C++: utility::down_cast(const class utility::options::OptionKey &) –> const class utility::options::StringOptionKey &

5. down_cast(s: utility::options::OptionKey) -> utility::options::FileOptionKey

C++: utility::down_cast(const class utility::options::OptionKey &) –> const class utility::options::FileOptionKey &

6. down_cast(s: utility::options::OptionKey) -> utility::options::PathOptionKey

C++: utility::down_cast(const class utility::options::OptionKey &) –> const class utility::options::PathOptionKey &

7. down_cast(s: utility::options::OptionKey) -> utility::options::AnyOptionKey

C++: utility::down_cast(const class utility::options::OptionKey &) –> const class utility::options::AnyOptionKey &

8. down_cast(s: utility::options::OptionKey) -> utility::options::BooleanVectorOptionKey

C++: utility::down_cast(const class utility::options::OptionKey &) –> const class utility::options::BooleanVectorOptionKey &

9. down_cast(s: utility::options::OptionKey) -> utility::options::IntegerVectorOptionKey

C++: utility::down_cast(const class utility::options::OptionKey &) –> const class utility::options::IntegerVectorOptionKey &

10. down_cast(s: utility::options::OptionKey) -> utility::options::RealVectorOptionKey

C++: utility::down_cast(const class utility::options::OptionKey &) –> const class utility::options::RealVectorOptionKey &

11. down_cast(s: utility::options::OptionKey) -> utility::options::ResidueChainVectorOptionKey

C++: utility::down_cast(const class utility::options::OptionKey &) –> const class utility::options::ResidueChainVectorOptionKey &

12. down_cast(s: utility::options::OptionKey) -> utility::options::StringVectorOptionKey

C++: utility::down_cast(const class utility::options::OptionKey &) –> const class utility::options::StringVectorOptionKey &

13. down_cast(s: utility::options::OptionKey) -> utility::options::FileVectorOptionKey

C++: utility::down_cast(const class utility::options::OptionKey &) –> const class utility::options::FileVectorOptionKey &

14. down_cast(s: utility::options::OptionKey) -> utility::options::PathVectorOptionKey

C++: utility::down_cast(const class utility::options::OptionKey &) –> const class utility::options::PathVectorOptionKey &

15. down_cast(s: utility::options::OptionKey) -> utility::options::AnyVectorOptionKey

C++: utility::down_cast(const class utility::options::OptionKey &) –> const class utility::options::AnyVectorOptionKey &

16. down_cast(s: utility::keys::Key) -> utility::keys::AutoKey<utility::options::Option, utility::keys::Key, utility::keys::NoClient>

C++: utility::down_cast(const class utility::keys::Key &) –> const class utility::keys::AutoKey<class utility::options::Option, class utility::keys::Key, class utility::keys::NoClient> &

pyrosetta.rosetta.utility.encode6bit(memory: int, length: int, jar: str) → None

C++: utility::encode6bit(const unsigned char *, unsigned int, class std::basic_string<char> &) –> void

pyrosetta.rosetta.utility.encode_24_to_32(i0: int, i1: int, i2: int, o0: int, o1: int, o2: int, o3: int) → None

C++: utility::encode_24_to_32(unsigned char, unsigned char, unsigned char, unsigned char &, unsigned char &, unsigned char &, unsigned char &) –> void

pyrosetta.rosetta.utility.endswith(haystack: str, needle: str) → bool

True iff haystack ends with needle

C++: utility::endswith(const class std::basic_string<char> &, const class std::basic_string<char> &) –> bool

pyrosetta.rosetta.utility.exit(*args, **kwargs)

Overloaded function.

1. exit(file: str, line: int, message: str) -> None
2. exit(file: str, line: int, message: str, status: int) -> None

Exit with file + line + message + optional status

C++: utility::exit(const class std::basic_string<char> &, const int, const class std::basic_string<char> &, const int) –> void

3. exit(file: str, line: int) -> None
4. exit(file: str, line: int, status: int) -> None

Exit with file + line + optional status

C++: utility::exit(const class std::basic_string<char> &, const int, const int) –> void

5. exit(status: int, file: str, line: int) -> None

Exit with file + line + status

Deprecated: For backwards compatibility with earlier version

C++: utility::exit(const int, const class std::basic_string<char> &, const int) –> void

pyrosetta.rosetta.utility.file_basename(full_path: str) → str

C++: utility::file_basename(const class std::basic_string<char> &) –> std::string

pyrosetta.rosetta.utility.file_contents(file_name: str) → str

Read the entire contents of a file into a string. All end-of-line characters are replaced

by “”. Throws a utility::excn::EXCN_msg_exception if the file cannot be opened.

C++: utility::file_contents(const class std::basic_string<char> &) –> std::string

pyrosetta.rosetta.utility.filename(path: str) → str

C++: utility::filename(const class std::basic_string<char> &) –> std::string

pyrosetta.rosetta.utility.fmt_real(: float, pad_left_newlen: int, decimal_places: int) → str

convert a Real to a string, padding left with spaces until total number of char on left is equal to pad_lef_n

C++: utility::fmt_real(double, const unsigned long, const unsigned long) –> std::string

pyrosetta.rosetta.utility.get_num_digits(value: int) → int

C++: utility::get_num_digits(unsigned long) –> unsigned long

pyrosetta.rosetta.utility.get_resnum_and_chain(s: str) → Tuple[pyrosetta.rosetta.std.vector_int, pyrosetta.rosetta.std.vector_char, pyrosetta.rosetta.std.vector_std_string]

converts string like “1-3 20-22” or “A:1-5 B:20-22” to vectors containing resnums and chains.

C++: utility::get_resnum_and_chain(const class std::basic_string<char> &) –> class std::tuple<class std::vector<int, class std::allocator<int> >, class std::vector<char, class std::allocator<char> >, class std::vector<std::string, class std::allocator<std::string > > >

pyrosetta.rosetta.utility.get_resnum_and_chain_and_segid(s: str, string_is_ok: bool) → Tuple[pyrosetta.rosetta.std.vector_int, pyrosetta.rosetta.std.vector_char, pyrosetta.rosetta.std.vector_std_string]

converts string like “1-3 20-22” or “A:1-5 B:20-22” to vectors containing resnums and chains.

C++: utility::get_resnum_and_chain_and_segid(const class std::basic_string<char> &, bool &) –> class std::tuple<class std::vector<int, class std::allocator<int> >, class std::vector<char, class std::allocator<char> >, class std::vector<std::string, class std::allocator<std::string > > >

pyrosetta.rosetta.utility.get_resnum_and_chain_from_one_tag(tag: str, resnum: pyrosetta.rosetta.std.vector_int, chains: pyrosetta.rosetta.std.vector_char, segids: pyrosetta.rosetta.std.vector_std_string) → bool

helper function for get_resnum_and_chain

C++: utility::get_resnum_and_chain_from_one_tag(const class std::basic_string<char> &, class std::vector<int, class std::allocator<int> > &, class std::vector<char, class std::allocator<char> > &, class std::vector<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> bool

pyrosetta.rosetta.utility.get_resnum_and_segid(s: str, string_is_ok: bool) → Tuple[pyrosetta.rosetta.std.vector_int, pyrosetta.rosetta.std.vector_std_string]

converts string like “1-3 20-22” or “A:1-5 B:20-22” to vectors containing resnums and chains.

C++: utility::get_resnum_and_segid(const class std::basic_string<char> &, bool &) –> struct std::pair<class std::vector<int, class std::allocator<int> >, class std::vector<std::string, class std::allocator<std::string > > >

pyrosetta.rosetta.utility.get_resnum_and_segid_from_one_tag(tag: str, resnum: pyrosetta.rosetta.std.vector_int, chains: pyrosetta.rosetta.std.vector_std_string) → bool

helper function for get_resnum_and_chain

C++: utility::get_resnum_and_segid_from_one_tag(const class std::basic_string<char> &, class std::vector<int, class std::allocator<int> > &, class std::vector<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> bool

pyrosetta.rosetta.utility.get_undefined_real() → float

Get a numeric value for Real that represents an “undefined” value

C++: utility::get_undefined_real() –> double

pyrosetta.rosetta.utility.get_undefined_size() → int

Get a numeric value for Size that represents an “undefined” value

C++: utility::get_undefined_size() –> unsigned long

pyrosetta.rosetta.utility.has_insertion_operator(*args, **kwargs)

Overloaded function.

1. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

2. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

3. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

4. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

5. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

6. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

7. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

8. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

9. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

10. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

11. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

12. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

13. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

14. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

15. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

16. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

17. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

18. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

19. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

20. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

21. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

22. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

23. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

24. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

25. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

26. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

27. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

28. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

29. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

30. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

31. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

32. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

33. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

34. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

35. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

36. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

37. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

38. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

39. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

40. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

41. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

42. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

43. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

44. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

45. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

46. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

47. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

48. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

49. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

50. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

51. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

52. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

53. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

54. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

55. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

56. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

57. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

58. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

59. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

60. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

61. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

62. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

63. has_insertion_operator() -> bool

C++: utility::has_insertion_operator() –> bool

pyrosetta.rosetta.utility.is_false_string(value_str: str) → bool

String accepted as a false value?

C++: utility::is_false_string(const class std::basic_string<char> &) –> bool

pyrosetta.rosetta.utility.is_string_numeric(input: str) → bool

C++: utility::is_string_numeric(const class std::basic_string<char> &) –> bool

pyrosetta.rosetta.utility.is_true_string(value_str: str) → bool

String accepted as a true value?

C++: utility::is_true_string(const class std::basic_string<char> &) –> bool

pyrosetta.rosetta.utility.is_undefined(*args, **kwargs)

Overloaded function.

1. is_undefined(val: int) -> bool

Check if a Size is undefined (i.e has the same value as utility::get_undefined_size() )

C++: utility::is_undefined(const unsigned long &) –> bool

2. is_undefined(val: float) -> bool

Check if a Real is undefined (i.e has the same value as utility::get_undefined_real() )

C++: utility::is_undefined(const double &) –> bool

pyrosetta.rosetta.utility.isinf(val: float) → bool

C++: utility::isinf(const double &) –> bool

pyrosetta.rosetta.utility.isnan(val: float) → bool

C++: utility::isnan(const double &) –> bool

pyrosetta.rosetta.utility.join(*args, **kwargs)

Overloaded function.

1. join(s: pyrosetta.rosetta.utility.vector1_std_string, connector: str) -> str

combine strings with anything

C++: utility::join(const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &, const class std::basic_string<char> &) –> std::string

2. join(s: pyrosetta.rosetta.std.vector_std_string, connector: str) -> str

combine strings with anything

C++: utility::join(const class std::vector<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &, const class std::basic_string<char> &) –> std::string

pyrosetta.rosetta.utility.lower(s: str) → str

Make a string Lowercase

C++: utility::lower(const class std::basic_string<char> &) –> std::string

pyrosetta.rosetta.utility.make_segtag_with_dashes(*args, **kwargs)

Overloaded function.

1. make_segtag_with_dashes(res_vector: pyrosetta.rosetta.utility.vector1_int, segid_vector: pyrosetta.rosetta.utility.vector1_std_string) -> str
2. make_segtag_with_dashes(res_vector: pyrosetta.rosetta.utility.vector1_int, segid_vector: pyrosetta.rosetta.utility.vector1_std_string, delimiter: str) -> str

C++: utility::make_segtag_with_dashes(class utility::vector1<int, class std::allocator<int> >, class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > >, const char) –> std::string

pyrosetta.rosetta.utility.make_tag(res_vector: pyrosetta.rosetta.utility.vector1_int) → str

C++: utility::make_tag(class utility::vector1<int, class std::allocator<int> >) –> std::string

pyrosetta.rosetta.utility.make_tag_with_dashes(*args, **kwargs)

Overloaded function.

1. make_tag_with_dashes(res_vector: pyrosetta.rosetta.utility.vector1_int) -> str
2. make_tag_with_dashes(res_vector: pyrosetta.rosetta.utility.vector1_int, delimiter: str) -> str

Compactifies vectors of ints: 1 2 3 9 10 11 to “1-3 9-11”

C++: utility::make_tag_with_dashes(class utility::vector1<int, class std::allocator<int> >, const char) –> std::string

3. make_tag_with_dashes(res_vector: pyrosetta.rosetta.utility.vector1_int, chain_vector: pyrosetta.rosetta.utility.vector1_char, segid_vector: pyrosetta.rosetta.utility.vector1_std_string) -> str
4. make_tag_with_dashes(res_vector: pyrosetta.rosetta.utility.vector1_int, chain_vector: pyrosetta.rosetta.utility.vector1_char, segid_vector: pyrosetta.rosetta.utility.vector1_std_string, delimiter: str) -> str

C++: utility::make_tag_with_dashes(class utility::vector1<int, class std::allocator<int> >, class utility::vector1<char, class std::allocator<char> >, class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > >, const char) –> std::string

pyrosetta.rosetta.utility.max(*args, **kwargs)

Overloaded function.

1. max(a: int, b: int) -> int

max( short int, short int )

C++: utility::max(const short, const short) –> short

2. max(a: int, b: int) -> int

max( int, int )

C++: utility::max(const int, const int) –> int

3. max(a: int, b: int) -> int

max( long int, long int )

C++: utility::max(const long, const long) –> long

4. max(a: int, b: int) -> int

max( unsigned short int, unsigned short int )

C++: utility::max(const unsigned short, const unsigned short) –> unsigned short

5. max(a: int, b: int) -> int

max( unsigned int, unsigned int )

C++: utility::max(const unsigned int, const unsigned int) –> unsigned int

6. max(a: int, b: int) -> int

max( unsigned long int, unsigned long int )

C++: utility::max(const unsigned long, const unsigned long) –> unsigned long

7. max(a: float, b: float) -> float

max( float, float )

C++: utility::max(const float, const float) –> float

8. max(a: float, b: float) -> float

max( double, double )

C++: utility::max(const double, const double) –> double

9. max(a: float, b: float) -> float

max( long double, long double )

C++: utility::max(const long double, const long double) –> long double

pyrosetta.rosetta.utility.min(*args, **kwargs)

Overloaded function.

1. min(a: int, b: int) -> int

min( short int, short int )

C++: utility::min(const short, const short) –> short

2. min(a: int, b: int) -> int

min( int, int )

C++: utility::min(const int, const int) –> int

3. min(a: int, b: int) -> int

min( long int, long int )

C++: utility::min(const long, const long) –> long

4. min(a: int, b: int) -> int

min( unsigned short int, unsigned short int )

C++: utility::min(const unsigned short, const unsigned short) –> unsigned short

5. min(a: int, b: int) -> int

min( unsigned int, unsigned int )

C++: utility::min(const unsigned int, const unsigned int) –> unsigned int

6. min(a: int, b: int) -> int

min( unsigned long int, unsigned long int )

C++: utility::min(const unsigned long, const unsigned long) –> unsigned long

7. min(a: float, b: float) -> float

min( float, float )

C++: utility::min(const float, const float) –> float

8. min(a: float, b: float) -> float

min( double, double )

C++: utility::min(const double, const double) –> double

9. min(a: float, b: float) -> float

min( long double, long double )

C++: utility::min(const long double, const long double) –> long double

pyrosetta.rosetta.utility.modulo(a: int, b: int) → int

Most folks use C’s “a % b” operator but it gives funny behavior for negative a.

This version came out of stack overflow.

C++: utility::modulo(const int &, const int &) –> unsigned long

pyrosetta.rosetta.utility.mpi_nprocs() → int

C++: utility::mpi_nprocs() –> int

pyrosetta.rosetta.utility.mpi_rank() → int

C++: utility::mpi_rank() –> int

pyrosetta.rosetta.utility.pad_left(*args, **kwargs)

Overloaded function.

1. pad_left(s: str, newlen: int) -> str
2. pad_left(s: str, newlen: int, pad_with: str) -> str

Add char to the left of the string

C++: utility::pad_left(class std::basic_string<char>, const unsigned long, char) –> std::string

3. pad_left(t: str, newlen: int) -> str
4. pad_left(t: str, newlen: int, pad_width: str) -> str

C++: utility::pad_left(const class std::basic_string<char> &, const unsigned long, char) –> std::string

pyrosetta.rosetta.utility.pad_right(*args, **kwargs)

Overloaded function.

1. pad_right(s: str, newlen: int) -> str
2. pad_right(s: str, newlen: int, pad_with: str) -> str

Add char to the right of a string

C++: utility::pad_right(class std::basic_string<char>, const unsigned long, char) –> std::string

3. pad_right(t: str, newlen: int) -> str
4. pad_right(t: str, newlen: int, pad_width: str) -> str

C++: utility::pad_right(const class std::basic_string<char> &, const unsigned long, char) –> std::string

pyrosetta.rosetta.utility.pathname(path: str) → str

C++: utility::pathname(const class std::basic_string<char> &) –> std::string

pyrosetta.rosetta.utility.quoted_split(s: str) → pyrosetta.rosetta.utility.vector1_std_string

Split a string by whitespace, but obey single and double quote marks, like the bash commandline

C++: utility::quoted_split(const class std::basic_string<char> &) –> class utility::vector1<std::string, class std::allocator<std::string > >

pyrosetta.rosetta.utility.rand_sleep() → None

C++: utility::rand_sleep() –> void

pyrosetta.rosetta.utility.receive_char_from_node(source: int) → str

Use MPI to receive a single char from a particular node.

C++: utility::receive_char_from_node(int) –> char

pyrosetta.rosetta.utility.receive_double_from_node(source: int) → float

Use MPI to receive a single double from a particular node.

C++: utility::receive_double_from_node(int) –> double

pyrosetta.rosetta.utility.receive_doubles_from_node(source: int) → pyrosetta.rosetta.utility.vector1_double

Use MPI to receive a vector of doubles from a particular node.

C++: utility::receive_doubles_from_node(int) –> class utility::vector1<double, class std::allocator<double> >

pyrosetta.rosetta.utility.receive_integer_from_anyone() → int

Use MPI to wait until some node sends an integer – usually its own mpi_rank

so that it can send further messages.

C++: utility::receive_integer_from_anyone() –> int

pyrosetta.rosetta.utility.receive_integer_from_node(source: int) → int

Use MPI to receive a single integer from a particular node.

C++: utility::receive_integer_from_node(int) –> int

pyrosetta.rosetta.utility.receive_integers_from_node(source: int) → pyrosetta.rosetta.utility.vector1_int

Use MPI to receive a vector of integers from a particular node.

C++: utility::receive_integers_from_node(int) –> class utility::vector1<int, class std::allocator<int> >

pyrosetta.rosetta.utility.receive_size_from_node(source: int) → int

Use MPI to receive a single unsigned (usually 64-bit) integer from a particular node.

C++: utility::receive_size_from_node(int) –> unsigned long

pyrosetta.rosetta.utility.receive_sizes_from_node(source: int) → pyrosetta.rosetta.utility.vector1_unsigned_long

Use MPI to receive a vector of integers from a particular node.

C++: utility::receive_sizes_from_node(int) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.utility.receive_string_from_node(source: int) → str

Use MPI to receive a string from a particular node.

C++: utility::receive_string_from_node(int) –> std::string

class pyrosetta.rosetta.utility.recent_history_queue

Bases: pybind11_builtins.pybind11_object

A class for keeping track of a subset of elements in a set that are pushed into a queue in a certain order, and which fall off the end of the queue in ther order in which they arrive. Elements in the set can be bumped to the front of the queue.

The queue is “in place”, so there are no calls to new or delete with repeated calls to push_to_front_of_history_queue().

The position in queue can be used to keep track of data for elements, where the position is understood not as the number of elements between the element and the front of the queue, but rather, an index that the object has in the “recent_history_queue_” data member – an array. If an element is in the queue with index X, and then it is pushed to the front of the history queue, its index will still be X.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.utility.recent_history_queue) -> None
2. __init__(self: pyrosetta.rosetta.utility.recent_history_queue, num_elements: int, history_size: int) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

assign(self: pyrosetta.rosetta.utility.recent_history_queue, : pyrosetta.rosetta.utility.recent_history_queue) → pyrosetta.rosetta.utility.recent_history_queue

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

clear(self: pyrosetta.rosetta.utility.recent_history_queue) → None

C++: utility::recent_history_queue::clear() –> void

curr_num_in_recent_history(self: pyrosetta.rosetta.utility.recent_history_queue) → int

C++: utility::recent_history_queue::curr_num_in_recent_history() const –> int

dynamic_memory_usage(self: pyrosetta.rosetta.utility.recent_history_queue) → int

C++: utility::recent_history_queue::dynamic_memory_usage() const –> unsigned int

end_of_queue(self: pyrosetta.rosetta.utility.recent_history_queue) → int

For unit-testing purposes

C++: utility::recent_history_queue::end_of_queue() const –> int

head_of_queue(self: pyrosetta.rosetta.utility.recent_history_queue) → int

For unit-testing purposes

C++: utility::recent_history_queue::head_of_queue() const –> int

history_size(*args, **kwargs)

Overloaded function.

1. history_size(self: pyrosetta.rosetta.utility.recent_history_queue, history_size: int) -> None

C++: utility::recent_history_queue::history_size(int) –> void

2. history_size(self: pyrosetta.rosetta.utility.recent_history_queue) -> int

C++: utility::recent_history_queue::history_size() const –> int

num_elements(*args, **kwargs)

Overloaded function.

1. num_elements(self: pyrosetta.rosetta.utility.recent_history_queue, num_elements: int) -> None

C++: utility::recent_history_queue::num_elements(int) –> void

2. num_elements(self: pyrosetta.rosetta.utility.recent_history_queue) -> int

C++: utility::recent_history_queue::num_elements() const –> int

pos_in_history_queue(self: pyrosetta.rosetta.utility.recent_history_queue, element: int) → int

Returns the position in the recent history for a given element in the set. Returns 0

if the element is not part of the recent history.

C++: utility::recent_history_queue::pos_in_history_queue(int) const –> int

push_to_front_of_history_queue(self: pyrosetta.rosetta.utility.recent_history_queue, element: int) → int

Push an element to the front of the recent history queue. This will likely bump

an element that had been in the recent history queue; in that event, this function returns the in-place index for that bumped element. If the new element doesn’t displace some other element (i.e. if the queue is either not yet full, or if the element was already in the queue), then this function returns a fictional index of “0”.

C++: utility::recent_history_queue::push_to_front_of_history_queue(int) –> int

pyrosetta.rosetta.utility.replace_environment_variables(input: str) → str

find all environment variables with the form ${VARIABLE}

and replace with the contents of that environment variable. if the environment variable does not exist, return string::npos

C++: utility::replace_environment_variables(class std::basic_string<char>) –> std::string

pyrosetta.rosetta.utility.replace_in(*args, **kwargs)

Overloaded function.

1. replace_in(s: str, from: str, to: str) -> None

C++: utility::replace_in(class std::basic_string<char> &, const char, const char *) –> void

2. replace_in(source: str, from: str, to: str) -> str

Generate new string from ‘source’ by replacing all occurrences of ‘from’ to ‘to’ string.

C++: utility::replace_in(const class std::basic_string<char> &, const class std::basic_string<char> &, const class std::basic_string<char> &) –> std::string

pyrosetta.rosetta.utility.replace_spaces(string_w_spaces: str, replacement: str) → str

replace space separations in a string with a connector such as ‘_’

C++: utility::replace_spaces(const class std::basic_string<char> &, const class std::basic_string<char> &) –> std::string

pyrosetta.rosetta.utility.round(val: float) → float

C++: utility::round(const double &) –> double

pyrosetta.rosetta.utility.same_ignoring_spaces(s1: str, s2: str) → bool

Compares two strings, ignoring spaces. Useful for comparing atom

name strings which have pdb-alignment built into them. Slightly dangerous if you consider the fact that atom names in the PDB are different for different indentation rules: ‘ CA ‘ is c-alpha. ‘CA ‘ is calcium.

C++: utility::same_ignoring_spaces(const class std::basic_string<char> &, const class std::basic_string<char> &) –> bool

pyrosetta.rosetta.utility.send_char_to_node(destination: int, message: str) → None

C++: utility::send_char_to_node(int, char) –> void

pyrosetta.rosetta.utility.send_double_to_node(destination: int, message: float) → None

C++: utility::send_double_to_node(int, double) –> void

pyrosetta.rosetta.utility.send_doubles_to_node(destination: int, message: pyrosetta.rosetta.utility.vector1_double) → None

C++: utility::send_doubles_to_node(int, const class utility::vector1<double, class std::allocator<double> > &) –> void

pyrosetta.rosetta.utility.send_integer_to_node(destination: int, message: int) → None

C++: utility::send_integer_to_node(int, int) –> void

pyrosetta.rosetta.utility.send_integers_to_node(destination: int, message: pyrosetta.rosetta.utility.vector1_int) → None

C++: utility::send_integers_to_node(int, const class utility::vector1<int, class std::allocator<int> > &) –> void

pyrosetta.rosetta.utility.send_size_to_node(destination: int, message: int) → None

Use MPI to send a single unsigned (usually 64-bit) integer to a particular node

C++: utility::send_size_to_node(int, unsigned long) –> void

pyrosetta.rosetta.utility.send_sizes_to_node(destination: int, message: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: utility::send_sizes_to_node(int, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

pyrosetta.rosetta.utility.send_string_to_node(source: int, message: str) → None

C++: utility::send_string_to_node(int, const class std::basic_string<char> &) –> void

class pyrosetta.rosetta.utility.simulate_mpi_message_type

Bases: pybind11_builtins.pybind11_object

This is for unit testing mpi code in a single processor. The idea is to buffer the messages in the SimulateMPIData stored in the SimulateMPI. To use this class, call initialize_simulation( nprocs ), then set the mpi rank can be set manually, and the functions in mpi_util are usable. By setting the mpi_rank to a different processor, other messages can be sent and received. See test/utility/simulate_mpi.cxxtest for examples.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(*args, **kwargs)

Overloaded function.

1. __eq__(self: pyrosetta.rosetta.utility.simulate_mpi_message_type, arg0: pyrosetta.rosetta.utility.simulate_mpi_message_type) -> bool
2. __eq__(self: pyrosetta.rosetta.utility.simulate_mpi_message_type, arg0: int) -> bool

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getstate__(self: pyrosetta.rosetta.utility.simulate_mpi_message_type) → tuple

__gt__

Return self>value.

__hash__(self: pyrosetta.rosetta.utility.simulate_mpi_message_type) → int

__init__(self: pyrosetta.rosetta.utility.simulate_mpi_message_type, arg0: int) → None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__int__(self: pyrosetta.rosetta.utility.simulate_mpi_message_type) → int

__le__

Return self<=value.

__lt__

Return self<value.

__ne__(*args, **kwargs)

Overloaded function.

1. __ne__(self: pyrosetta.rosetta.utility.simulate_mpi_message_type, arg0: pyrosetta.rosetta.utility.simulate_mpi_message_type) -> bool
2. __ne__(self: pyrosetta.rosetta.utility.simulate_mpi_message_type, arg0: int) -> bool

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__(self: pyrosetta.rosetta.utility.simulate_mpi_message_type) → str

__setattr__

Implement setattr(self, name, value).

__setstate__(self: pyrosetta.rosetta.utility.simulate_mpi_message_type, arg0: tuple) → None

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

pyrosetta.rosetta.utility.slurp(in: pyrosetta.rosetta.std.istream, out: str) → None

Take all of the contents from the std::istream “in” and put them in the std::string “out”.

Useful for reading the full contents of a file into a string.

C++: utility::slurp(class std::basic_istream<char> &, class std::basic_string<char> &) –> void

pyrosetta.rosetta.utility.split(s: str) → pyrosetta.rosetta.utility.vector1_std_string

split given std::string using ‘ ‘ symbol.

C++: utility::split(const class std::basic_string<char> &) –> class utility::vector1<std::string, class std::allocator<std::string > >

pyrosetta.rosetta.utility.split_by_newlines(s: str) → pyrosetta.rosetta.std.vector_std_string

Split string by new line symbols, return vector of string.

C++: utility::split_by_newlines(const class std::basic_string<char> &) –> class std::vector<std::string, class std::allocator<std::string > >

pyrosetta.rosetta.utility.split_to_list(s: str) → pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

split given std::string using ‘ ‘ symbol.

C++: utility::split_to_list(const class std::basic_string<char> &) –> class std::list<std::string, class std::allocator<std::string > >

pyrosetta.rosetta.utility.split_to_set(s: str) → pyrosetta.rosetta.std.set_std_string_std_less_std_string_std_allocator_std_string_t

split given std::string to a set using ‘ ‘ symbol.

C++: utility::split_to_set(const class std::basic_string<char> &) –> class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > >

pyrosetta.rosetta.utility.split_whitespace(s: str) → pyrosetta.rosetta.utility.vector1_std_string

split given std::string using whitespace as a separator.

Unlike string_split_multi_delim(), any group of mixed whitespace counts only as a single seperator.

C++: utility::split_whitespace(const class std::basic_string<char> &) –> class utility::vector1<std::string, class std::allocator<std::string > >

pyrosetta.rosetta.utility.startswith(haystack: str, needle: str) → bool

True iff haystack starts with needle

C++: utility::startswith(const class std::basic_string<char> &, const class std::basic_string<char> &) –> bool

pyrosetta.rosetta.utility.string2Real(st: str) → float

convert a string to a Real, returns numeric::get_undefined_real() on failure

C++: utility::string2Real(class std::basic_string<char>) –> double

pyrosetta.rosetta.utility.string2Size(st: str) → int

convert a string to a Size, returns numeric::get_undefined_size() on failure

C++: utility::string2Size(class std::basic_string<char>) –> unsigned long

pyrosetta.rosetta.utility.string2float(st: str) → float

convert a string to a float, returns -1 on failure

C++: utility::string2float(class std::basic_string<char>) –> float

pyrosetta.rosetta.utility.string2int(st: str) → int

convert a string to an int, returns -1 on failure

C++: utility::string2int(class std::basic_string<char>) –> int

pyrosetta.rosetta.utility.string2uint(x: str, y: int) → None

C++: utility::string2uint(const class std::basic_string<char> &, unsigned int *) –> void

pyrosetta.rosetta.utility.string_split(*args, **kwargs)

Overloaded function.

1. string_split(in: str) -> pyrosetta.rosetta.utility.vector1_std_string
2. string_split(in: str, splitchar: str) -> pyrosetta.rosetta.utility.vector1_std_string

split to vector1< std::string > using arbitrary split character

C++: utility::string_split(const class std::basic_string<char> &, char) –> class utility::vector1<std::string, class std::allocator<std::string > >

pyrosetta.rosetta.utility.string_split_multi_delim(*args, **kwargs)

Overloaded function.

1. string_split_multi_delim(in: str) -> pyrosetta.rosetta.utility.vector1_std_string
2. string_split_multi_delim(in: str, splitchars: str) -> pyrosetta.rosetta.utility.vector1_std_string

split to vector< std::string > using any of arbitrary split characters

C++: utility::string_split_multi_delim(const class std::basic_string<char> &, class std::basic_string<char>) –> class utility::vector1<std::string, class std::allocator<std::string > >

pyrosetta.rosetta.utility.string_split_simple(*args, **kwargs)

Overloaded function.

1. string_split_simple(in: str) -> pyrosetta.rosetta.utility.vector1_std_string
2. string_split_simple(in: str, splitchar: str) -> pyrosetta.rosetta.utility.vector1_std_string

split to vector1< std::string > using arbitrary split character, but no empty strings (closer to python string::split)

C++: utility::string_split_simple(const class std::basic_string<char> &, char) –> class utility::vector1<std::string, class std::allocator<std::string > >

pyrosetta.rosetta.utility.string_to_sha1(input_string: str) → str

C++: utility::string_to_sha1(const class std::basic_string<char> &) –> std::string

pyrosetta.rosetta.utility.strip(*args, **kwargs)

Overloaded function.

1. strip(source: str) -> str
2. strip(source: str, c: str) -> str

Return a copy of the string with leading and trailing characters removed

C++: utility::strip(const class std::basic_string<char> &, char) –> std::string

3. strip(source: str, drop: str) -> str

Return a copy of the string with leading and trailing characters removed

Any charachters in drop will be removed For the in place version, see trim()

C++: utility::strip(const class std::basic_string<char> &, const class std::basic_string<char> &) –> std::string

class pyrosetta.rosetta.utility.subset_mapping

Bases: pybind11_builtins.pybind11_object

This class handles the bookeeping to map between a set of integer ids in the “source” enumeration to a subset of those ids – the destination enumartion. Elements in the source enumeration that do not map to elements in the destination enumeration are represented by the value 0. Both enumerations should count from 1. Once the class has been initialized, this class offers O(1) mapping between elements in the enumerations.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.utility.subset_mapping) -> None
2. __init__(self: pyrosetta.rosetta.utility.subset_mapping, source_enumeration_size: int) -> None
3. __init__(self: pyrosetta.rosetta.utility.subset_mapping, arg0: pyrosetta.rosetta.utility.subset_mapping) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

assign(self: pyrosetta.rosetta.utility.subset_mapping, rhs: pyrosetta.rosetta.utility.subset_mapping) → pyrosetta.rosetta.utility.subset_mapping

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

d2s(self: pyrosetta.rosetta.utility.subset_mapping, destination_id: int) → int

Map from the id of an element in the destination enumeration to an id

in the source enumeration. This is guaranteed to return a non-zero value.

C++: utility::subset_mapping::d2s(unsigned long) const –> unsigned long

destination_size(self: pyrosetta.rosetta.utility.subset_mapping) → int

The number of elements in the destination enumeration – this

represents the number of calls that have been made to set_next_correspondence()

C++: utility::subset_mapping::destination_size() const –> unsigned long

reserve_destination_size(self: pyrosetta.rosetta.utility.subset_mapping, : int) → None

If you know the size of the destination enumeration, then you can save

some under-the-hood vector resizing operations by informing the subset_mapping its size up front. This call must proceed the first call to set_next_correspondence

C++: utility::subset_mapping::reserve_destination_size(unsigned long) –> void

s2d(self: pyrosetta.rosetta.utility.subset_mapping, source_id: int) → int

Map from the id of an element in source enumeration to an id in the

the destination enumeration, which may in fact be UNMAPPED.

C++: utility::subset_mapping::s2d(unsigned long) const –> unsigned long

set_next_correspondence(self: pyrosetta.rosetta.utility.subset_mapping, source_id: int) → None

Inform the mapping of the next source-enumeration id that should be mapped

to a destination-enumeration id. This will increase the size of the destination enumeration by one. It is not essential that the source-enumeration ids appear in sorted order, however, by construction, the destination ids will be in sorted order.

C++: utility::subset_mapping::set_next_correspondence(unsigned long) –> void

set_source_size(self: pyrosetta.rosetta.utility.subset_mapping, : int) → None

Required before the first call to set_next_correspondence may be called.

The size of the source enumeration must be known before the mapping may begin

C++: utility::subset_mapping::set_source_size(unsigned long) –> void

source_id_is_mapped(self: pyrosetta.rosetta.utility.subset_mapping, source_id: int) → bool

C++: utility::subset_mapping::source_id_is_mapped(unsigned long) const –> bool

source_size(self: pyrosetta.rosetta.utility.subset_mapping) → int

The number of elements in the source enumeration

C++: utility::subset_mapping::source_size() const –> unsigned long

pyrosetta.rosetta.utility.swap4_aligned(v: capsule, ndata: int) → None

C++: utility::swap4_aligned(void *, long) –> void

pyrosetta.rosetta.utility.sys_sleep(seconds: float) → None

Sleep for a specified number of seconds

C++: utility::sys_sleep(const double) –> void

pyrosetta.rosetta.utility.timestamp() → str

Generate timestamp string

C++: utility::timestamp() –> std::string

pyrosetta.rosetta.utility.timestamp_short() → str

Generate timestamp string, short format

C++: utility::timestamp_short() –> std::string

pyrosetta.rosetta.utility.to_string(*args, **kwargs)

Overloaded function.

1. to_string(t: float) -> str

C++: utility::to_string(const double &) –> std::string

2. to_string(t: int) -> str

C++: utility::to_string(const unsigned long &) –> std::string

3. to_string(t: int) -> str

C++: utility::to_string(const long &) –> std::string

4. to_string(t: str) -> str

C++: utility::to_string(const char &) –> std::string

pyrosetta.rosetta.utility.trim(*args, **kwargs)

Overloaded function.

1. trim(s: str) -> None
2. trim(s: str, drop: str) -> None

Remove any charachters in “drop” from the front and back of the string.

Use strip() for the value-return version

C++: utility::trim(class std::basic_string<char> &, const class std::basic_string<char> &) –> void

3. trim(s: str) -> str
4. trim(s: str, drop: str) -> str

Ambiguious with the trim( std::string & s ) – Deprecated:

use strip() instead for return-value trimming

C++: utility::trim(const class std::basic_string<char> &, const class std::basic_string<char> &) –> std::string

pyrosetta.rosetta.utility.trimmed_compare(s1: str, s2: str) → bool

compares two strings ignoring leading and trailing spaces

C++: utility::trimmed_compare(const class std::basic_string<char> &, const class std::basic_string<char> &) –> bool

pyrosetta.rosetta.utility.upper(s: str) → str

Make a string Uppercase

C++: utility::upper(const class std::basic_string<char> &) –> std::string