raw_data

Bindings for core::io::raw_data namespace

class pyrosetta.rosetta.core.io.raw_data.DecoyFileData

Bases: RawFileData

assign(self: pyrosetta.rosetta.core.io.raw_data.DecoyFileData, : pyrosetta.rosetta.core.io.raw_data.DecoyFileData) → pyrosetta.rosetta.core.io.raw_data.DecoyFileData

C++: core::io::raw_data::DecoyFileData::operator=(const class core::io::raw_data::DecoyFileData &) –> class core::io::raw_data::DecoyFileData &

begin(self: pyrosetta.rosetta.core.io.raw_data.RawFileData) → core::io::raw_data::RawFileData::iterator

Returns an iterator to the start of the members of this container.

C++: core::io::raw_data::RawFileData::begin() –> class core::io::raw_data::RawFileData::iterator

begin_const(self: pyrosetta.rosetta.core.io.raw_data.RawFileData) → core::io::raw_data::RawFileData::const_iterator

C++: core::io::raw_data::RawFileData::begin_const() const –> class core::io::raw_data::RawFileData::const_iterator

clear_structure_map(self: pyrosetta.rosetta.core.io.raw_data.RawFileData) → None

Remove all of the RawStruct objects from this object.

C++: core::io::raw_data::RawFileData::clear_structure_map() –> void

class const_iterator

Bases: pybind11_object

const_iterator class for RawFileData container.

arrow(self: pyrosetta.rosetta.core.io.raw_data.RawFileData.const_iterator) → pyrosetta.rosetta.core.io.raw_data.RawStruct

C++: core::io::raw_data::RawFileData::const_iterator::operator->() const –> class std::shared_ptr<class core::io::raw_data::RawStruct>

assign(self: pyrosetta.rosetta.core.io.raw_data.RawFileData.const_iterator, src: pyrosetta.rosetta.core.io.raw_data.RawFileData.const_iterator) → pyrosetta.rosetta.core.io.raw_data.RawFileData.const_iterator

C++: core::io::raw_data::RawFileData::const_iterator::operator=(const class core::io::raw_data::RawFileData::const_iterator &) –> class core::io::raw_data::RawFileData::const_iterator &

dereference(self: pyrosetta.rosetta.core.io.raw_data.RawFileData.const_iterator) → pyrosetta.rosetta.core.io.raw_data.RawStruct

C++: core::io::raw_data::RawFileData::const_iterator::operator*() const –> class std::shared_ptr<class core::io::raw_data::RawStruct>

pre_increment(self: pyrosetta.rosetta.core.io.raw_data.RawFileData.const_iterator) → pyrosetta.rosetta.core.io.raw_data.RawFileData.const_iterator

C++: core::io::raw_data::RawFileData::const_iterator::operator++() –> class core::io::raw_data::RawFileData::const_iterator &

end(self: pyrosetta.rosetta.core.io.raw_data.RawFileData) → core::io::raw_data::RawFileData::iterator

Returns an iterator to the end of the members of this container.

C++: core::io::raw_data::RawFileData::end() –> class core::io::raw_data::RawFileData::iterator

end_const(self: pyrosetta.rosetta.core.io.raw_data.RawFileData) → core::io::raw_data::RawFileData::const_iterator

C++: core::io::raw_data::RawFileData::end_const() const –> class core::io::raw_data::RawFileData::const_iterator

class iterator

Bases: pybind11_object

Iterator class for RawFileData container.

arrow(self: pyrosetta.rosetta.core.io.raw_data.RawFileData.iterator) → pyrosetta.rosetta.core.io.raw_data.RawStruct

C++: core::io::raw_data::RawFileData::iterator::operator->() –> class std::shared_ptr<class core::io::raw_data::RawStruct>

assign(self: pyrosetta.rosetta.core.io.raw_data.RawFileData.iterator, src: pyrosetta.rosetta.core.io.raw_data.RawFileData.iterator) → pyrosetta.rosetta.core.io.raw_data.RawFileData.iterator

C++: core::io::raw_data::RawFileData::iterator::operator=(const class core::io::raw_data::RawFileData::iterator &) –> class core::io::raw_data::RawFileData::iterator &

dereference(self: pyrosetta.rosetta.core.io.raw_data.RawFileData.iterator) → pyrosetta.rosetta.core.io.raw_data.RawStruct

C++: core::io::raw_data::RawFileData::iterator::operator*() const –> class std::shared_ptr<class core::io::raw_data::RawStruct>

pre_increment(self: pyrosetta.rosetta.core.io.raw_data.RawFileData.iterator) → pyrosetta.rosetta.core.io.raw_data.RawFileData.iterator

C++: core::io::raw_data::RawFileData::iterator::operator++() –> class core::io::raw_data::RawFileData::iterator &

nres(self: pyrosetta.rosetta.core.io.raw_data.RawFileData) → int
Returns the number of residues in the first structure in this object. Not

guaranteed to be fixed for all structures in this container.

C++: core::io::raw_data::RawFileData::nres() const –> int

read_tags_fast(self: pyrosetta.rosetta.core.io.raw_data.RawFileData, filename: str) → pyrosetta.rosetta.utility.vector1_std_string
quickly read a list of tags from a silent-input file. Only checks lines beginning

with SCORE: strings.

C++: core::io::raw_data::RawFileData::read_tags_fast(const std::string &) const –> class utility::vector1<std::string, class std::allocator<std::string > >

sequence(self: pyrosetta.rosetta.core.io.raw_data.RawFileData) → str
Returns the sequence of the first structure in this object. Not

guaranteed to be fixed for all structures in this container.

C++: core::io::raw_data::RawFileData::sequence() const –> std::string

size(self: pyrosetta.rosetta.core.io.raw_data.RawFileData) → int

Returns the number of structures contained in this container.

C++: core::io::raw_data::RawFileData::size() const –> int

write_all(self: pyrosetta.rosetta.core.io.raw_data.RawFileData, filename: str, score_map: pyrosetta.rosetta.std.map_std_string_double) → None

write all RawStruct objects in the structure_map_ to the given filename.

C++: core::io::raw_data::RawFileData::write_all(const std::string &, const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &) –> void

write_pose(self: pyrosetta.rosetta.core.io.raw_data.DecoyFileData, pose: pyrosetta.rosetta.core.pose.Pose, score_map: pyrosetta.rosetta.std.map_std_string_double, tag: str, fullatom: bool) → bool

C++: core::io::raw_data::DecoyFileData::write_pose(const class core::pose::Pose &, const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &, std::string, bool) –> bool

write_struct(self: pyrosetta.rosetta.core.io.raw_data.DecoyFileData, s: core::io::raw_data::DecoyStruct, score_map: pyrosetta.rosetta.std.map_std_string_double) → bool

C++: core::io::raw_data::DecoyFileData::write_struct(const class core::io::raw_data::DecoyStruct, const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &) –> bool

class pyrosetta.rosetta.core.io.raw_data.DecoyStruct

Bases: RawStruct

assign(self: pyrosetta.rosetta.core.io.raw_data.DecoyStruct, : pyrosetta.rosetta.core.io.raw_data.DecoyStruct) → pyrosetta.rosetta.core.io.raw_data.DecoyStruct

C++: core::io::raw_data::DecoyStruct::operator=(const class core::io::raw_data::DecoyStruct &) –> class core::io::raw_data::DecoyStruct &

chi(*args, **kwargs)

Overloaded function.

  1. chi(self: pyrosetta.rosetta.core.io.raw_data.DecoyStruct, seqpos: int) -> pyrosetta.rosetta.utility.vector1_double

C++: core::io::raw_data::DecoyStruct::chi(unsigned int) const –> class utility::vector1<double, class std::allocator<double> >

  1. chi(self: pyrosetta.rosetta.core.io.raw_data.DecoyStruct, seqpos: int, chis: pyrosetta.rosetta.utility.vector1_double) -> None

C++: core::io::raw_data::DecoyStruct::chi(unsigned int, class utility::vector1<double, class std::allocator<double> >) –> void

coords(*args, **kwargs)

Overloaded function.

  1. coords(self: pyrosetta.rosetta.core.io.raw_data.DecoyStruct, seqpos: int) -> pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::io::raw_data::DecoyStruct::coords(unsigned int) const –> class numeric::xyzVector<double>

  1. coords(self: pyrosetta.rosetta.core.io.raw_data.DecoyStruct, seqpos: int, coords: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: core::io::raw_data::DecoyStruct::coords(unsigned int, class numeric::xyzVector<double>) –> void

decoy_tag(*args, **kwargs)

Overloaded function.

  1. decoy_tag(self: pyrosetta.rosetta.core.io.raw_data.RawStruct) -> str

returns the tag associated with this RawStruct

C++: core::io::raw_data::RawStruct::decoy_tag() –> std::string

  1. decoy_tag(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, tag: str) -> None

sets the tag associated with this RawStruct

C++: core::io::raw_data::RawStruct::decoy_tag(std::string) –> void

fill_pose(*args, **kwargs)

Overloaded function.

  1. fill_pose(self: pyrosetta.rosetta.core.io.raw_data.DecoyStruct, pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: core::io::raw_data::DecoyStruct::fill_pose(class core::pose::Pose &) –> void

  1. fill_pose(self: pyrosetta.rosetta.core.io.raw_data.DecoyStruct, pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) -> None

C++: core::io::raw_data::DecoyStruct::fill_pose(class core::pose::Pose &, const class core::chemical::ResidueTypeSet &) –> void

fullatom(*args, **kwargs)

Overloaded function.

  1. fullatom(self: pyrosetta.rosetta.core.io.raw_data.DecoyStruct) -> bool

data getters/setters

C++: core::io::raw_data::DecoyStruct::fullatom() const –> bool

  1. fullatom(self: pyrosetta.rosetta.core.io.raw_data.DecoyStruct, fullatom: bool) -> None

C++: core::io::raw_data::DecoyStruct::fullatom(bool) –> void

get_debug_rmsd(self: pyrosetta.rosetta.core.io.raw_data.DecoyStruct) → float
calculates the RMSD between the C-alpha atoms of a Pose built from the torsions in this

DecoyStruct and the C-alpha atoms from this DecoyStruct.

C++: core::io::raw_data::DecoyStruct::get_debug_rmsd() –> double

nres(*args, **kwargs)

Overloaded function.

  1. nres(self: pyrosetta.rosetta.core.io.raw_data.RawStruct) -> int

data access methods.

C++: core::io::raw_data::RawStruct::nres() –> unsigned long

  1. nres(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, nres: int) -> None

returns the number of residues in this RawStruct

C++: core::io::raw_data::RawStruct::nres(unsigned long) –> void

omega(*args, **kwargs)

Overloaded function.

  1. omega(self: pyrosetta.rosetta.core.io.raw_data.DecoyStruct, seqpos: int) -> float

C++: core::io::raw_data::DecoyStruct::omega(unsigned int) const –> double

  1. omega(self: pyrosetta.rosetta.core.io.raw_data.DecoyStruct, seqpos: int, omega: float) -> None

C++: core::io::raw_data::DecoyStruct::omega(unsigned int, double) –> void

phi(*args, **kwargs)

Overloaded function.

  1. phi(self: pyrosetta.rosetta.core.io.raw_data.DecoyStruct, seqpos: int) -> float

C++: core::io::raw_data::DecoyStruct::phi(unsigned int) const –> double

  1. phi(self: pyrosetta.rosetta.core.io.raw_data.DecoyStruct, seqpos: int, phi: float) -> None

C++: core::io::raw_data::DecoyStruct::phi(unsigned int, double) –> void

print_conformation(self: pyrosetta.rosetta.core.io.raw_data.DecoyStruct, output: pyrosetta.rosetta.std.ostream) → None

C++: core::io::raw_data::DecoyStruct::print_conformation(std::ostream &) const –> void

print_header(*args, **kwargs)

Overloaded function.

  1. print_header(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, out: pyrosetta.rosetta.std.ostream, score_map: pyrosetta.rosetta.std.map_std_string_double) -> None

  2. print_header(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, out: pyrosetta.rosetta.std.ostream, score_map: pyrosetta.rosetta.std.map_std_string_double, string_map: pyrosetta.rosetta.std.map_std_string_std_string) -> None

  3. print_header(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, out: pyrosetta.rosetta.std.ostream, score_map: pyrosetta.rosetta.std.map_std_string_double, string_map: pyrosetta.rosetta.std.map_std_string_std_string, print_sequence: bool) -> None

print out a header line to the given ozstream. In a rosetta++ silent-file, this contained the lines

SEQUENCE: <protein sequence>: <list of score-types>.

C++: core::io::raw_data::RawStruct::print_header(std::ostream &, const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &, const class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &, bool) const –> void

print_scores(*args, **kwargs)

Overloaded function.

  1. print_scores(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, out: pyrosetta.rosetta.std.ostream, score_map: pyrosetta.rosetta.std.map_std_string_double) -> None

  2. print_scores(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, out: pyrosetta.rosetta.std.ostream, score_map: pyrosetta.rosetta.std.map_std_string_double, string_map: pyrosetta.rosetta.std.map_std_string_std_string) -> None

print out a SCORE line to the given ozstream.

C++: core::io::raw_data::RawStruct::print_scores(std::ostream &, const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &, const class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &) const –> void

psi(*args, **kwargs)

Overloaded function.

  1. psi(self: pyrosetta.rosetta.core.io.raw_data.DecoyStruct, seqpos: int) -> float

C++: core::io::raw_data::DecoyStruct::psi(unsigned int) const –> double

  1. psi(self: pyrosetta.rosetta.core.io.raw_data.DecoyStruct, seqpos: int, psi: float) -> None

C++: core::io::raw_data::DecoyStruct::psi(unsigned int, double) –> void

resize(self: pyrosetta.rosetta.core.io.raw_data.DecoyStruct, nres_in: int) → None

C++: core::io::raw_data::DecoyStruct::resize(const unsigned long) –> void

secstruct(*args, **kwargs)

Overloaded function.

  1. secstruct(self: pyrosetta.rosetta.core.io.raw_data.DecoyStruct, seqpos: int) -> str

C++: core::io::raw_data::DecoyStruct::secstruct(unsigned int) const –> char

  1. secstruct(self: pyrosetta.rosetta.core.io.raw_data.DecoyStruct, seqpos: int, ss: str) -> None

C++: core::io::raw_data::DecoyStruct::secstruct(unsigned int, char) –> void

sequence(*args, **kwargs)

Overloaded function.

  1. sequence(self: pyrosetta.rosetta.core.io.raw_data.RawStruct) -> str

returns the sequence for this RawStruct

C++: core::io::raw_data::RawStruct::sequence() –> std::string

  1. sequence(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, sequence: str) -> None

sets the sequence for this RawStruct

C++: core::io::raw_data::RawStruct::sequence(std::string) –> void

class pyrosetta.rosetta.core.io.raw_data.DisulfideFile

Bases: pybind11_object

Parses and stores a disulfide file.

Initiallizing a DisulfideFile is a lightweight operation. The heavy lifting occurs the first time disulfides() is called. This parses the file and caches the resulting pairs of residues. Subsequent calls to disulfides() are fast since they don’t reparse the file but merely reinterpret the results in terms of the specified.

The disulfide file format is pretty flexible. It looks for three kinds of lines:

  • ‘12 42’ Lines with two integers are interpreted as a disulfide bond, indexed by internal rosetta residue number, i.e. the 12th and 42nd residues from the start of the pose.

  • ‘12A 42A’ If a single character is appended to the numbers, DisulfideFile assumes that these refer to the pdb number and chain, i.e. the residues of chain A numbered 12 and 42 in the pdb.

  • ‘SSBOND 1 CYS A 12 CYS A 42’ The

    PDB format for disulfide bond annotations.

All lines not matching these criteria are silently ignored. This implies that whole pdb files can usually be used unaltered as disulfide files, since the SSBOND entries are extracted and all else is ignored.

Question from rhiju, 2014 – I don’t see handling of ‘12A’ or SSBOND cases in

DisulfideFile.cc – is someone going to check that in?

class NumberingSystem

Bases: pybind11_object

distinguish between PDB numbering and internal Rosetta numbering

unknown_num should be avoided, as one of the other types can generally be infered from the existance of a chain specifier.

Members:

pdb_num

rosetta_num

unknown_num

property name
pdb_num = <NumberingSystem.pdb_num: 0>
rosetta_num = <NumberingSystem.rosetta_num: 1>
unknown_num = <NumberingSystem.unknown_num: 2>
property value
class ResNum

Bases: pybind11_object

represents a residue of either pdb or rosetta numbering.

pdb numbers should include a chain character; rosetta numbers have chain==0

property chain
property n
property type
disulfides(*args, **kwargs)

Overloaded function.

  1. disulfides(self: pyrosetta.rosetta.core.io.raw_data.DisulfideFile, disulfides: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) -> None

Get a list of disulfide bonds declared in the file

C++: core::io::raw_data::DisulfideFile::disulfides(class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &) const –> void

  1. disulfides(self: pyrosetta.rosetta.core.io.raw_data.DisulfideFile, disulfides: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, pose: pyrosetta.rosetta.core.pose.Pose) -> None

Get a list of disulfide bonds declared in the file

(renumbered to rosetta numbering if necessary)

C++: core::io::raw_data::DisulfideFile::disulfides(class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &, const class core::pose::Pose &) const –> void

filename(self: pyrosetta.rosetta.core.io.raw_data.DisulfideFile) → str

Accessor for the filename

C++: core::io::raw_data::DisulfideFile::filename() const –> const std::string &

pdb_num = <NumberingSystem.pdb_num: 0>
read_in_and_set_disulfides(self: pyrosetta.rosetta.core.io.raw_data.DisulfideFile, pose: pyrosetta.rosetta.core.pose.Pose) → None
Get a list of disulfide bonds declared in the file

(renumbered to rosetta numbering if necessary)

also manually set the disulfides in the conformation of the provided pose (this is a necessary workaround for dealing with multiple disulfide specification files in PyRosetta

C++: core::io::raw_data::DisulfideFile::read_in_and_set_disulfides(class core::pose::Pose &) –> void

rosetta_num = <NumberingSystem.rosetta_num: 1>
unknown_num = <NumberingSystem.unknown_num: 2>
class pyrosetta.rosetta.core.io.raw_data.RawFileData

Bases: pybind11_object

Abstract base class for classes that writes different types of silent-files that contain a mixture of Struct objects which are expected to be uniquely identified by some sort of string-based tag.

assign(self: pyrosetta.rosetta.core.io.raw_data.RawFileData, : pyrosetta.rosetta.core.io.raw_data.RawFileData) → pyrosetta.rosetta.core.io.raw_data.RawFileData

C++: core::io::raw_data::RawFileData::operator=(const class core::io::raw_data::RawFileData &) –> class core::io::raw_data::RawFileData &

begin(self: pyrosetta.rosetta.core.io.raw_data.RawFileData) → core::io::raw_data::RawFileData::iterator

Returns an iterator to the start of the members of this container.

C++: core::io::raw_data::RawFileData::begin() –> class core::io::raw_data::RawFileData::iterator

begin_const(self: pyrosetta.rosetta.core.io.raw_data.RawFileData) → core::io::raw_data::RawFileData::const_iterator

C++: core::io::raw_data::RawFileData::begin_const() const –> class core::io::raw_data::RawFileData::const_iterator

clear_structure_map(self: pyrosetta.rosetta.core.io.raw_data.RawFileData) → None

Remove all of the RawStruct objects from this object.

C++: core::io::raw_data::RawFileData::clear_structure_map() –> void

class const_iterator

Bases: pybind11_object

const_iterator class for RawFileData container.

arrow(self: pyrosetta.rosetta.core.io.raw_data.RawFileData.const_iterator) → pyrosetta.rosetta.core.io.raw_data.RawStruct

C++: core::io::raw_data::RawFileData::const_iterator::operator->() const –> class std::shared_ptr<class core::io::raw_data::RawStruct>

assign(self: pyrosetta.rosetta.core.io.raw_data.RawFileData.const_iterator, src: pyrosetta.rosetta.core.io.raw_data.RawFileData.const_iterator) → pyrosetta.rosetta.core.io.raw_data.RawFileData.const_iterator

C++: core::io::raw_data::RawFileData::const_iterator::operator=(const class core::io::raw_data::RawFileData::const_iterator &) –> class core::io::raw_data::RawFileData::const_iterator &

dereference(self: pyrosetta.rosetta.core.io.raw_data.RawFileData.const_iterator) → pyrosetta.rosetta.core.io.raw_data.RawStruct

C++: core::io::raw_data::RawFileData::const_iterator::operator*() const –> class std::shared_ptr<class core::io::raw_data::RawStruct>

pre_increment(self: pyrosetta.rosetta.core.io.raw_data.RawFileData.const_iterator) → pyrosetta.rosetta.core.io.raw_data.RawFileData.const_iterator

C++: core::io::raw_data::RawFileData::const_iterator::operator++() –> class core::io::raw_data::RawFileData::const_iterator &

end(self: pyrosetta.rosetta.core.io.raw_data.RawFileData) → core::io::raw_data::RawFileData::iterator

Returns an iterator to the end of the members of this container.

C++: core::io::raw_data::RawFileData::end() –> class core::io::raw_data::RawFileData::iterator

end_const(self: pyrosetta.rosetta.core.io.raw_data.RawFileData) → core::io::raw_data::RawFileData::const_iterator

C++: core::io::raw_data::RawFileData::end_const() const –> class core::io::raw_data::RawFileData::const_iterator

class iterator

Bases: pybind11_object

Iterator class for RawFileData container.

arrow(self: pyrosetta.rosetta.core.io.raw_data.RawFileData.iterator) → pyrosetta.rosetta.core.io.raw_data.RawStruct

C++: core::io::raw_data::RawFileData::iterator::operator->() –> class std::shared_ptr<class core::io::raw_data::RawStruct>

assign(self: pyrosetta.rosetta.core.io.raw_data.RawFileData.iterator, src: pyrosetta.rosetta.core.io.raw_data.RawFileData.iterator) → pyrosetta.rosetta.core.io.raw_data.RawFileData.iterator

C++: core::io::raw_data::RawFileData::iterator::operator=(const class core::io::raw_data::RawFileData::iterator &) –> class core::io::raw_data::RawFileData::iterator &

dereference(self: pyrosetta.rosetta.core.io.raw_data.RawFileData.iterator) → pyrosetta.rosetta.core.io.raw_data.RawStruct

C++: core::io::raw_data::RawFileData::iterator::operator*() const –> class std::shared_ptr<class core::io::raw_data::RawStruct>

pre_increment(self: pyrosetta.rosetta.core.io.raw_data.RawFileData.iterator) → pyrosetta.rosetta.core.io.raw_data.RawFileData.iterator

C++: core::io::raw_data::RawFileData::iterator::operator++() –> class core::io::raw_data::RawFileData::iterator &

nres(self: pyrosetta.rosetta.core.io.raw_data.RawFileData) → int
Returns the number of residues in the first structure in this object. Not

guaranteed to be fixed for all structures in this container.

C++: core::io::raw_data::RawFileData::nres() const –> int

read_tags_fast(self: pyrosetta.rosetta.core.io.raw_data.RawFileData, filename: str) → pyrosetta.rosetta.utility.vector1_std_string
quickly read a list of tags from a silent-input file. Only checks lines beginning

with SCORE: strings.

C++: core::io::raw_data::RawFileData::read_tags_fast(const std::string &) const –> class utility::vector1<std::string, class std::allocator<std::string > >

sequence(self: pyrosetta.rosetta.core.io.raw_data.RawFileData) → str
Returns the sequence of the first structure in this object. Not

guaranteed to be fixed for all structures in this container.

C++: core::io::raw_data::RawFileData::sequence() const –> std::string

size(self: pyrosetta.rosetta.core.io.raw_data.RawFileData) → int

Returns the number of structures contained in this container.

C++: core::io::raw_data::RawFileData::size() const –> int

write_all(self: pyrosetta.rosetta.core.io.raw_data.RawFileData, filename: str, score_map: pyrosetta.rosetta.std.map_std_string_double) → None

write all RawStruct objects in the structure_map_ to the given filename.

C++: core::io::raw_data::RawFileData::write_all(const std::string &, const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &) –> void

class pyrosetta.rosetta.core.io.raw_data.RawStruct

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, : pyrosetta.rosetta.core.io.raw_data.RawStruct) → pyrosetta.rosetta.core.io.raw_data.RawStruct

C++: core::io::raw_data::RawStruct::operator=(const class core::io::raw_data::RawStruct &) –> class core::io::raw_data::RawStruct &

decoy_tag(*args, **kwargs)

Overloaded function.

  1. decoy_tag(self: pyrosetta.rosetta.core.io.raw_data.RawStruct) -> str

returns the tag associated with this RawStruct

C++: core::io::raw_data::RawStruct::decoy_tag() –> std::string

  1. decoy_tag(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, tag: str) -> None

sets the tag associated with this RawStruct

C++: core::io::raw_data::RawStruct::decoy_tag(std::string) –> void

fill_pose(*args, **kwargs)

Overloaded function.

  1. fill_pose(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, pose: pyrosetta.rosetta.core.pose.Pose) -> None

Fill a Pose with the conformation information in this RawStruct and the FA_STANDARD

ResidueTypeSet. This is a virtual method which must be implemented by classes derived from RawStruct.

C++: core::io::raw_data::RawStruct::fill_pose(class core::pose::Pose &) –> void

  1. fill_pose(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) -> None

Fill a Pose with the conformation information in this RawStruct and the ResidueTypeSet

provided by the caller. This is a virtual method which must be implemented by classes derived from RawStruct.

C++: core::io::raw_data::RawStruct::fill_pose(class core::pose::Pose &, const class core::chemical::ResidueTypeSet &) –> void

get_debug_rmsd(self: pyrosetta.rosetta.core.io.raw_data.RawStruct) → float
Do some sort of comparison between the actual RMSD of this silent-struct and

the cached coordinates. Used for RawStruct objects that are rebuild from torsions or other shortened representations of data.

C++: core::io::raw_data::RawStruct::get_debug_rmsd() –> double

nres(*args, **kwargs)

Overloaded function.

  1. nres(self: pyrosetta.rosetta.core.io.raw_data.RawStruct) -> int

data access methods.

C++: core::io::raw_data::RawStruct::nres() –> unsigned long

  1. nres(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, nres: int) -> None

returns the number of residues in this RawStruct

C++: core::io::raw_data::RawStruct::nres(unsigned long) –> void

print_conformation(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, out: pyrosetta.rosetta.std.ostream) → None

C++: core::io::raw_data::RawStruct::print_conformation(std::ostream &) const –> void

print_header(*args, **kwargs)

Overloaded function.

  1. print_header(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, out: pyrosetta.rosetta.std.ostream, score_map: pyrosetta.rosetta.std.map_std_string_double) -> None

  2. print_header(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, out: pyrosetta.rosetta.std.ostream, score_map: pyrosetta.rosetta.std.map_std_string_double, string_map: pyrosetta.rosetta.std.map_std_string_std_string) -> None

  3. print_header(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, out: pyrosetta.rosetta.std.ostream, score_map: pyrosetta.rosetta.std.map_std_string_double, string_map: pyrosetta.rosetta.std.map_std_string_std_string, print_sequence: bool) -> None

print out a header line to the given ozstream. In a rosetta++ silent-file, this contained the lines

SEQUENCE: <protein sequence>: <list of score-types>.

C++: core::io::raw_data::RawStruct::print_header(std::ostream &, const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &, const class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &, bool) const –> void

print_scores(*args, **kwargs)

Overloaded function.

  1. print_scores(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, out: pyrosetta.rosetta.std.ostream, score_map: pyrosetta.rosetta.std.map_std_string_double) -> None

  2. print_scores(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, out: pyrosetta.rosetta.std.ostream, score_map: pyrosetta.rosetta.std.map_std_string_double, string_map: pyrosetta.rosetta.std.map_std_string_std_string) -> None

print out a SCORE line to the given ozstream.

C++: core::io::raw_data::RawStruct::print_scores(std::ostream &, const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &, const class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &) const –> void

sequence(*args, **kwargs)

Overloaded function.

  1. sequence(self: pyrosetta.rosetta.core.io.raw_data.RawStruct) -> str

returns the sequence for this RawStruct

C++: core::io::raw_data::RawStruct::sequence() –> std::string

  1. sequence(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, sequence: str) -> None

sets the sequence for this RawStruct

C++: core::io::raw_data::RawStruct::sequence(std::string) –> void

class pyrosetta.rosetta.core.io.raw_data.ScoreFileData

Bases: RawFileData

assign(self: pyrosetta.rosetta.core.io.raw_data.ScoreFileData, : pyrosetta.rosetta.core.io.raw_data.ScoreFileData) → pyrosetta.rosetta.core.io.raw_data.ScoreFileData

C++: core::io::raw_data::ScoreFileData::operator=(const class core::io::raw_data::ScoreFileData &) –> class core::io::raw_data::ScoreFileData &

begin(self: pyrosetta.rosetta.core.io.raw_data.RawFileData) → core::io::raw_data::RawFileData::iterator

Returns an iterator to the start of the members of this container.

C++: core::io::raw_data::RawFileData::begin() –> class core::io::raw_data::RawFileData::iterator

begin_const(self: pyrosetta.rosetta.core.io.raw_data.RawFileData) → core::io::raw_data::RawFileData::const_iterator

C++: core::io::raw_data::RawFileData::begin_const() const –> class core::io::raw_data::RawFileData::const_iterator

clear_structure_map(self: pyrosetta.rosetta.core.io.raw_data.RawFileData) → None

Remove all of the RawStruct objects from this object.

C++: core::io::raw_data::RawFileData::clear_structure_map() –> void

class const_iterator

Bases: pybind11_object

const_iterator class for RawFileData container.

arrow(self: pyrosetta.rosetta.core.io.raw_data.RawFileData.const_iterator) → pyrosetta.rosetta.core.io.raw_data.RawStruct

C++: core::io::raw_data::RawFileData::const_iterator::operator->() const –> class std::shared_ptr<class core::io::raw_data::RawStruct>

assign(self: pyrosetta.rosetta.core.io.raw_data.RawFileData.const_iterator, src: pyrosetta.rosetta.core.io.raw_data.RawFileData.const_iterator) → pyrosetta.rosetta.core.io.raw_data.RawFileData.const_iterator

C++: core::io::raw_data::RawFileData::const_iterator::operator=(const class core::io::raw_data::RawFileData::const_iterator &) –> class core::io::raw_data::RawFileData::const_iterator &

dereference(self: pyrosetta.rosetta.core.io.raw_data.RawFileData.const_iterator) → pyrosetta.rosetta.core.io.raw_data.RawStruct

C++: core::io::raw_data::RawFileData::const_iterator::operator*() const –> class std::shared_ptr<class core::io::raw_data::RawStruct>

pre_increment(self: pyrosetta.rosetta.core.io.raw_data.RawFileData.const_iterator) → pyrosetta.rosetta.core.io.raw_data.RawFileData.const_iterator

C++: core::io::raw_data::RawFileData::const_iterator::operator++() –> class core::io::raw_data::RawFileData::const_iterator &

end(self: pyrosetta.rosetta.core.io.raw_data.RawFileData) → core::io::raw_data::RawFileData::iterator

Returns an iterator to the end of the members of this container.

C++: core::io::raw_data::RawFileData::end() –> class core::io::raw_data::RawFileData::iterator

end_const(self: pyrosetta.rosetta.core.io.raw_data.RawFileData) → core::io::raw_data::RawFileData::const_iterator

C++: core::io::raw_data::RawFileData::end_const() const –> class core::io::raw_data::RawFileData::const_iterator

class iterator

Bases: pybind11_object

Iterator class for RawFileData container.

arrow(self: pyrosetta.rosetta.core.io.raw_data.RawFileData.iterator) → pyrosetta.rosetta.core.io.raw_data.RawStruct

C++: core::io::raw_data::RawFileData::iterator::operator->() –> class std::shared_ptr<class core::io::raw_data::RawStruct>

assign(self: pyrosetta.rosetta.core.io.raw_data.RawFileData.iterator, src: pyrosetta.rosetta.core.io.raw_data.RawFileData.iterator) → pyrosetta.rosetta.core.io.raw_data.RawFileData.iterator

C++: core::io::raw_data::RawFileData::iterator::operator=(const class core::io::raw_data::RawFileData::iterator &) –> class core::io::raw_data::RawFileData::iterator &

dereference(self: pyrosetta.rosetta.core.io.raw_data.RawFileData.iterator) → pyrosetta.rosetta.core.io.raw_data.RawStruct

C++: core::io::raw_data::RawFileData::iterator::operator*() const –> class std::shared_ptr<class core::io::raw_data::RawStruct>

pre_increment(self: pyrosetta.rosetta.core.io.raw_data.RawFileData.iterator) → pyrosetta.rosetta.core.io.raw_data.RawFileData.iterator

C++: core::io::raw_data::RawFileData::iterator::operator++() –> class core::io::raw_data::RawFileData::iterator &

nres(self: pyrosetta.rosetta.core.io.raw_data.RawFileData) → int
Returns the number of residues in the first structure in this object. Not

guaranteed to be fixed for all structures in this container.

C++: core::io::raw_data::RawFileData::nres() const –> int

read_tags_fast(self: pyrosetta.rosetta.core.io.raw_data.RawFileData, filename: str) → pyrosetta.rosetta.utility.vector1_std_string
quickly read a list of tags from a silent-input file. Only checks lines beginning

with SCORE: strings.

C++: core::io::raw_data::RawFileData::read_tags_fast(const std::string &) const –> class utility::vector1<std::string, class std::allocator<std::string > >

sequence(self: pyrosetta.rosetta.core.io.raw_data.RawFileData) → str
Returns the sequence of the first structure in this object. Not

guaranteed to be fixed for all structures in this container.

C++: core::io::raw_data::RawFileData::sequence() const –> std::string

size(self: pyrosetta.rosetta.core.io.raw_data.RawFileData) → int

Returns the number of structures contained in this container.

C++: core::io::raw_data::RawFileData::size() const –> int

write_all(self: pyrosetta.rosetta.core.io.raw_data.RawFileData, filename: str, score_map: pyrosetta.rosetta.std.map_std_string_double) → None

write all RawStruct objects in the structure_map_ to the given filename.

C++: core::io::raw_data::RawFileData::write_all(const std::string &, const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &) –> void

write_pose(*args, **kwargs)

Overloaded function.

  1. write_pose(self: pyrosetta.rosetta.core.io.raw_data.ScoreFileData, pose: pyrosetta.rosetta.core.pose.Pose, score_map: pyrosetta.rosetta.std.map_std_string_double, tag: str) -> bool

  2. write_pose(self: pyrosetta.rosetta.core.io.raw_data.ScoreFileData, pose: pyrosetta.rosetta.core.pose.Pose, score_map: pyrosetta.rosetta.std.map_std_string_double, tag: str, string_map: pyrosetta.rosetta.std.map_std_string_std_string) -> bool

C++: core::io::raw_data::ScoreFileData::write_pose(const class core::pose::Pose &, const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &, std::string, const class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &) –> bool

write_struct(*args, **kwargs)

Overloaded function.

  1. write_struct(self: pyrosetta.rosetta.core.io.raw_data.ScoreFileData, s: pyrosetta.rosetta.core.io.raw_data.RawStruct, score_map: pyrosetta.rosetta.std.map_std_string_double) -> bool

  2. write_struct(self: pyrosetta.rosetta.core.io.raw_data.ScoreFileData, s: pyrosetta.rosetta.core.io.raw_data.RawStruct, score_map: pyrosetta.rosetta.std.map_std_string_double, string_map: pyrosetta.rosetta.std.map_std_string_std_string) -> bool

C++: core::io::raw_data::ScoreFileData::write_struct(const class std::shared_ptr<class core::io::raw_data::RawStruct>, const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &, const class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &) –> bool

class pyrosetta.rosetta.core.io.raw_data.ScoreMap

Bases: pybind11_object

static add_arbitrary_score_data_from_pose(pose: pyrosetta.rosetta.core.pose.Pose, score_map: pyrosetta.rosetta.std.map_std_string_double) → None

Add data set as PoseExtraScores (ARBITRARY_FLOAT_DATA) and SimpleMetrics (SIMPLE_METRIC_DATA).

C++: core::io::raw_data::ScoreMap::add_arbitrary_score_data_from_pose(const class core::pose::Pose &, class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &) –> void

static add_arbitrary_string_data_from_pose(pose: pyrosetta.rosetta.core.pose.Pose, string_map: pyrosetta.rosetta.std.map_std_string_std_string) → None

Add data set as PoseExtraScores (ARBITRARY_STRING_DATA) and SimpleMetrics (SIMPLE_METRIC_DATA).

C++: core::io::raw_data::ScoreMap::add_arbitrary_string_data_from_pose(const class core::pose::Pose &, class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &) –> void

static add_energies_data_from_scored_pose(pose: pyrosetta.rosetta.core.pose.Pose, scores: pyrosetta.rosetta.std.map_std_string_double) → None

Add energies to scores map.

C++: core::io::raw_data::ScoreMap::add_energies_data_from_scored_pose(const class core::pose::Pose &, class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &) –> void

assign(self: pyrosetta.rosetta.core.io.raw_data.ScoreMap, : pyrosetta.rosetta.core.io.raw_data.ScoreMap) → pyrosetta.rosetta.core.io.raw_data.ScoreMap

C++: core::io::raw_data::ScoreMap::operator=(const class core::io::raw_data::ScoreMap &) –> class core::io::raw_data::ScoreMap &

static get_arbitrary_score_data_from_pose(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.map_std_string_double

Return by value version of extra score data.

Get data set as PoseExtraScores (ARBITRARY_FLOAT_DATA) and SimpleMetrics (SIMPLE_METRIC_DATA).

C++: core::io::raw_data::ScoreMap::get_arbitrary_score_data_from_pose(const class core::pose::Pose &) –> class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > >

static get_arbitrary_string_data_from_pose(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.map_std_string_std_string

Return by value version of extra string data.

Get data set as PoseExtraScores (ARBITRARY_STRING_DATA) and SimpleMetrics (SIMPLE_METRIC_DATA).

C++: core::io::raw_data::ScoreMap::get_arbitrary_string_data_from_pose(const class core::pose::Pose &) –> class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > >

static get_energies_map_from_scored_pose(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.map_std_string_double

generates a (nonzero) (weighted) scoremap assuming the pose is already scored (note const w.r.t. pose)

C++: core::io::raw_data::ScoreMap::get_energies_map_from_scored_pose(const class core::pose::Pose &) –> class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > >

static print(score_map: pyrosetta.rosetta.std.map_std_string_double, out: pyrosetta.rosetta.std.ostream) → None

print out the values in the scoremap

C++: core::io::raw_data::ScoreMap::print(const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &, std::ostream &) –> void

static score_and_add_energies_to_map(score_map: pyrosetta.rosetta.std.map_std_string_double, score_fxn: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose) → None

Scores and grabs (nonzero, weighted) energies map.

C++: core::io::raw_data::ScoreMap::score_and_add_energies_to_map(class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &, class std::shared_ptr<const class core::scoring::ScoreFunction>, class core::pose::Pose &) –> void

class pyrosetta.rosetta.core.io.raw_data.ScoreStructJSON

Bases: RawStruct

assign(self: pyrosetta.rosetta.core.io.raw_data.ScoreStructJSON, : pyrosetta.rosetta.core.io.raw_data.ScoreStructJSON) → pyrosetta.rosetta.core.io.raw_data.ScoreStructJSON

C++: core::io::raw_data::ScoreStructJSON::operator=(const class core::io::raw_data::ScoreStructJSON &) –> class core::io::raw_data::ScoreStructJSON &

decoy_tag(*args, **kwargs)

Overloaded function.

  1. decoy_tag(self: pyrosetta.rosetta.core.io.raw_data.RawStruct) -> str

returns the tag associated with this RawStruct

C++: core::io::raw_data::RawStruct::decoy_tag() –> std::string

  1. decoy_tag(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, tag: str) -> None

sets the tag associated with this RawStruct

C++: core::io::raw_data::RawStruct::decoy_tag(std::string) –> void

fill_pose(*args, **kwargs)

Overloaded function.

  1. fill_pose(self: pyrosetta.rosetta.core.io.raw_data.ScoreStructJSON, : pyrosetta.rosetta.core.pose.Pose) -> None

C++: core::io::raw_data::ScoreStructJSON::fill_pose(class core::pose::Pose &) –> void

  1. fill_pose(self: pyrosetta.rosetta.core.io.raw_data.ScoreStructJSON, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.chemical.ResidueTypeSet) -> None

C++: core::io::raw_data::ScoreStructJSON::fill_pose(class core::pose::Pose &, const class core::chemical::ResidueTypeSet &) –> void

get_debug_rmsd(self: pyrosetta.rosetta.core.io.raw_data.ScoreStructJSON) → float

C++: core::io::raw_data::ScoreStructJSON::get_debug_rmsd() –> double

nres(*args, **kwargs)

Overloaded function.

  1. nres(self: pyrosetta.rosetta.core.io.raw_data.RawStruct) -> int

data access methods.

C++: core::io::raw_data::RawStruct::nres() –> unsigned long

  1. nres(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, nres: int) -> None

returns the number of residues in this RawStruct

C++: core::io::raw_data::RawStruct::nres(unsigned long) –> void

print_conformation(self: pyrosetta.rosetta.core.io.raw_data.ScoreStructJSON, : pyrosetta.rosetta.std.ostream) → None

C++: core::io::raw_data::ScoreStructJSON::print_conformation(std::ostream &) const –> void

print_header(self: pyrosetta.rosetta.core.io.raw_data.ScoreStructJSON, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.std.map_std_string_double, : pyrosetta.rosetta.std.map_std_string_std_string, : bool) → None

C++: core::io::raw_data::ScoreStructJSON::print_header(std::ostream &, const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &, const class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &, bool) const –> void

print_scores(*args, **kwargs)

Overloaded function.

  1. print_scores(self: pyrosetta.rosetta.core.io.raw_data.ScoreStructJSON, out: pyrosetta.rosetta.std.ostream, score_map: pyrosetta.rosetta.std.map_std_string_double) -> None

  2. print_scores(self: pyrosetta.rosetta.core.io.raw_data.ScoreStructJSON, out: pyrosetta.rosetta.std.ostream, score_map: pyrosetta.rosetta.std.map_std_string_double, string_map: pyrosetta.rosetta.std.map_std_string_std_string) -> None

C++: core::io::raw_data::ScoreStructJSON::print_scores(std::ostream &, const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &, const class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &) const –> void

sequence(*args, **kwargs)

Overloaded function.

  1. sequence(self: pyrosetta.rosetta.core.io.raw_data.RawStruct) -> str

returns the sequence for this RawStruct

C++: core::io::raw_data::RawStruct::sequence() –> std::string

  1. sequence(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, sequence: str) -> None

sets the sequence for this RawStruct

C++: core::io::raw_data::RawStruct::sequence(std::string) –> void

class pyrosetta.rosetta.core.io.raw_data.ScoreStructText

Bases: RawStruct

assign(self: pyrosetta.rosetta.core.io.raw_data.ScoreStructText, : pyrosetta.rosetta.core.io.raw_data.ScoreStructText) → pyrosetta.rosetta.core.io.raw_data.ScoreStructText

C++: core::io::raw_data::ScoreStructText::operator=(const class core::io::raw_data::ScoreStructText &) –> class core::io::raw_data::ScoreStructText &

decoy_tag(*args, **kwargs)

Overloaded function.

  1. decoy_tag(self: pyrosetta.rosetta.core.io.raw_data.RawStruct) -> str

returns the tag associated with this RawStruct

C++: core::io::raw_data::RawStruct::decoy_tag() –> std::string

  1. decoy_tag(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, tag: str) -> None

sets the tag associated with this RawStruct

C++: core::io::raw_data::RawStruct::decoy_tag(std::string) –> void

fill_pose(*args, **kwargs)

Overloaded function.

  1. fill_pose(self: pyrosetta.rosetta.core.io.raw_data.ScoreStructText, : pyrosetta.rosetta.core.pose.Pose) -> None

Fill a Pose with the conformation information in this RawStruct and the FA_STANDARD

ResidueTypeSet. This is a virtual method which must be implemented by classes derived from RawStruct.

C++: core::io::raw_data::ScoreStructText::fill_pose(class core::pose::Pose &) –> void

  1. fill_pose(self: pyrosetta.rosetta.core.io.raw_data.ScoreStructText, : pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) -> None

Fill a Pose with the conformation information in this RawStruct and the ResidueTypeSet

provided by the caller. This is a virtual method which must be implemented by classes derived from RawStruct.

C++: core::io::raw_data::ScoreStructText::fill_pose(class core::pose::Pose &, const class core::chemical::ResidueTypeSet &) –> void

get_debug_rmsd(self: pyrosetta.rosetta.core.io.raw_data.ScoreStructText) → float

C++: core::io::raw_data::ScoreStructText::get_debug_rmsd() –> double

nres(*args, **kwargs)

Overloaded function.

  1. nres(self: pyrosetta.rosetta.core.io.raw_data.RawStruct) -> int

data access methods.

C++: core::io::raw_data::RawStruct::nres() –> unsigned long

  1. nres(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, nres: int) -> None

returns the number of residues in this RawStruct

C++: core::io::raw_data::RawStruct::nres(unsigned long) –> void

print_conformation(self: pyrosetta.rosetta.core.io.raw_data.ScoreStructText, out: pyrosetta.rosetta.std.ostream) → None

C++: core::io::raw_data::ScoreStructText::print_conformation(std::ostream &) const –> void

print_header(*args, **kwargs)

Overloaded function.

  1. print_header(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, out: pyrosetta.rosetta.std.ostream, score_map: pyrosetta.rosetta.std.map_std_string_double) -> None

  2. print_header(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, out: pyrosetta.rosetta.std.ostream, score_map: pyrosetta.rosetta.std.map_std_string_double, string_map: pyrosetta.rosetta.std.map_std_string_std_string) -> None

  3. print_header(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, out: pyrosetta.rosetta.std.ostream, score_map: pyrosetta.rosetta.std.map_std_string_double, string_map: pyrosetta.rosetta.std.map_std_string_std_string, print_sequence: bool) -> None

print out a header line to the given ozstream. In a rosetta++ silent-file, this contained the lines

SEQUENCE: <protein sequence>: <list of score-types>.

C++: core::io::raw_data::RawStruct::print_header(std::ostream &, const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &, const class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &, bool) const –> void

print_scores(*args, **kwargs)

Overloaded function.

  1. print_scores(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, out: pyrosetta.rosetta.std.ostream, score_map: pyrosetta.rosetta.std.map_std_string_double) -> None

  2. print_scores(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, out: pyrosetta.rosetta.std.ostream, score_map: pyrosetta.rosetta.std.map_std_string_double, string_map: pyrosetta.rosetta.std.map_std_string_std_string) -> None

print out a SCORE line to the given ozstream.

C++: core::io::raw_data::RawStruct::print_scores(std::ostream &, const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &, const class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &) const –> void

sequence(*args, **kwargs)

Overloaded function.

  1. sequence(self: pyrosetta.rosetta.core.io.raw_data.RawStruct) -> str

returns the sequence for this RawStruct

C++: core::io::raw_data::RawStruct::sequence() –> std::string

  1. sequence(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, sequence: str) -> None

sets the sequence for this RawStruct

C++: core::io::raw_data::RawStruct::sequence(std::string) –> void