silent

Bindings for core::io::silent namespace

class pyrosetta.rosetta.core.io.silent.BinarySilentStruct

Bases: SilentStruct

CA_rmsd(self: pyrosetta.rosetta.core.io.silent.BinarySilentStruct, other_pss: pyrosetta.rosetta.core.io.silent.BinarySilentStruct) → float

C++: core::io::silent::BinarySilentStruct::CA_rmsd(class core::io::silent::BinarySilentStruct) –> double

add_chain_ending(self: pyrosetta.rosetta.core.io.silent.BinarySilentStruct, seqpos: int) → None

C++: core::io::silent::BinarySilentStruct::add_chain_ending(const unsigned long) –> void

add_comment(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str, value: str) → None

add a named comment to this SilentStruct object.

Similar to methods for playing with energies, but mapping is string => string rather than string => Real.

C++: core::io::silent::SilentStruct::add_comment(std::string, std::string) –> void

add_energy(*args, **kwargs)

Overloaded function.

1. add_energy(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str, value: float) -> None

2. add_energy(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str, value: float, weight: float) -> None

add a score of a given name and value to this SilentStruct.

Takes an optional weight that defaults to 1.0.

C++: core::io::silent::SilentStruct::add_energy(const std::string &, double, double) –> void

add_jump(self: pyrosetta.rosetta.core.io.silent.BinarySilentStruct, jump: pyrosetta.rosetta.core.kinematics.Jump) → None

C++: core::io::silent::BinarySilentStruct::add_jump(class core::kinematics::Jump) –> void

add_other_struct(self: pyrosetta.rosetta.core.io.silent.SilentStruct, silent_struct: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

C++: core::io::silent::SilentStruct::add_other_struct(class std::shared_ptr<class core::io::silent::SilentStruct>) –> void

add_parent_remark(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str, value: str) → None

C++: core::io::silent::SilentStruct::add_parent_remark(const std::string &, const std::string &) –> void

add_string_value(*args, **kwargs)

Overloaded function.

1. add_string_value(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str, value: str) -> None

2. add_string_value(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str, value: str, index: int) -> None

add a non-floating point score of a given name and value to this

SilentStruct.

C++: core::io::silent::SilentStruct::add_string_value(const std::string &, const std::string &, const int) –> void

add_submotif_info_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line_stream: pyrosetta.rosetta.std.istream) → None

C++: core::io::silent::SilentStruct::add_submotif_info_from_line(std::istream &) –> void

assign(self: pyrosetta.rosetta.core.io.silent.BinarySilentStruct, src: pyrosetta.rosetta.core.io.silent.BinarySilentStruct) → pyrosetta.rosetta.core.io.silent.BinarySilentStruct

Assignment operator.

C++: core::io::silent::BinarySilentStruct::operator=(const class core::io::silent::BinarySilentStruct &) –> class core::io::silent::BinarySilentStruct &

chain_endings(*args, **kwargs)

Overloaded function.

1. chain_endings(self: pyrosetta.rosetta.core.io.silent.BinarySilentStruct, endings: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::io::silent::BinarySilentStruct::chain_endings(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

2. chain_endings(self: pyrosetta.rosetta.core.io.silent.BinarySilentStruct) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::io::silent::BinarySilentStruct::chain_endings() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

chain_endings_str(self: pyrosetta.rosetta.core.io.silent.BinarySilentStruct) → str

C++: core::io::silent::BinarySilentStruct::chain_endings_str() const –> std::string

clear_comments(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

C++: core::io::silent::SilentStruct::clear_comments() –> void

clear_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

Clear all of the energies in the SilentStruct. Doesn’t just

zero the energies, it entirely removes all knowledge of all energies from this SilentStruct.

C++: core::io::silent::SilentStruct::clear_energies() –> void

clone(self: pyrosetta.rosetta.core.io.silent.BinarySilentStruct) → pyrosetta.rosetta.core.io.silent.SilentStruct

C++: core::io::silent::BinarySilentStruct::clone() const –> class std::shared_ptr<class core::io::silent::SilentStruct>

comment_from_line(*args, **kwargs)

Overloaded function.

1. comment_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line: str) -> None

C++: core::io::silent::SilentStruct::comment_from_line(const std::string &) –> void

2. comment_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line: str, include_silentfile_comments: bool) -> None

Creates and adds a comment from an input REMARK line

Input comment line, of the format “REMARK key value [value]*”

If true, ‘REMARK XXX SILENTFILE’ lines will be added to comments.

C++: core::io::silent::SilentStruct::comment_from_line(const std::string &, const bool) –> void

copy_scores(self: pyrosetta.rosetta.core.io.silent.SilentStruct, src_ss: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

Copy the score information in the given SilentStruct into

this SilentStruct.

C++: core::io::silent::SilentStruct::copy_scores(const class core::io::silent::SilentStruct &) –> void

decoy_tag(*args, **kwargs)

Overloaded function.

1. decoy_tag(self: pyrosetta.rosetta.core.io.silent.SilentStruct) -> str

returns the tag associated with this SilentStruct.

C++: core::io::silent::SilentStruct::decoy_tag() const –> std::string

2. decoy_tag(self: pyrosetta.rosetta.core.io.silent.SilentStruct, tag: str) -> None

sets the tag associated with this SilentStruct.

C++: core::io::silent::SilentStruct::decoy_tag(const std::string &) –> void

energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.utility.vector1_core_io_silent_SilentEnergy

Returns the vector of SilentEnergy objects associated with

this SilentStruct object.

C++: core::io::silent::SilentStruct::energies() const –> class utility::vector1<class core::io::silent::SilentEnergy, class std::allocator<class core::io::silent::SilentEnergy> >

energies_from_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

Initialize this SilentStruct’s energies from the given Pose.

This sets energies, energy weights, and the output widths for the energies.

C++: core::io::silent::SilentStruct::energies_from_pose(const class core::pose::Pose &) –> void

energies_into_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

Put the energy information from this SilentStruct into the

pose. Energies that correspond to a ScoreType are put into the pose.energies().total_energies() EnergyMap, all other energies are put into the ARBITRARY_FLOAT_DATA map in the pose DataCache. Also sets the scorefxn_weights in the Energies object using the information from this SilentStruct.

C++: core::io::silent::SilentStruct::energies_into_pose(class core::pose::Pose &) const –> void

energy_names(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → core::io::silent::EnergyNames

Returns the EnergyNames that this SilentStruct contains.

C++: core::io::silent::SilentStruct::energy_names() const –> class core::io::silent::EnergyNames

erase_comment(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str) → None

C++: core::io::silent::SilentStruct::erase_comment(const std::string &) –> void

figure_out_residue_numbers_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line_stream: pyrosetta.rosetta.std.istream) → None

C++: core::io::silent::SilentStruct::figure_out_residue_numbers_from_line(std::istream &) –> void

figure_out_segment_ids_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line_stream: pyrosetta.rosetta.std.istream) → None

C++: core::io::silent::SilentStruct::figure_out_segment_ids_from_line(std::istream &) –> void

fill_other_struct_list(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: core::io::silent::SilentStruct::fill_other_struct_list(const class core::pose::Pose &) –> void

fill_pose(*args, **kwargs)

Overloaded function.

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

2. fill_pose(self: pyrosetta.rosetta.core.io.silent.BinarySilentStruct, pose: pyrosetta.rosetta.core.pose.Pose, metapatches: bool) -> None

Configure the conformation of the given Pose with the

conformational data within this BinarySilentStruct. Calls pose.clear() and rebuilds Pose from scratch using FA_STANDARD residue types.

C++: core::io::silent::BinarySilentStruct::fill_pose(class core::pose::Pose &, const bool) const –> void

3. fill_pose(self: pyrosetta.rosetta.core.io.silent.BinarySilentStruct, pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) -> None

4. fill_pose(self: pyrosetta.rosetta.core.io.silent.BinarySilentStruct, pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, metapatches: bool) -> None

Configure the conformation of the given Pose with the

conformational data within this BinarySilentStruct. Calls pose.clear() and rebuilds Pose from scratch using the user-specified residue types.

C++: core::io::silent::BinarySilentStruct::fill_pose(class core::pose::Pose &, const class core::chemical::ResidueTypeSet &, const bool) const –> void

fill_struct(self: pyrosetta.rosetta.core.io.silent.BinarySilentStruct, pose: pyrosetta.rosetta.core.pose.Pose, tag: str) → None

opposite of fill_pose

C++: core::io::silent::BinarySilentStruct::fill_struct(const class core::pose::Pose &, const std::string &) –> void

fill_struct_with_residue_numbers(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: core::io::silent::SilentStruct::fill_struct_with_residue_numbers(const class core::pose::Pose &) –> void

fill_struct_with_submotif_info_list(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: core::io::silent::SilentStruct::fill_struct_with_submotif_info_list(const class core::pose::Pose &) –> void

finish_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

calls optH if command line requests optH.

must be called by derived classes.

C++: core::io::silent::SilentStruct::finish_pose(class core::pose::Pose &) const –> void

fold_tree(*args, **kwargs)

Overloaded function.

1. fold_tree(self: pyrosetta.rosetta.core.io.silent.BinarySilentStruct, f: pyrosetta.rosetta.core.kinematics.FoldTree) -> None

C++: core::io::silent::BinarySilentStruct::fold_tree(class core::kinematics::FoldTree) –> void

2. fold_tree(self: pyrosetta.rosetta.core.io.silent.BinarySilentStruct) -> pyrosetta.rosetta.core.kinematics.FoldTree

C++: core::io::silent::BinarySilentStruct::fold_tree() const –> const class core::kinematics::FoldTree &

force_bitflip(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → bool

Gets whether conversion from big-endian to little-endian (or the converse) should be forced

when a binary silent structure is initialized from lines.

C++: core::io::silent::SilentStruct::force_bitflip() const –> bool

full_model_info_into_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: core::io::silent::SilentStruct::full_model_info_into_pose(class core::pose::Pose &) const –> void

full_model_parameters(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → core::pose::full_model_info::FullModelParameters

C++: core::io::silent::SilentStruct::full_model_parameters() const –> class std::shared_ptr<const class core::pose::full_model_info::FullModelParameters>

fullatom(*args, **kwargs)

Overloaded function.

1. fullatom(self: pyrosetta.rosetta.core.io.silent.BinarySilentStruct) -> bool

C++: core::io::silent::BinarySilentStruct::fullatom() const –> bool

2. fullatom(self: pyrosetta.rosetta.core.io.silent.BinarySilentStruct, fullatom: bool) -> None

C++: core::io::silent::BinarySilentStruct::fullatom(bool) –> void

get_CA_xyz(self: pyrosetta.rosetta.core.io.silent.BinarySilentStruct) → pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t

returns the positions of the CA atoms

C++: core::io::silent::BinarySilentStruct::get_CA_xyz() const –> class ObjexxFCL::FArray2D<double>

get_all_comments(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.std.map_std_string_std_string

C++: core::io::silent::SilentStruct::get_all_comments() const –> class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > >

get_comment(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str) → str

C++: core::io::silent::SilentStruct::get_comment(const std::string &) const –> std::string

get_debug_rmsd(self: pyrosetta.rosetta.core.io.silent.BinarySilentStruct) → float

calculates the RMSD between the C-alpha atoms of a Pose built from

the torsions in this ProteinSilentStruct and the C-alpha atoms from this ProteinSilentStruct.

C++: core::io::silent::BinarySilentStruct::get_debug_rmsd() –> double

get_energy(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str) → float

Returns the energy associated with the given scorename if this

SilentStruct has an energy for that scorename. Otherwise returns 0.

C++: core::io::silent::SilentStruct::get_energy(const std::string &) const –> double

get_parent_remark(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str) → str

C++: core::io::silent::SilentStruct::get_parent_remark(const std::string &) const –> std::string

get_parent_remark_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line: str) → None

C++: core::io::silent::SilentStruct::get_parent_remark_from_line(const std::string &) –> void

get_self_ptr(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.core.io.silent.SilentStruct

C++: core::io::silent::SilentStruct::get_self_ptr() –> class std::shared_ptr<class core::io::silent::SilentStruct>

get_silent_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.utility.vector1_core_io_silent_SilentEnergy

C++: core::io::silent::SilentStruct::get_silent_energies() –> class utility::vector1<class core::io::silent::SilentEnergy, class std::allocator<class core::io::silent::SilentEnergy> >

get_silent_energy(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str) → pyrosetta.rosetta.core.io.silent.SilentEnergy

Returns the SilentEnergy associated with this scorename.

C++: core::io::silent::SilentStruct::get_silent_energy(const std::string &) const –> const class core::io::silent::SilentEnergy &

get_string_value(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str) → str

Returns the energy associated with the given scorename if this

SilentStruct has an energy for that scorename. Otherwise returns 0.

C++: core::io::silent::SilentStruct::get_string_value(const std::string &) const –> const std::string &

has_comment(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str) → bool

C++: core::io::silent::SilentStruct::has_comment(const std::string &) const –> bool

has_energy(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str) → bool

returns true if this SilentStruct has an energy for the given

scorename, returns false otherwise.

C++: core::io::silent::SilentStruct::has_energy(const std::string &) const –> bool

has_parent_remark(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str) → bool

C++: core::io::silent::SilentStruct::has_parent_remark(const std::string &) const –> bool

init_from_lines(*args, **kwargs)

Overloaded function.

1. init_from_lines(self: pyrosetta.rosetta.core.io.silent.BinarySilentStruct, lines: pyrosetta.rosetta.utility.vector1_std_string, container: pyrosetta.rosetta.core.io.silent.SilentFileData) -> bool

Initialize object from a set of lines.

Does not skip read from container.

C++: core::io::silent::BinarySilentStruct::init_from_lines(const class utility::vector1<std::string, class std::allocator<std::string > > &, class core::io::silent::SilentFileData &) –> bool

2. init_from_lines(self: pyrosetta.rosetta.core.io.silent.BinarySilentStruct, lines: pyrosetta.rosetta.utility.vector1_std_string, container: pyrosetta.rosetta.core.io.silent.SilentFileData, skip_read_from_container: bool) -> bool

Initialize object from a set of lines.

If skip_read_from_container is true, then the container object is not used.

C++: core::io::silent::BinarySilentStruct::init_from_lines(const class utility::vector1<std::string, class std::allocator<std::string > > &, class core::io::silent::SilentFileData &, const bool) –> bool

is_symmetric(self: pyrosetta.rosetta.core.io.silent.BinarySilentStruct) → bool

C++: core::io::silent::BinarySilentStruct::is_symmetric() const –> bool

jump(self: pyrosetta.rosetta.core.io.silent.BinarySilentStruct, jump_num: int) → pyrosetta.rosetta.core.kinematics.RT

C++: core::io::silent::BinarySilentStruct::jump(unsigned long) const –> const class core::kinematics::RT &

mem_footprint(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → int

C++: core::io::silent::SilentStruct::mem_footprint() const –> unsigned long

nonconst_other_struct_list(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_io_silent_SilentStruct_t

C++: core::io::silent::SilentStruct::nonconst_other_struct_list() –> class utility::vector1<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &

nres(*args, **kwargs)

Overloaded function.

1. nres(self: pyrosetta.rosetta.core.io.silent.SilentStruct) -> int

returns the number of residues contained by this

SilentStruct.

C++: core::io::silent::SilentStruct::nres() const –> unsigned long

2. nres(self: pyrosetta.rosetta.core.io.silent.SilentStruct, nres: int) -> None

returns the number of residues in this SilentStruct.

C++: core::io::silent::SilentStruct::nres(unsigned long) –> void

one_letter_sequence(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → str

strip […] comment from seqeunce_ and return pure

one-letter sequence

C++: core::io::silent::SilentStruct::one_letter_sequence() const –> std::string

options(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.core.io.silent.SilentFileOptions

C++: core::io::silent::SilentStruct::options() const –> const class core::io::silent::SilentFileOptions &

other_struct_list(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_io_silent_SilentStruct_t

C++: core::io::silent::SilentStruct::other_struct_list() const –> const class utility::vector1<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &

parse_chain_endings(self: pyrosetta.rosetta.core.io.silent.BinarySilentStruct, stream: pyrosetta.rosetta.std.istream) → None

C++: core::io::silent::BinarySilentStruct::parse_chain_endings(std::istream &) –> void

parse_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct, input: pyrosetta.rosetta.std.istream, energy_names: pyrosetta.rosetta.utility.vector1_std_string) → None

C++: core::io::silent::SilentStruct::parse_energies(std::istream &, const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

precision(*args, **kwargs)

Overloaded function.

1. precision(self: pyrosetta.rosetta.core.io.silent.SilentStruct, precision: int) -> None

C++: core::io::silent::SilentStruct::precision(unsigned long) –> void

2. precision(self: pyrosetta.rosetta.core.io.silent.SilentStruct) -> int

C++: core::io::silent::SilentStruct::precision() const –> unsigned long

print_comments(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None

print the comments in this SilentStruct.

C++: core::io::silent::SilentStruct::print_comments(std::ostream &) const –> void

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

Prints the conformation information within this

BinarySilentStruct to the given std::ostream.

C++: core::io::silent::BinarySilentStruct::print_conformation(std::ostream &) const –> void

print_header(self: pyrosetta.rosetta.core.io.silent.BinarySilentStruct, out: pyrosetta.rosetta.std.ostream) → None

print header information

C++: core::io::silent::BinarySilentStruct::print_header(std::ostream &) const –> void

print_parent_remarks(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None

C++: core::io::silent::SilentStruct::print_parent_remarks(std::ostream &) const –> void

print_residue_numbers(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None

print the resnum in this SilentStruct, if filled.

C++: core::io::silent::SilentStruct::print_residue_numbers(std::ostream &) const –> void

print_score_header(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None

only print SCORE: header line

C++: core::io::silent::SilentStruct::print_score_header(std::ostream &) const –> void

print_scores(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None

print out a SCORE line to the given ozstream.

C++: core::io::silent::SilentStruct::print_scores(std::ostream &) const –> void

print_submotif_info(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None

print the submotif_info in this SilentStruct, if filled.

C++: core::io::silent::SilentStruct::print_submotif_info(std::ostream &) const –> void

read_score_headers(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line: str, enames: pyrosetta.rosetta.utility.vector1_std_string, container: core::io::silent::SilentFileData) → None

C++: core::io::silent::SilentStruct::read_score_headers(const std::string &, class utility::vector1<std::string, class std::allocator<std::string > > &, class core::io::silent::SilentFileData &) –> void

read_sequence(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line: str) → bool

C++: core::io::silent::SilentStruct::read_sequence(const std::string &) –> bool

rename_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

C++: core::io::silent::SilentStruct::rename_energies() –> void

residue_numbers_into_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: core::io::silent::SilentStruct::residue_numbers_into_pose(class core::pose::Pose &) const –> void

resize(self: pyrosetta.rosetta.core.io.silent.BinarySilentStruct, nres_in: int) → None

Re-dimension the storage capacity of this BinarySilentStruct to the given number of residues.

C++: core::io::silent::BinarySilentStruct::resize(const unsigned long) –> void

scoreline_prefix(*args, **kwargs)

Overloaded function.

1. scoreline_prefix(self: pyrosetta.rosetta.core.io.silent.SilentStruct, prefix: str) -> None

C++: core::io::silent::SilentStruct::scoreline_prefix(const std::string &) –> void

2. scoreline_prefix(self: pyrosetta.rosetta.core.io.silent.SilentStruct) -> str

C++: core::io::silent::SilentStruct::scoreline_prefix() const –> std::string

secstruct(*args, **kwargs)

Overloaded function.

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

C++: core::io::silent::BinarySilentStruct::secstruct(unsigned int) const –> char

2. secstruct(self: pyrosetta.rosetta.core.io.silent.BinarySilentStruct, seqpos: int, ss: str) -> None

C++: core::io::silent::BinarySilentStruct::secstruct(unsigned int, char) –> void

sequence(*args, **kwargs)

Overloaded function.

1. sequence(self: pyrosetta.rosetta.core.io.silent.SilentStruct) -> pyrosetta.rosetta.core.sequence.AnnotatedSequence

returns the sequence associated with this SilentStruct.

C++: core::io::silent::SilentStruct::sequence() const –> const class core::sequence::AnnotatedSequence &

2. sequence(self: pyrosetta.rosetta.core.io.silent.SilentStruct, sequence: pyrosetta.rosetta.core.sequence.AnnotatedSequence) -> None

sets the sequence for this SilentStruct.

C++: core::io::silent::SilentStruct::sequence(const class core::sequence::AnnotatedSequence &) –> void

set_chains(self: pyrosetta.rosetta.core.io.silent.SilentStruct, chains: pyrosetta.rosetta.utility.vector1_char) → None

C++: core::io::silent::SilentStruct::set_chains(const class utility::vector1<char, class std::allocator<char> > &) –> void

set_decoy_tag(self: pyrosetta.rosetta.core.io.silent.SilentStruct, tag: str) → None

set the tag associate with this SilentStruct

C++: core::io::silent::SilentStruct::set_decoy_tag(const std::string &) –> void

set_force_bitflip(self: pyrosetta.rosetta.core.io.silent.SilentStruct, setting: bool) → None

Sets whether conversion from big-endian to little-endian (or the converse) should be forced

when a binary silent structure is initialized from lines.

C++: core::io::silent::SilentStruct::set_force_bitflip(const bool) –> void

set_full_model_parameters(self: pyrosetta.rosetta.core.io.silent.SilentStruct, setting: core::pose::full_model_info::FullModelParameters) → None

C++: core::io::silent::SilentStruct::set_full_model_parameters(class std::shared_ptr<const class core::pose::full_model_info::FullModelParameters>) –> void

set_residue_numbers(self: pyrosetta.rosetta.core.io.silent.SilentStruct, residue_numbers: pyrosetta.rosetta.utility.vector1_int) → None

C++: core::io::silent::SilentStruct::set_residue_numbers(const class utility::vector1<int, class std::allocator<int> > &) –> void

set_segment_IDs(self: pyrosetta.rosetta.core.io.silent.SilentStruct, segids: pyrosetta.rosetta.utility.vector1_std_string) → None

C++: core::io::silent::SilentStruct::set_segment_IDs(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_tag_from_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

Sets the tag from the Pose DataCache.

C++: core::io::silent::SilentStruct::set_tag_from_pose(const class core::pose::Pose &) –> void

set_valid_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct, valid: pyrosetta.rosetta.utility.vector1_std_string) → None

C++: core::io::silent::SilentStruct::set_valid_energies(class utility::vector1<std::string, class std::allocator<std::string > >) –> void

setup_other_poses(self: pyrosetta.rosetta.core.io.silent.BinarySilentStruct, pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → None

for stepwise modeling, setup other_poses inside full_model_info

C++: core::io::silent::BinarySilentStruct::setup_other_poses(class core::pose::Pose &, const class core::chemical::ResidueTypeSet &) const –> void

shared_from_this(self: pyrosetta.rosetta.core.io.silent.BinarySilentStruct) → pyrosetta.rosetta.core.io.silent.BinarySilentStruct

C++: core::io::silent::BinarySilentStruct::shared_from_this() –> class std::shared_ptr<class core::io::silent::BinarySilentStruct>

silent_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct, new_se: pyrosetta.rosetta.utility.vector1_core_io_silent_SilentEnergy) → None

sets the silent_energies for this SilentStruct.

C++: core::io::silent::SilentStruct::silent_energies(const class utility::vector1<class core::io::silent::SilentEnergy, class std::allocator<class core::io::silent::SilentEnergy> > &) –> void

sort_silent_scores(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

sort all the silent energies by their name.

C++: core::io::silent::SilentStruct::sort_silent_scores() –> void

symmetry_info(*args, **kwargs)

Overloaded function.

1. symmetry_info(self: pyrosetta.rosetta.core.io.silent.BinarySilentStruct, s: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) -> None

C++: core::io::silent::BinarySilentStruct::symmetry_info(class core::conformation::symmetry::SymmetryInfo &) –> void

2. symmetry_info(self: pyrosetta.rosetta.core.io.silent.BinarySilentStruct) -> pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo

C++: core::io::silent::BinarySilentStruct::symmetry_info() const –> class std::shared_ptr<const class core::conformation::symmetry::SymmetryInfo>

class pyrosetta.rosetta.core.io.silent.BinarySilentStructCreator

Bases: SilentStructCreator

creator for the BinarySilentStruct class

assign(self: pyrosetta.rosetta.core.io.silent.BinarySilentStructCreator, : pyrosetta.rosetta.core.io.silent.BinarySilentStructCreator) → pyrosetta.rosetta.core.io.silent.BinarySilentStructCreator

C++: core::io::silent::BinarySilentStructCreator::operator=(const class core::io::silent::BinarySilentStructCreator &) –> class core::io::silent::BinarySilentStructCreator &

create_silent_struct(self: pyrosetta.rosetta.core.io.silent.BinarySilentStructCreator, : pyrosetta.rosetta.core.io.silent.SilentFileOptions) → pyrosetta.rosetta.core.io.silent.SilentStruct

C++: core::io::silent::BinarySilentStructCreator::create_silent_struct(const class core::io::silent::SilentFileOptions &) const –> class std::shared_ptr<class core::io::silent::SilentStruct>

keyname(self: pyrosetta.rosetta.core.io.silent.BinarySilentStructCreator) → str

C++: core::io::silent::BinarySilentStructCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.io.silent.EnergyNames

Bases: SharedSilentData

assign(self: pyrosetta.rosetta.core.io.silent.EnergyNames, : pyrosetta.rosetta.core.io.silent.EnergyNames) → pyrosetta.rosetta.core.io.silent.EnergyNames

C++: core::io::silent::EnergyNames::operator=(const class core::io::silent::EnergyNames &) –> class core::io::silent::EnergyNames &

energy_names(*args, **kwargs)

Overloaded function.

1. energy_names(self: pyrosetta.rosetta.core.io.silent.EnergyNames, new_e_names: pyrosetta.rosetta.utility.vector1_std_string) -> None

C++: core::io::silent::EnergyNames::energy_names(class utility::vector1<std::string, class std::allocator<std::string > >) –> void

2. energy_names(self: pyrosetta.rosetta.core.io.silent.EnergyNames) -> pyrosetta.rosetta.utility.vector1_std_string

C++: core::io::silent::EnergyNames::energy_names() const –> class utility::vector1<std::string, class std::allocator<std::string > >

class pyrosetta.rosetta.core.io.silent.ProteinSilentStructCreator

Bases: SilentStructCreator

creator for the ProteinSilentStruct class

assign(self: pyrosetta.rosetta.core.io.silent.ProteinSilentStructCreator, : pyrosetta.rosetta.core.io.silent.ProteinSilentStructCreator) → pyrosetta.rosetta.core.io.silent.ProteinSilentStructCreator

C++: core::io::silent::ProteinSilentStructCreator::operator=(const class core::io::silent::ProteinSilentStructCreator &) –> class core::io::silent::ProteinSilentStructCreator &

create_silent_struct(self: pyrosetta.rosetta.core.io.silent.ProteinSilentStructCreator, : pyrosetta.rosetta.core.io.silent.SilentFileOptions) → pyrosetta.rosetta.core.io.silent.SilentStruct

C++: core::io::silent::ProteinSilentStructCreator::create_silent_struct(const class core::io::silent::SilentFileOptions &) const –> class std::shared_ptr<class core::io::silent::SilentStruct>

keyname(self: pyrosetta.rosetta.core.io.silent.ProteinSilentStructCreator) → str

C++: core::io::silent::ProteinSilentStructCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator

Bases: SilentStructCreator

creator for the ProteinSilentStruct_SinglePrec class

assign(self: pyrosetta.rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator, : pyrosetta.rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator) → pyrosetta.rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator

C++: core::io::silent::ProteinSilentStruct_SinglePrecCreator::operator=(const class core::io::silent::ProteinSilentStruct_SinglePrecCreator &) –> class core::io::silent::ProteinSilentStruct_SinglePrecCreator &

create_silent_struct(self: pyrosetta.rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator, : pyrosetta.rosetta.core.io.silent.SilentFileOptions) → pyrosetta.rosetta.core.io.silent.SilentStruct

C++: core::io::silent::ProteinSilentStruct_SinglePrecCreator::create_silent_struct(const class core::io::silent::SilentFileOptions &) const –> class std::shared_ptr<class core::io::silent::SilentStruct>

keyname(self: pyrosetta.rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator) → str

C++: core::io::silent::ProteinSilentStruct_SinglePrecCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.io.silent.RNA_SilentStruct

Bases: SilentStruct

CA_rmsd(self: pyrosetta.rosetta.core.io.silent.RNA_SilentStruct, other_pss: pyrosetta.rosetta.core.io.silent.RNA_SilentStruct) → float

C++: core::io::silent::RNA_SilentStruct::CA_rmsd(class core::io::silent::RNA_SilentStruct) –> double

add_comment(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str, value: str) → None

add a named comment to this SilentStruct object.

Similar to methods for playing with energies, but mapping is string => string rather than string => Real.

C++: core::io::silent::SilentStruct::add_comment(std::string, std::string) –> void

add_energy(*args, **kwargs)

Overloaded function.

1. add_energy(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str, value: float) -> None

2. add_energy(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str, value: float, weight: float) -> None

add a score of a given name and value to this SilentStruct.

Takes an optional weight that defaults to 1.0.

C++: core::io::silent::SilentStruct::add_energy(const std::string &, double, double) –> void

add_jump(self: pyrosetta.rosetta.core.io.silent.RNA_SilentStruct, jump: pyrosetta.rosetta.core.kinematics.Jump) → None

C++: core::io::silent::RNA_SilentStruct::add_jump(const class core::kinematics::Jump &) –> void

add_other_struct(self: pyrosetta.rosetta.core.io.silent.SilentStruct, silent_struct: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

C++: core::io::silent::SilentStruct::add_other_struct(class std::shared_ptr<class core::io::silent::SilentStruct>) –> void

add_parent_remark(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str, value: str) → None

C++: core::io::silent::SilentStruct::add_parent_remark(const std::string &, const std::string &) –> void

add_string_value(*args, **kwargs)

Overloaded function.

1. add_string_value(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str, value: str) -> None

2. add_string_value(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str, value: str, index: int) -> None

add a non-floating point score of a given name and value to this

SilentStruct.

C++: core::io::silent::SilentStruct::add_string_value(const std::string &, const std::string &, const int) –> void

add_submotif_info_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line_stream: pyrosetta.rosetta.std.istream) → None

C++: core::io::silent::SilentStruct::add_submotif_info_from_line(std::istream &) –> void

assign(self: pyrosetta.rosetta.core.io.silent.RNA_SilentStruct, src: pyrosetta.rosetta.core.io.silent.RNA_SilentStruct) → pyrosetta.rosetta.core.io.silent.RNA_SilentStruct

Test if this RNA_SilentStruct is equal to the given RNA_SilentStruct in terms of conformation.

Doesn’t check energies.

C++: core::io::silent::RNA_SilentStruct::operator=(const class core::io::silent::RNA_SilentStruct &) –> class core::io::silent::RNA_SilentStruct &

chi(self: pyrosetta.rosetta.core.io.silent.RNA_SilentStruct, seqpos: int, torsion_num: int) → float

C++: core::io::silent::RNA_SilentStruct::chi(const unsigned long &, const unsigned long &) const –> double

chi_torsions(self: pyrosetta.rosetta.core.io.silent.RNA_SilentStruct, seqpos: int) → pyrosetta.rosetta.utility.vector1_double

C++: core::io::silent::RNA_SilentStruct::chi_torsions(unsigned long) const –> class utility::vector1<double, class std::allocator<double> >

clear_comments(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

C++: core::io::silent::SilentStruct::clear_comments() –> void

clear_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

Clear all of the energies in the SilentStruct. Doesn’t just

zero the energies, it entirely removes all knowledge of all energies from this SilentStruct.

C++: core::io::silent::SilentStruct::clear_energies() –> void

clone(self: pyrosetta.rosetta.core.io.silent.RNA_SilentStruct) → pyrosetta.rosetta.core.io.silent.SilentStruct

C++: core::io::silent::RNA_SilentStruct::clone() const –> class std::shared_ptr<class core::io::silent::SilentStruct>

comment_from_line(*args, **kwargs)

Overloaded function.

1. comment_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line: str) -> None

C++: core::io::silent::SilentStruct::comment_from_line(const std::string &) –> void

2. comment_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line: str, include_silentfile_comments: bool) -> None

Creates and adds a comment from an input REMARK line

Input comment line, of the format “REMARK key value [value]*”

If true, ‘REMARK XXX SILENTFILE’ lines will be added to comments.

C++: core::io::silent::SilentStruct::comment_from_line(const std::string &, const bool) –> void

coords(*args, **kwargs)

Overloaded function.

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

C++: core::io::silent::RNA_SilentStruct::coords(unsigned long) const –> class numeric::xyzVector<double>

2. coords(self: pyrosetta.rosetta.core.io.silent.RNA_SilentStruct) -> pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t

C++: core::io::silent::RNA_SilentStruct::coords() const –> class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >

copy_scores(self: pyrosetta.rosetta.core.io.silent.SilentStruct, src_ss: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

Copy the score information in the given SilentStruct into

this SilentStruct.

C++: core::io::silent::SilentStruct::copy_scores(const class core::io::silent::SilentStruct &) –> void

decoy_tag(*args, **kwargs)

Overloaded function.

1. decoy_tag(self: pyrosetta.rosetta.core.io.silent.SilentStruct) -> str

returns the tag associated with this SilentStruct.

C++: core::io::silent::SilentStruct::decoy_tag() const –> std::string

2. decoy_tag(self: pyrosetta.rosetta.core.io.silent.SilentStruct, tag: str) -> None

sets the tag associated with this SilentStruct.

C++: core::io::silent::SilentStruct::decoy_tag(const std::string &) –> void

energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.utility.vector1_core_io_silent_SilentEnergy

Returns the vector of SilentEnergy objects associated with

this SilentStruct object.

C++: core::io::silent::SilentStruct::energies() const –> class utility::vector1<class core::io::silent::SilentEnergy, class std::allocator<class core::io::silent::SilentEnergy> >

energies_from_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

Initialize this SilentStruct’s energies from the given Pose.

This sets energies, energy weights, and the output widths for the energies.

C++: core::io::silent::SilentStruct::energies_from_pose(const class core::pose::Pose &) –> void

energies_into_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

Put the energy information from this SilentStruct into the

pose. Energies that correspond to a ScoreType are put into the pose.energies().total_energies() EnergyMap, all other energies are put into the ARBITRARY_FLOAT_DATA map in the pose DataCache. Also sets the scorefxn_weights in the Energies object using the information from this SilentStruct.

C++: core::io::silent::SilentStruct::energies_into_pose(class core::pose::Pose &) const –> void

energy_names(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → core::io::silent::EnergyNames

Returns the EnergyNames that this SilentStruct contains.

C++: core::io::silent::SilentStruct::energy_names() const –> class core::io::silent::EnergyNames

erase_comment(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str) → None

C++: core::io::silent::SilentStruct::erase_comment(const std::string &) –> void

figure_out_residue_numbers_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line_stream: pyrosetta.rosetta.std.istream) → None

C++: core::io::silent::SilentStruct::figure_out_residue_numbers_from_line(std::istream &) –> void

figure_out_segment_ids_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line_stream: pyrosetta.rosetta.std.istream) → None

C++: core::io::silent::SilentStruct::figure_out_segment_ids_from_line(std::istream &) –> void

fill_other_struct_list(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: core::io::silent::SilentStruct::fill_other_struct_list(const class core::pose::Pose &) –> void

fill_pose(*args, **kwargs)

Overloaded function.

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

2. fill_pose(self: pyrosetta.rosetta.core.io.silent.RNA_SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose, metapatches: bool) -> None

Configure the conformation of the given Pose with the conformational data within this RNA_SilentStruct.

Calls pose.clear() and rebuilds Pose from scratch using FA_STANDARD residue types.

C++: core::io::silent::RNA_SilentStruct::fill_pose(class core::pose::Pose &, const bool) const –> void

3. fill_pose(self: pyrosetta.rosetta.core.io.silent.RNA_SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) -> None

4. fill_pose(self: pyrosetta.rosetta.core.io.silent.RNA_SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, metapatches: bool) -> None

Configure the conformation of the given Pose with the conformational data within

this RNA_SilentStruct. Calls pose.clear() and rebuilds Pose from scratch using the user-specified residue types.

C++: core::io::silent::RNA_SilentStruct::fill_pose(class core::pose::Pose &, const class core::chemical::ResidueTypeSet &, const bool) const –> void

fill_struct(self: pyrosetta.rosetta.core.io.silent.RNA_SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose, tag: str) → None

opposite of fill_pose

C++: core::io::silent::RNA_SilentStruct::fill_struct(const class core::pose::Pose &, const std::string &) –> void

fill_struct_with_residue_numbers(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: core::io::silent::SilentStruct::fill_struct_with_residue_numbers(const class core::pose::Pose &) –> void

fill_struct_with_submotif_info_list(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: core::io::silent::SilentStruct::fill_struct_with_submotif_info_list(const class core::pose::Pose &) –> void

finish_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

calls optH if command line requests optH.

must be called by derived classes.

C++: core::io::silent::SilentStruct::finish_pose(class core::pose::Pose &) const –> void

fold_tree(self: pyrosetta.rosetta.core.io.silent.RNA_SilentStruct) → pyrosetta.rosetta.core.kinematics.FoldTree

C++: core::io::silent::RNA_SilentStruct::fold_tree() const –> const class core::kinematics::FoldTree &

force_bitflip(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → bool

Gets whether conversion from big-endian to little-endian (or the converse) should be forced

when a binary silent structure is initialized from lines.

C++: core::io::silent::SilentStruct::force_bitflip() const –> bool

full_model_info_into_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: core::io::silent::SilentStruct::full_model_info_into_pose(class core::pose::Pose &) const –> void

full_model_parameters(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → core::pose::full_model_info::FullModelParameters

C++: core::io::silent::SilentStruct::full_model_parameters() const –> class std::shared_ptr<const class core::pose::full_model_info::FullModelParameters>

fullatom(*args, **kwargs)

Overloaded function.

1. fullatom(self: pyrosetta.rosetta.core.io.silent.RNA_SilentStruct) -> bool

data getters/setters

C++: core::io::silent::RNA_SilentStruct::fullatom() const –> bool

2. fullatom(self: pyrosetta.rosetta.core.io.silent.RNA_SilentStruct, fullatom: bool) -> None

C++: core::io::silent::RNA_SilentStruct::fullatom(bool) –> void

get_CA_xyz(self: pyrosetta.rosetta.core.io.silent.RNA_SilentStruct) → pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t

returns the positions of the CA atoms in this RNA_SilentStruct.

Useful for RMS calculations.

C++: core::io::silent::RNA_SilentStruct::get_CA_xyz() const –> class ObjexxFCL::FArray2D<double>

get_all_comments(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.std.map_std_string_std_string

C++: core::io::silent::SilentStruct::get_all_comments() const –> class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > >

get_comment(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str) → str

C++: core::io::silent::SilentStruct::get_comment(const std::string &) const –> std::string

get_debug_rmsd(self: pyrosetta.rosetta.core.io.silent.RNA_SilentStruct) → float

calculates the RMSD between the C-alpha atoms of a Pose built from the torsions in this

RNA_SilentStruct and the C-alpha atoms from this RNA_SilentStruct.

C++: core::io::silent::RNA_SilentStruct::get_debug_rmsd() –> double

get_energy(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str) → float

Returns the energy associated with the given scorename if this

SilentStruct has an energy for that scorename. Otherwise returns 0.

C++: core::io::silent::SilentStruct::get_energy(const std::string &) const –> double

get_parent_remark(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str) → str

C++: core::io::silent::SilentStruct::get_parent_remark(const std::string &) const –> std::string

get_parent_remark_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line: str) → None

C++: core::io::silent::SilentStruct::get_parent_remark_from_line(const std::string &) –> void

get_self_ptr(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.core.io.silent.SilentStruct

C++: core::io::silent::SilentStruct::get_self_ptr() –> class std::shared_ptr<class core::io::silent::SilentStruct>

get_silent_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.utility.vector1_core_io_silent_SilentEnergy

C++: core::io::silent::SilentStruct::get_silent_energies() –> class utility::vector1<class core::io::silent::SilentEnergy, class std::allocator<class core::io::silent::SilentEnergy> >

get_silent_energy(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str) → pyrosetta.rosetta.core.io.silent.SilentEnergy

Returns the SilentEnergy associated with this scorename.

C++: core::io::silent::SilentStruct::get_silent_energy(const std::string &) const –> const class core::io::silent::SilentEnergy &

get_string_value(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str) → str

Returns the energy associated with the given scorename if this

SilentStruct has an energy for that scorename. Otherwise returns 0.

C++: core::io::silent::SilentStruct::get_string_value(const std::string &) const –> const std::string &

has_comment(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str) → bool

C++: core::io::silent::SilentStruct::has_comment(const std::string &) const –> bool

has_energy(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str) → bool

returns true if this SilentStruct has an energy for the given

scorename, returns false otherwise.

C++: core::io::silent::SilentStruct::has_energy(const std::string &) const –> bool

has_parent_remark(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str) → bool

C++: core::io::silent::SilentStruct::has_parent_remark(const std::string &) const –> bool

init_from_lines(self: pyrosetta.rosetta.core.io.silent.RNA_SilentStruct, lines: pyrosetta.rosetta.utility.vector1_std_string, container: pyrosetta.rosetta.core.io.silent.SilentFileData) → bool

Tells this RNA_SilentStruct object to initialize itself from the given set of lines. Lines should

be of the format

C++: core::io::silent::RNA_SilentStruct::init_from_lines(const class utility::vector1<std::string, class std::allocator<std::string > > &, class core::io::silent::SilentFileData &) –> bool

jump(self: pyrosetta.rosetta.core.io.silent.RNA_SilentStruct, jump_num: int) → pyrosetta.rosetta.core.kinematics.Jump

C++: core::io::silent::RNA_SilentStruct::jump(const unsigned long &) const –> const class core::kinematics::Jump &

mainchain_torsion(self: pyrosetta.rosetta.core.io.silent.RNA_SilentStruct, seqpos: int, torsion_num: int) → float

C++: core::io::silent::RNA_SilentStruct::mainchain_torsion(const unsigned long &, const unsigned long &) const –> double

mainchain_torsions(self: pyrosetta.rosetta.core.io.silent.RNA_SilentStruct, seqpos: int) → pyrosetta.rosetta.utility.vector1_double

C++: core::io::silent::RNA_SilentStruct::mainchain_torsions(unsigned long) const –> class utility::vector1<double, class std::allocator<double> >

mem_footprint(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → int

C++: core::io::silent::SilentStruct::mem_footprint() const –> unsigned long

nonconst_other_struct_list(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_io_silent_SilentStruct_t

C++: core::io::silent::SilentStruct::nonconst_other_struct_list() –> class utility::vector1<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &

nres(*args, **kwargs)

Overloaded function.

1. nres(self: pyrosetta.rosetta.core.io.silent.SilentStruct) -> int

returns the number of residues contained by this

SilentStruct.

C++: core::io::silent::SilentStruct::nres() const –> unsigned long

2. nres(self: pyrosetta.rosetta.core.io.silent.SilentStruct, nres: int) -> None

returns the number of residues in this SilentStruct.

C++: core::io::silent::SilentStruct::nres(unsigned long) –> void

one_letter_sequence(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → str

strip […] comment from seqeunce_ and return pure

one-letter sequence

C++: core::io::silent::SilentStruct::one_letter_sequence() const –> std::string

options(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.core.io.silent.SilentFileOptions

C++: core::io::silent::SilentStruct::options() const –> const class core::io::silent::SilentFileOptions &

other_struct_list(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_io_silent_SilentStruct_t

C++: core::io::silent::SilentStruct::other_struct_list() const –> const class utility::vector1<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &

parse_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct, input: pyrosetta.rosetta.std.istream, energy_names: pyrosetta.rosetta.utility.vector1_std_string) → None

C++: core::io::silent::SilentStruct::parse_energies(std::istream &, const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

precision(*args, **kwargs)

Overloaded function.

1. precision(self: pyrosetta.rosetta.core.io.silent.SilentStruct, precision: int) -> None

C++: core::io::silent::SilentStruct::precision(unsigned long) –> void

2. precision(self: pyrosetta.rosetta.core.io.silent.SilentStruct) -> int

C++: core::io::silent::SilentStruct::precision() const –> unsigned long

print_comments(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None

print the comments in this SilentStruct.

C++: core::io::silent::SilentStruct::print_comments(std::ostream &) const –> void

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

Prints the conformation information within this RNA_SilentStruct to the given std::ostream.

C++: core::io::silent::RNA_SilentStruct::print_conformation(std::ostream &) const –> void

print_header(self: pyrosetta.rosetta.core.io.silent.RNA_SilentStruct, out: pyrosetta.rosetta.std.ostream) → None

print header information

C++: core::io::silent::RNA_SilentStruct::print_header(std::ostream &) const –> void

print_parent_remarks(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None

C++: core::io::silent::SilentStruct::print_parent_remarks(std::ostream &) const –> void

print_residue_numbers(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None

print the resnum in this SilentStruct, if filled.

C++: core::io::silent::SilentStruct::print_residue_numbers(std::ostream &) const –> void

print_score_header(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None

only print SCORE: header line

C++: core::io::silent::SilentStruct::print_score_header(std::ostream &) const –> void

print_scores(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None

print out a SCORE line to the given ozstream.

C++: core::io::silent::SilentStruct::print_scores(std::ostream &) const –> void

print_submotif_info(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None

print the submotif_info in this SilentStruct, if filled.

C++: core::io::silent::SilentStruct::print_submotif_info(std::ostream &) const –> void

read_score_headers(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line: str, enames: pyrosetta.rosetta.utility.vector1_std_string, container: core::io::silent::SilentFileData) → None

C++: core::io::silent::SilentStruct::read_score_headers(const std::string &, class utility::vector1<std::string, class std::allocator<std::string > > &, class core::io::silent::SilentFileData &) –> void

read_sequence(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line: str) → bool

C++: core::io::silent::SilentStruct::read_sequence(const std::string &) –> bool

rename_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

C++: core::io::silent::SilentStruct::rename_energies() –> void

residue_numbers_into_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: core::io::silent::SilentStruct::residue_numbers_into_pose(class core::pose::Pose &) const –> void

resize(self: pyrosetta.rosetta.core.io.silent.RNA_SilentStruct, nres_in: int) → None

Re-dimension the storage capacity of this RNA_SilentStruct to the given number of residues.

C++: core::io::silent::RNA_SilentStruct::resize(const unsigned long) –> void

scoreline_prefix(*args, **kwargs)

Overloaded function.

1. scoreline_prefix(self: pyrosetta.rosetta.core.io.silent.SilentStruct, prefix: str) -> None

C++: core::io::silent::SilentStruct::scoreline_prefix(const std::string &) –> void

2. scoreline_prefix(self: pyrosetta.rosetta.core.io.silent.SilentStruct) -> str

C++: core::io::silent::SilentStruct::scoreline_prefix() const –> std::string

secstruct(self: pyrosetta.rosetta.core.io.silent.RNA_SilentStruct, seqpos: int) → str

C++: core::io::silent::RNA_SilentStruct::secstruct(unsigned long) const –> char

sequence(*args, **kwargs)

Overloaded function.

1. sequence(self: pyrosetta.rosetta.core.io.silent.SilentStruct) -> pyrosetta.rosetta.core.sequence.AnnotatedSequence

returns the sequence associated with this SilentStruct.

C++: core::io::silent::SilentStruct::sequence() const –> const class core::sequence::AnnotatedSequence &

2. sequence(self: pyrosetta.rosetta.core.io.silent.SilentStruct, sequence: pyrosetta.rosetta.core.sequence.AnnotatedSequence) -> None

sets the sequence for this SilentStruct.

C++: core::io::silent::SilentStruct::sequence(const class core::sequence::AnnotatedSequence &) –> void

set_chains(self: pyrosetta.rosetta.core.io.silent.SilentStruct, chains: pyrosetta.rosetta.utility.vector1_char) → None

C++: core::io::silent::SilentStruct::set_chains(const class utility::vector1<char, class std::allocator<char> > &) –> void

set_chi_torsions(self: pyrosetta.rosetta.core.io.silent.RNA_SilentStruct, seqpos: int, torsions: pyrosetta.rosetta.utility.vector1_double) → None

C++: core::io::silent::RNA_SilentStruct::set_chi_torsions(const unsigned long &, class utility::vector1<double, class std::allocator<double> > &) –> void

set_coords(self: pyrosetta.rosetta.core.io.silent.RNA_SilentStruct, seqpos: int, coords: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

C++: core::io::silent::RNA_SilentStruct::set_coords(const unsigned long &, const class numeric::xyzVector<double> &) –> void

set_decoy_tag(self: pyrosetta.rosetta.core.io.silent.SilentStruct, tag: str) → None

set the tag associate with this SilentStruct

C++: core::io::silent::SilentStruct::set_decoy_tag(const std::string &) –> void

set_fold_tree(self: pyrosetta.rosetta.core.io.silent.RNA_SilentStruct, f: pyrosetta.rosetta.core.kinematics.FoldTree) → None

C++: core::io::silent::RNA_SilentStruct::set_fold_tree(const class core::kinematics::FoldTree &) –> void

set_force_bitflip(self: pyrosetta.rosetta.core.io.silent.SilentStruct, setting: bool) → None

Sets whether conversion from big-endian to little-endian (or the converse) should be forced

when a binary silent structure is initialized from lines.

C++: core::io::silent::SilentStruct::set_force_bitflip(const bool) –> void

set_full_model_parameters(self: pyrosetta.rosetta.core.io.silent.SilentStruct, setting: core::pose::full_model_info::FullModelParameters) → None

C++: core::io::silent::SilentStruct::set_full_model_parameters(class std::shared_ptr<const class core::pose::full_model_info::FullModelParameters>) –> void

set_mainchain_torsions(self: pyrosetta.rosetta.core.io.silent.RNA_SilentStruct, seqpos: int, torsions: pyrosetta.rosetta.utility.vector1_double) → None

C++: core::io::silent::RNA_SilentStruct::set_mainchain_torsions(const unsigned long &, class utility::vector1<double, class std::allocator<double> > &) –> void

set_non_main_chain_sugar_coords(self: pyrosetta.rosetta.core.io.silent.RNA_SilentStruct, seqpos: int, vecs: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t) → None

C++: core::io::silent::RNA_SilentStruct::set_non_main_chain_sugar_coords(const unsigned long &, const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) –> void

set_residue_numbers(self: pyrosetta.rosetta.core.io.silent.SilentStruct, residue_numbers: pyrosetta.rosetta.utility.vector1_int) → None

C++: core::io::silent::SilentStruct::set_residue_numbers(const class utility::vector1<int, class std::allocator<int> > &) –> void

set_secstruct(self: pyrosetta.rosetta.core.io.silent.RNA_SilentStruct, seqpos: int, ss: str) → None

C++: core::io::silent::RNA_SilentStruct::set_secstruct(const unsigned long &, const char &) –> void

set_segment_IDs(self: pyrosetta.rosetta.core.io.silent.SilentStruct, segids: pyrosetta.rosetta.utility.vector1_std_string) → None

C++: core::io::silent::SilentStruct::set_segment_IDs(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_tag_from_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

Sets the tag from the Pose DataCache.

C++: core::io::silent::SilentStruct::set_tag_from_pose(const class core::pose::Pose &) –> void

set_valid_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct, valid: pyrosetta.rosetta.utility.vector1_std_string) → None

C++: core::io::silent::SilentStruct::set_valid_energies(class utility::vector1<std::string, class std::allocator<std::string > >) –> void

silent_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct, new_se: pyrosetta.rosetta.utility.vector1_core_io_silent_SilentEnergy) → None

sets the silent_energies for this SilentStruct.

C++: core::io::silent::SilentStruct::silent_energies(const class utility::vector1<class core::io::silent::SilentEnergy, class std::allocator<class core::io::silent::SilentEnergy> > &) –> void

sort_silent_scores(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

sort all the silent energies by their name.

C++: core::io::silent::SilentStruct::sort_silent_scores() –> void

class pyrosetta.rosetta.core.io.silent.RNA_SilentStructCreator

Bases: SilentStructCreator

creator for the RNA_SilentStruct class

assign(self: pyrosetta.rosetta.core.io.silent.RNA_SilentStructCreator, : pyrosetta.rosetta.core.io.silent.RNA_SilentStructCreator) → pyrosetta.rosetta.core.io.silent.RNA_SilentStructCreator

C++: core::io::silent::RNA_SilentStructCreator::operator=(const class core::io::silent::RNA_SilentStructCreator &) –> class core::io::silent::RNA_SilentStructCreator &

create_silent_struct(self: pyrosetta.rosetta.core.io.silent.RNA_SilentStructCreator, : pyrosetta.rosetta.core.io.silent.SilentFileOptions) → pyrosetta.rosetta.core.io.silent.SilentStruct

C++: core::io::silent::RNA_SilentStructCreator::create_silent_struct(const class core::io::silent::SilentFileOptions &) const –> class std::shared_ptr<class core::io::silent::SilentStruct>

keyname(self: pyrosetta.rosetta.core.io.silent.RNA_SilentStructCreator) → str

C++: core::io::silent::RNA_SilentStructCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct

Bases: SilentStruct

add_comment(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str, value: str) → None

add a named comment to this SilentStruct object.

Similar to methods for playing with energies, but mapping is string => string rather than string => Real.

C++: core::io::silent::SilentStruct::add_comment(std::string, std::string) –> void

add_energy(*args, **kwargs)

Overloaded function.

1. add_energy(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str, value: float) -> None

2. add_energy(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str, value: float, weight: float) -> None

add a score of a given name and value to this SilentStruct.

Takes an optional weight that defaults to 1.0.

C++: core::io::silent::SilentStruct::add_energy(const std::string &, double, double) –> void

add_jump(self: pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct, jump: pyrosetta.rosetta.core.kinematics.Jump) → None

C++: core::io::silent::RigidBodySilentStruct::add_jump(const class core::kinematics::Jump &) –> void

add_other_struct(self: pyrosetta.rosetta.core.io.silent.SilentStruct, silent_struct: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

C++: core::io::silent::SilentStruct::add_other_struct(class std::shared_ptr<class core::io::silent::SilentStruct>) –> void

add_parent_remark(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str, value: str) → None

C++: core::io::silent::SilentStruct::add_parent_remark(const std::string &, const std::string &) –> void

add_rt(self: pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct, rt: pyrosetta.rosetta.core.kinematics.RT) → None

C++: core::io::silent::RigidBodySilentStruct::add_rt(const class core::kinematics::RT &) –> void

add_string_value(*args, **kwargs)

Overloaded function.

1. add_string_value(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str, value: str) -> None

2. add_string_value(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str, value: str, index: int) -> None

add a non-floating point score of a given name and value to this

SilentStruct.

C++: core::io::silent::SilentStruct::add_string_value(const std::string &, const std::string &, const int) –> void

add_submotif_info_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line_stream: pyrosetta.rosetta.std.istream) → None

C++: core::io::silent::SilentStruct::add_submotif_info_from_line(std::istream &) –> void

assign(self: pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct, src: pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct) → pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct

Test if this RigidBodySilentStruct is equal to the given

RigidBodySilentStruct in terms of conformation. Doesn’t check energies.

C++: core::io::silent::RigidBodySilentStruct::operator=(const class core::io::silent::RigidBodySilentStruct &) –> class core::io::silent::RigidBodySilentStruct &

clear_comments(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

C++: core::io::silent::SilentStruct::clear_comments() –> void

clear_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

Clear all of the energies in the SilentStruct. Doesn’t just

zero the energies, it entirely removes all knowledge of all energies from this SilentStruct.

C++: core::io::silent::SilentStruct::clear_energies() –> void

clone(self: pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct) → pyrosetta.rosetta.core.io.silent.SilentStruct

Returns a new RigidBodySilentStruct with a copy of the information

in this RigidBodySilentStruct.

C++: core::io::silent::RigidBodySilentStruct::clone() const –> class std::shared_ptr<class core::io::silent::SilentStruct>

comment_from_line(*args, **kwargs)

Overloaded function.

1. comment_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line: str) -> None

C++: core::io::silent::SilentStruct::comment_from_line(const std::string &) –> void

2. comment_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line: str, include_silentfile_comments: bool) -> None

Creates and adds a comment from an input REMARK line

Input comment line, of the format “REMARK key value [value]*”

If true, ‘REMARK XXX SILENTFILE’ lines will be added to comments.

C++: core::io::silent::SilentStruct::comment_from_line(const std::string &, const bool) –> void

copy_scores(self: pyrosetta.rosetta.core.io.silent.SilentStruct, src_ss: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

Copy the score information in the given SilentStruct into

this SilentStruct.

C++: core::io::silent::SilentStruct::copy_scores(const class core::io::silent::SilentStruct &) –> void

decoy_tag(*args, **kwargs)

Overloaded function.

1. decoy_tag(self: pyrosetta.rosetta.core.io.silent.SilentStruct) -> str

returns the tag associated with this SilentStruct.

C++: core::io::silent::SilentStruct::decoy_tag() const –> std::string

2. decoy_tag(self: pyrosetta.rosetta.core.io.silent.SilentStruct, tag: str) -> None

sets the tag associated with this SilentStruct.

C++: core::io::silent::SilentStruct::decoy_tag(const std::string &) –> void

energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.utility.vector1_core_io_silent_SilentEnergy

Returns the vector of SilentEnergy objects associated with

this SilentStruct object.

C++: core::io::silent::SilentStruct::energies() const –> class utility::vector1<class core::io::silent::SilentEnergy, class std::allocator<class core::io::silent::SilentEnergy> >

energies_from_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

Initialize this SilentStruct’s energies from the given Pose.

This sets energies, energy weights, and the output widths for the energies.

C++: core::io::silent::SilentStruct::energies_from_pose(const class core::pose::Pose &) –> void

energies_into_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

Put the energy information from this SilentStruct into the

pose. Energies that correspond to a ScoreType are put into the pose.energies().total_energies() EnergyMap, all other energies are put into the ARBITRARY_FLOAT_DATA map in the pose DataCache. Also sets the scorefxn_weights in the Energies object using the information from this SilentStruct.

C++: core::io::silent::SilentStruct::energies_into_pose(class core::pose::Pose &) const –> void

energy_names(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → core::io::silent::EnergyNames

Returns the EnergyNames that this SilentStruct contains.

C++: core::io::silent::SilentStruct::energy_names() const –> class core::io::silent::EnergyNames

erase_comment(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str) → None

C++: core::io::silent::SilentStruct::erase_comment(const std::string &) –> void

figure_out_residue_numbers_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line_stream: pyrosetta.rosetta.std.istream) → None

C++: core::io::silent::SilentStruct::figure_out_residue_numbers_from_line(std::istream &) –> void

figure_out_segment_ids_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line_stream: pyrosetta.rosetta.std.istream) → None

C++: core::io::silent::SilentStruct::figure_out_segment_ids_from_line(std::istream &) –> void

fill_other_struct_list(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: core::io::silent::SilentStruct::fill_other_struct_list(const class core::pose::Pose &) –> void

fill_pose(*args, **kwargs)

Overloaded function.

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

2. fill_pose(self: pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct, pose: pyrosetta.rosetta.core.pose.Pose, metapatches: bool) -> None

Configure the conformation of the given Pose with the

conformational data within this RigidBodySilentStruct. sets the jump stored in the RigidBodySilentStruct

C++: core::io::silent::RigidBodySilentStruct::fill_pose(class core::pose::Pose &, const bool) const –> void

3. fill_pose(self: pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct, pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) -> None

4. fill_pose(self: pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct, pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, metapatches: bool) -> None

Configure the conformation of the given Pose with the

conformational data within this RigidBodySilentStruct.

C++: core::io::silent::RigidBodySilentStruct::fill_pose(class core::pose::Pose &, const class core::chemical::ResidueTypeSet &, const bool) const –> void

fill_struct(*args, **kwargs)

Overloaded function.

1. fill_struct(self: pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) -> None

2. fill_struct(self: pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct, pose: pyrosetta.rosetta.core.pose.Pose, tag: str) -> None

opposite of fill_pose

C++: core::io::silent::RigidBodySilentStruct::fill_struct(const class core::pose::Pose &, const std::string &) –> void

fill_struct_with_residue_numbers(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: core::io::silent::SilentStruct::fill_struct_with_residue_numbers(const class core::pose::Pose &) –> void

fill_struct_with_submotif_info_list(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: core::io::silent::SilentStruct::fill_struct_with_submotif_info_list(const class core::pose::Pose &) –> void

finish_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

calls optH if command line requests optH.

must be called by derived classes.

C++: core::io::silent::SilentStruct::finish_pose(class core::pose::Pose &) const –> void

fold_tree(*args, **kwargs)

Overloaded function.

1. fold_tree(self: pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct, : pyrosetta.rosetta.core.kinematics.FoldTree) -> None

C++: core::io::silent::RigidBodySilentStruct::fold_tree(const class core::kinematics::FoldTree &) –> void

2. fold_tree(self: pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct) -> pyrosetta.rosetta.core.kinematics.FoldTree

C++: core::io::silent::RigidBodySilentStruct::fold_tree() const –> const class core::kinematics::FoldTree &

force_bitflip(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → bool

Gets whether conversion from big-endian to little-endian (or the converse) should be forced

when a binary silent structure is initialized from lines.

C++: core::io::silent::SilentStruct::force_bitflip() const –> bool

full_model_info_into_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: core::io::silent::SilentStruct::full_model_info_into_pose(class core::pose::Pose &) const –> void

full_model_parameters(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → core::pose::full_model_info::FullModelParameters

C++: core::io::silent::SilentStruct::full_model_parameters() const –> class std::shared_ptr<const class core::pose::full_model_info::FullModelParameters>

get_CA_xyz(self: pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct) → pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t

C++: core::io::silent::RigidBodySilentStruct::get_CA_xyz() const –> class ObjexxFCL::FArray2D<double>

get_all_comments(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.std.map_std_string_std_string

C++: core::io::silent::SilentStruct::get_all_comments() const –> class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > >

get_comment(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str) → str

C++: core::io::silent::SilentStruct::get_comment(const std::string &) const –> std::string

get_debug_rmsd(self: pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct) → float

calculates the RMSD between the C-alpha atoms of a Pose built from

the torsions in this RigidBodySilentStruct and the C-alpha atoms from this RigidBodySilentStruct.

C++: core::io::silent::RigidBodySilentStruct::get_debug_rmsd() –> double

get_energy(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str) → float

Returns the energy associated with the given scorename if this

SilentStruct has an energy for that scorename. Otherwise returns 0.

C++: core::io::silent::SilentStruct::get_energy(const std::string &) const –> double

get_parent_remark(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str) → str

C++: core::io::silent::SilentStruct::get_parent_remark(const std::string &) const –> std::string

get_parent_remark_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line: str) → None

C++: core::io::silent::SilentStruct::get_parent_remark_from_line(const std::string &) –> void

get_self_ptr(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.core.io.silent.SilentStruct

C++: core::io::silent::SilentStruct::get_self_ptr() –> class std::shared_ptr<class core::io::silent::SilentStruct>

get_silent_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.utility.vector1_core_io_silent_SilentEnergy

C++: core::io::silent::SilentStruct::get_silent_energies() –> class utility::vector1<class core::io::silent::SilentEnergy, class std::allocator<class core::io::silent::SilentEnergy> >

get_silent_energy(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str) → pyrosetta.rosetta.core.io.silent.SilentEnergy

Returns the SilentEnergy associated with this scorename.

C++: core::io::silent::SilentStruct::get_silent_energy(const std::string &) const –> const class core::io::silent::SilentEnergy &

get_string_value(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str) → str

Returns the energy associated with the given scorename if this

SilentStruct has an energy for that scorename. Otherwise returns 0.

C++: core::io::silent::SilentStruct::get_string_value(const std::string &) const –> const std::string &

has_comment(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str) → bool

C++: core::io::silent::SilentStruct::has_comment(const std::string &) const –> bool

has_energy(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str) → bool

returns true if this SilentStruct has an energy for the given

scorename, returns false otherwise.

C++: core::io::silent::SilentStruct::has_energy(const std::string &) const –> bool

has_parent_remark(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str) → bool

C++: core::io::silent::SilentStruct::has_parent_remark(const std::string &) const –> bool

init_from_lines(self: pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct, lines: pyrosetta.rosetta.utility.vector1_std_string, container: pyrosetta.rosetta.core.io.silent.SilentFileData) → bool

Tells this RigidBodySilentStruct object to initialize itself from

C++: core::io::silent::RigidBodySilentStruct::init_from_lines(const class utility::vector1<std::string, class std::allocator<std::string > > &, class core::io::silent::SilentFileData &) –> bool

is_symmetric(self: pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct) → bool

C++: core::io::silent::RigidBodySilentStruct::is_symmetric() const –> bool

jump(self: pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct, jump_num: int) → pyrosetta.rosetta.core.kinematics.RT

C++: core::io::silent::RigidBodySilentStruct::jump(const unsigned long) const –> const class core::kinematics::RT &

mem_footprint(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → int

C++: core::io::silent::SilentStruct::mem_footprint() const –> unsigned long

njumps(self: pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct) → int

returns the number of jumps held in this container.

C++: core::io::silent::RigidBodySilentStruct::njumps() const –> unsigned long

nonconst_other_struct_list(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_io_silent_SilentStruct_t

C++: core::io::silent::SilentStruct::nonconst_other_struct_list() –> class utility::vector1<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &

nres(*args, **kwargs)

Overloaded function.

1. nres(self: pyrosetta.rosetta.core.io.silent.SilentStruct) -> int

returns the number of residues contained by this

SilentStruct.

C++: core::io::silent::SilentStruct::nres() const –> unsigned long

2. nres(self: pyrosetta.rosetta.core.io.silent.SilentStruct, nres: int) -> None

returns the number of residues in this SilentStruct.

C++: core::io::silent::SilentStruct::nres(unsigned long) –> void

one_letter_sequence(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → str

strip […] comment from seqeunce_ and return pure

one-letter sequence

C++: core::io::silent::SilentStruct::one_letter_sequence() const –> std::string

options(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.core.io.silent.SilentFileOptions

C++: core::io::silent::SilentStruct::options() const –> const class core::io::silent::SilentFileOptions &

other_struct_list(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_io_silent_SilentStruct_t

C++: core::io::silent::SilentStruct::other_struct_list() const –> const class utility::vector1<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &

parse_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct, input: pyrosetta.rosetta.std.istream, energy_names: pyrosetta.rosetta.utility.vector1_std_string) → None

C++: core::io::silent::SilentStruct::parse_energies(std::istream &, const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

precision(*args, **kwargs)

Overloaded function.

1. precision(self: pyrosetta.rosetta.core.io.silent.SilentStruct, precision: int) -> None

C++: core::io::silent::SilentStruct::precision(unsigned long) –> void

2. precision(self: pyrosetta.rosetta.core.io.silent.SilentStruct) -> int

C++: core::io::silent::SilentStruct::precision() const –> unsigned long

print_comments(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None

print the comments in this SilentStruct.

C++: core::io::silent::SilentStruct::print_comments(std::ostream &) const –> void

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

Prints the conformation information within this

C++: core::io::silent::RigidBodySilentStruct::print_conformation(std::ostream &) const –> void

print_header(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → 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::silent::SilentStruct::print_header(std::ostream &) const –> void

print_parent_remarks(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None

C++: core::io::silent::SilentStruct::print_parent_remarks(std::ostream &) const –> void

print_residue_numbers(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None

print the resnum in this SilentStruct, if filled.

C++: core::io::silent::SilentStruct::print_residue_numbers(std::ostream &) const –> void

print_score_header(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None

only print SCORE: header line

C++: core::io::silent::SilentStruct::print_score_header(std::ostream &) const –> void

print_scores(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None

print out a SCORE line to the given ozstream.

C++: core::io::silent::SilentStruct::print_scores(std::ostream &) const –> void

print_submotif_info(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None

print the submotif_info in this SilentStruct, if filled.

C++: core::io::silent::SilentStruct::print_submotif_info(std::ostream &) const –> void

read_score_headers(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line: str, enames: pyrosetta.rosetta.utility.vector1_std_string, container: core::io::silent::SilentFileData) → None

C++: core::io::silent::SilentStruct::read_score_headers(const std::string &, class utility::vector1<std::string, class std::allocator<std::string > > &, class core::io::silent::SilentFileData &) –> void

read_sequence(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line: str) → bool

C++: core::io::silent::SilentStruct::read_sequence(const std::string &) –> bool

rename_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

C++: core::io::silent::SilentStruct::rename_energies() –> void

residue_numbers_into_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: core::io::silent::SilentStruct::residue_numbers_into_pose(class core::pose::Pose &) const –> void

scoreline_prefix(*args, **kwargs)

Overloaded function.

1. scoreline_prefix(self: pyrosetta.rosetta.core.io.silent.SilentStruct, prefix: str) -> None

C++: core::io::silent::SilentStruct::scoreline_prefix(const std::string &) –> void

2. scoreline_prefix(self: pyrosetta.rosetta.core.io.silent.SilentStruct) -> str

C++: core::io::silent::SilentStruct::scoreline_prefix() const –> std::string

sequence(*args, **kwargs)

Overloaded function.

1. sequence(self: pyrosetta.rosetta.core.io.silent.SilentStruct) -> pyrosetta.rosetta.core.sequence.AnnotatedSequence

returns the sequence associated with this SilentStruct.

C++: core::io::silent::SilentStruct::sequence() const –> const class core::sequence::AnnotatedSequence &

2. sequence(self: pyrosetta.rosetta.core.io.silent.SilentStruct, sequence: pyrosetta.rosetta.core.sequence.AnnotatedSequence) -> None

sets the sequence for this SilentStruct.

C++: core::io::silent::SilentStruct::sequence(const class core::sequence::AnnotatedSequence &) –> void

set_chains(self: pyrosetta.rosetta.core.io.silent.SilentStruct, chains: pyrosetta.rosetta.utility.vector1_char) → None

C++: core::io::silent::SilentStruct::set_chains(const class utility::vector1<char, class std::allocator<char> > &) –> void

set_decoy_tag(self: pyrosetta.rosetta.core.io.silent.SilentStruct, tag: str) → None

set the tag associate with this SilentStruct

C++: core::io::silent::SilentStruct::set_decoy_tag(const std::string &) –> void

set_force_bitflip(self: pyrosetta.rosetta.core.io.silent.SilentStruct, setting: bool) → None

Sets whether conversion from big-endian to little-endian (or the converse) should be forced

when a binary silent structure is initialized from lines.

C++: core::io::silent::SilentStruct::set_force_bitflip(const bool) –> void

set_full_model_parameters(self: pyrosetta.rosetta.core.io.silent.SilentStruct, setting: core::pose::full_model_info::FullModelParameters) → None

C++: core::io::silent::SilentStruct::set_full_model_parameters(class std::shared_ptr<const class core::pose::full_model_info::FullModelParameters>) –> void

set_residue_numbers(self: pyrosetta.rosetta.core.io.silent.SilentStruct, residue_numbers: pyrosetta.rosetta.utility.vector1_int) → None

C++: core::io::silent::SilentStruct::set_residue_numbers(const class utility::vector1<int, class std::allocator<int> > &) –> void

set_segment_IDs(self: pyrosetta.rosetta.core.io.silent.SilentStruct, segids: pyrosetta.rosetta.utility.vector1_std_string) → None

C++: core::io::silent::SilentStruct::set_segment_IDs(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_tag_from_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

Sets the tag from the Pose DataCache.

C++: core::io::silent::SilentStruct::set_tag_from_pose(const class core::pose::Pose &) –> void

set_valid_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct, valid: pyrosetta.rosetta.utility.vector1_std_string) → None

C++: core::io::silent::SilentStruct::set_valid_energies(class utility::vector1<std::string, class std::allocator<std::string > >) –> void

silent_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct, new_se: pyrosetta.rosetta.utility.vector1_core_io_silent_SilentEnergy) → None

sets the silent_energies for this SilentStruct.

C++: core::io::silent::SilentStruct::silent_energies(const class utility::vector1<class core::io::silent::SilentEnergy, class std::allocator<class core::io::silent::SilentEnergy> > &) –> void

sort_silent_scores(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

sort all the silent energies by their name.

C++: core::io::silent::SilentStruct::sort_silent_scores() –> void

symmetry_info(*args, **kwargs)

Overloaded function.

1. symmetry_info(self: pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct, s: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) -> None

C++: core::io::silent::RigidBodySilentStruct::symmetry_info(class core::conformation::symmetry::SymmetryInfo &) –> void

2. symmetry_info(self: pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct) -> pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo

C++: core::io::silent::RigidBodySilentStruct::symmetry_info() const –> class std::shared_ptr<const class core::conformation::symmetry::SymmetryInfo>

class pyrosetta.rosetta.core.io.silent.RigidBodySilentStructCreator

Bases: SilentStructCreator

creator for the RigidBodySilentStruct class

assign(self: pyrosetta.rosetta.core.io.silent.RigidBodySilentStructCreator, : pyrosetta.rosetta.core.io.silent.RigidBodySilentStructCreator) → pyrosetta.rosetta.core.io.silent.RigidBodySilentStructCreator

C++: core::io::silent::RigidBodySilentStructCreator::operator=(const class core::io::silent::RigidBodySilentStructCreator &) –> class core::io::silent::RigidBodySilentStructCreator &

create_silent_struct(self: pyrosetta.rosetta.core.io.silent.RigidBodySilentStructCreator, : pyrosetta.rosetta.core.io.silent.SilentFileOptions) → pyrosetta.rosetta.core.io.silent.SilentStruct

C++: core::io::silent::RigidBodySilentStructCreator::create_silent_struct(const class core::io::silent::SilentFileOptions &) const –> class std::shared_ptr<class core::io::silent::SilentStruct>

keyname(self: pyrosetta.rosetta.core.io.silent.RigidBodySilentStructCreator) → str

C++: core::io::silent::RigidBodySilentStructCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct

Bases: SilentStruct

add_comment(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str, value: str) → None

add a named comment to this SilentStruct object.

Similar to methods for playing with energies, but mapping is string => string rather than string => Real.

C++: core::io::silent::SilentStruct::add_comment(std::string, std::string) –> void

add_energy(*args, **kwargs)

Overloaded function.

1. add_energy(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str, value: float) -> None

2. add_energy(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str, value: float, weight: float) -> None

add a score of a given name and value to this SilentStruct.

Takes an optional weight that defaults to 1.0.

C++: core::io::silent::SilentStruct::add_energy(const std::string &, double, double) –> void

add_other_struct(self: pyrosetta.rosetta.core.io.silent.SilentStruct, silent_struct: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

C++: core::io::silent::SilentStruct::add_other_struct(class std::shared_ptr<class core::io::silent::SilentStruct>) –> void

add_parent_remark(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str, value: str) → None

C++: core::io::silent::SilentStruct::add_parent_remark(const std::string &, const std::string &) –> void

add_string_value(*args, **kwargs)

Overloaded function.

1. add_string_value(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str, value: str) -> None

2. add_string_value(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str, value: str, index: int) -> None

add a non-floating point score of a given name and value to this

SilentStruct.

C++: core::io::silent::SilentStruct::add_string_value(const std::string &, const std::string &, const int) –> void

add_submotif_info_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line_stream: pyrosetta.rosetta.std.istream) → None

C++: core::io::silent::SilentStruct::add_submotif_info_from_line(std::istream &) –> void

assign(self: pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct, src: pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct) → pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct

Test if this ScoreFileSilentStruct is equal to the given ScoreFileSilentStruct in

terms of conformation. Doesn’t check energies.

C++: core::io::silent::ScoreFileSilentStruct::operator=(const class core::io::silent::ScoreFileSilentStruct &) –> class core::io::silent::ScoreFileSilentStruct &

clear_comments(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

C++: core::io::silent::SilentStruct::clear_comments() –> void

clear_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

Clear all of the energies in the SilentStruct. Doesn’t just

zero the energies, it entirely removes all knowledge of all energies from this SilentStruct.

C++: core::io::silent::SilentStruct::clear_energies() –> void

clone(self: pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct) → pyrosetta.rosetta.core.io.silent.SilentStruct

C++: core::io::silent::ScoreFileSilentStruct::clone() const –> class std::shared_ptr<class core::io::silent::SilentStruct>

comment_from_line(*args, **kwargs)

Overloaded function.

1. comment_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line: str) -> None

C++: core::io::silent::SilentStruct::comment_from_line(const std::string &) –> void

2. comment_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line: str, include_silentfile_comments: bool) -> None

Creates and adds a comment from an input REMARK line

Input comment line, of the format “REMARK key value [value]*”

If true, ‘REMARK XXX SILENTFILE’ lines will be added to comments.

C++: core::io::silent::SilentStruct::comment_from_line(const std::string &, const bool) –> void

copy_scores(self: pyrosetta.rosetta.core.io.silent.SilentStruct, src_ss: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

Copy the score information in the given SilentStruct into

this SilentStruct.

C++: core::io::silent::SilentStruct::copy_scores(const class core::io::silent::SilentStruct &) –> void

decoy_tag(*args, **kwargs)

Overloaded function.

1. decoy_tag(self: pyrosetta.rosetta.core.io.silent.SilentStruct) -> str

returns the tag associated with this SilentStruct.

C++: core::io::silent::SilentStruct::decoy_tag() const –> std::string

2. decoy_tag(self: pyrosetta.rosetta.core.io.silent.SilentStruct, tag: str) -> None

sets the tag associated with this SilentStruct.

C++: core::io::silent::SilentStruct::decoy_tag(const std::string &) –> void

energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.utility.vector1_core_io_silent_SilentEnergy

Returns the vector of SilentEnergy objects associated with

this SilentStruct object.

C++: core::io::silent::SilentStruct::energies() const –> class utility::vector1<class core::io::silent::SilentEnergy, class std::allocator<class core::io::silent::SilentEnergy> >

energies_from_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

Initialize this SilentStruct’s energies from the given Pose.

This sets energies, energy weights, and the output widths for the energies.

C++: core::io::silent::SilentStruct::energies_from_pose(const class core::pose::Pose &) –> void

energies_into_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

Put the energy information from this SilentStruct into the

pose. Energies that correspond to a ScoreType are put into the pose.energies().total_energies() EnergyMap, all other energies are put into the ARBITRARY_FLOAT_DATA map in the pose DataCache. Also sets the scorefxn_weights in the Energies object using the information from this SilentStruct.

C++: core::io::silent::SilentStruct::energies_into_pose(class core::pose::Pose &) const –> void

energy_names(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → core::io::silent::EnergyNames

Returns the EnergyNames that this SilentStruct contains.

C++: core::io::silent::SilentStruct::energy_names() const –> class core::io::silent::EnergyNames

erase_comment(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str) → None

C++: core::io::silent::SilentStruct::erase_comment(const std::string &) –> void

figure_out_residue_numbers_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line_stream: pyrosetta.rosetta.std.istream) → None

C++: core::io::silent::SilentStruct::figure_out_residue_numbers_from_line(std::istream &) –> void

figure_out_segment_ids_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line_stream: pyrosetta.rosetta.std.istream) → None

C++: core::io::silent::SilentStruct::figure_out_segment_ids_from_line(std::istream &) –> void

fill_other_struct_list(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: core::io::silent::SilentStruct::fill_other_struct_list(const class core::pose::Pose &) –> void

fill_pose(*args, **kwargs)

Overloaded function.

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

2. fill_pose(self: pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct, pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, metapatches: bool) -> None

Configure the conformation of the given Pose with the

conformational data within this ScoreFileSilentStruct. Calls pose.clear() and rebuilds Pose from scratch using the / user-specified residue types.

C++: core::io::silent::ScoreFileSilentStruct::fill_pose(class core::pose::Pose &, const class core::chemical::ResidueTypeSet &, const bool) const –> void

fill_struct(self: pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct, pose: pyrosetta.rosetta.core.pose.Pose, tag: str) → None

opposite of fill_pose

C++: core::io::silent::ScoreFileSilentStruct::fill_struct(const class core::pose::Pose &, const std::string &) –> void

fill_struct_with_residue_numbers(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: core::io::silent::SilentStruct::fill_struct_with_residue_numbers(const class core::pose::Pose &) –> void

fill_struct_with_submotif_info_list(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: core::io::silent::SilentStruct::fill_struct_with_submotif_info_list(const class core::pose::Pose &) –> void

finish_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

calls optH if command line requests optH.

must be called by derived classes.

C++: core::io::silent::SilentStruct::finish_pose(class core::pose::Pose &) const –> void

force_bitflip(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → bool

Gets whether conversion from big-endian to little-endian (or the converse) should be forced

when a binary silent structure is initialized from lines.

C++: core::io::silent::SilentStruct::force_bitflip() const –> bool

full_model_info_into_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: core::io::silent::SilentStruct::full_model_info_into_pose(class core::pose::Pose &) const –> void

full_model_parameters(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → core::pose::full_model_info::FullModelParameters

C++: core::io::silent::SilentStruct::full_model_parameters() const –> class std::shared_ptr<const class core::pose::full_model_info::FullModelParameters>

get_CA_xyz(self: pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct) → pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t

returns the positions of the CA atoms in this ScoreFileSilentStruct.

Useful for RMS calculations.

C++: core::io::silent::ScoreFileSilentStruct::get_CA_xyz() const –> class ObjexxFCL::FArray2D<double>

get_all_comments(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.std.map_std_string_std_string

C++: core::io::silent::SilentStruct::get_all_comments() const –> class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > >

get_comment(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str) → str

C++: core::io::silent::SilentStruct::get_comment(const std::string &) const –> std::string

get_debug_rmsd(self: pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct) → float

calculates the RMSD between the C-alpha atoms of a Pose built from the torsions in this

ScoreFileSilentStruct and the C-alpha atoms from this ScoreFileSilentStruct.

C++: core::io::silent::ScoreFileSilentStruct::get_debug_rmsd() –> double

get_energy(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str) → float

Returns the energy associated with the given scorename if this

SilentStruct has an energy for that scorename. Otherwise returns 0.

C++: core::io::silent::SilentStruct::get_energy(const std::string &) const –> double

get_parent_remark(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str) → str

C++: core::io::silent::SilentStruct::get_parent_remark(const std::string &) const –> std::string

get_parent_remark_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line: str) → None

C++: core::io::silent::SilentStruct::get_parent_remark_from_line(const std::string &) –> void

get_self_ptr(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.core.io.silent.SilentStruct

C++: core::io::silent::SilentStruct::get_self_ptr() –> class std::shared_ptr<class core::io::silent::SilentStruct>

get_silent_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.utility.vector1_core_io_silent_SilentEnergy

C++: core::io::silent::SilentStruct::get_silent_energies() –> class utility::vector1<class core::io::silent::SilentEnergy, class std::allocator<class core::io::silent::SilentEnergy> >

get_silent_energy(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str) → pyrosetta.rosetta.core.io.silent.SilentEnergy

Returns the SilentEnergy associated with this scorename.

C++: core::io::silent::SilentStruct::get_silent_energy(const std::string &) const –> const class core::io::silent::SilentEnergy &

get_string_value(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str) → str

Returns the energy associated with the given scorename if this

SilentStruct has an energy for that scorename. Otherwise returns 0.

C++: core::io::silent::SilentStruct::get_string_value(const std::string &) const –> const std::string &

has_comment(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str) → bool

C++: core::io::silent::SilentStruct::has_comment(const std::string &) const –> bool

has_energy(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str) → bool

returns true if this SilentStruct has an energy for the given

scorename, returns false otherwise.

C++: core::io::silent::SilentStruct::has_energy(const std::string &) const –> bool

has_parent_remark(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str) → bool

C++: core::io::silent::SilentStruct::has_parent_remark(const std::string &) const –> bool

init_from_lines(self: pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct, lines: pyrosetta.rosetta.utility.vector1_std_string, container: pyrosetta.rosetta.core.io.silent.SilentFileData) → bool

Tells this ScoreFileSilentStruct object to initialize itself from the given set of lines.

Only initializes energies.

C++: core::io::silent::ScoreFileSilentStruct::init_from_lines(const class utility::vector1<std::string, class std::allocator<std::string > > &, class core::io::silent::SilentFileData &) –> bool

mem_footprint(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → int

C++: core::io::silent::SilentStruct::mem_footprint() const –> unsigned long

nonconst_other_struct_list(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_io_silent_SilentStruct_t

C++: core::io::silent::SilentStruct::nonconst_other_struct_list() –> class utility::vector1<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &

nres(*args, **kwargs)

Overloaded function.

1. nres(self: pyrosetta.rosetta.core.io.silent.SilentStruct) -> int

returns the number of residues contained by this

SilentStruct.

C++: core::io::silent::SilentStruct::nres() const –> unsigned long

2. nres(self: pyrosetta.rosetta.core.io.silent.SilentStruct, nres: int) -> None

returns the number of residues in this SilentStruct.

C++: core::io::silent::SilentStruct::nres(unsigned long) –> void

one_letter_sequence(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → str

strip […] comment from seqeunce_ and return pure

one-letter sequence

C++: core::io::silent::SilentStruct::one_letter_sequence() const –> std::string

options(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.core.io.silent.SilentFileOptions

C++: core::io::silent::SilentStruct::options() const –> const class core::io::silent::SilentFileOptions &

other_struct_list(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_io_silent_SilentStruct_t

C++: core::io::silent::SilentStruct::other_struct_list() const –> const class utility::vector1<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &

parse_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct, input: pyrosetta.rosetta.std.istream, energy_names: pyrosetta.rosetta.utility.vector1_std_string) → None

C++: core::io::silent::SilentStruct::parse_energies(std::istream &, const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

precision(*args, **kwargs)

Overloaded function.

1. precision(self: pyrosetta.rosetta.core.io.silent.SilentStruct, precision: int) -> None

C++: core::io::silent::SilentStruct::precision(unsigned long) –> void

2. precision(self: pyrosetta.rosetta.core.io.silent.SilentStruct) -> int

C++: core::io::silent::SilentStruct::precision() const –> unsigned long

print_comments(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None

print the comments in this SilentStruct.

C++: core::io::silent::SilentStruct::print_comments(std::ostream &) const –> void

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

Prints the conformation information within this ScoreFileSilentStruct

to the given std::ostream.

C++: core::io::silent::ScoreFileSilentStruct::print_conformation(std::ostream &) const –> void

print_header(self: pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct, out: pyrosetta.rosetta.std.ostream) → None

Prints the header information within this ScoreFileSilentStruct

to the given std::ostream.

C++: core::io::silent::ScoreFileSilentStruct::print_header(std::ostream &) const –> void

print_parent_remarks(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None

C++: core::io::silent::SilentStruct::print_parent_remarks(std::ostream &) const –> void

print_residue_numbers(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None

print the resnum in this SilentStruct, if filled.

C++: core::io::silent::SilentStruct::print_residue_numbers(std::ostream &) const –> void

print_score_header(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None

only print SCORE: header line

C++: core::io::silent::SilentStruct::print_score_header(std::ostream &) const –> void

print_scores(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None

print out a SCORE line to the given ozstream.

C++: core::io::silent::SilentStruct::print_scores(std::ostream &) const –> void

print_submotif_info(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None

print the submotif_info in this SilentStruct, if filled.

C++: core::io::silent::SilentStruct::print_submotif_info(std::ostream &) const –> void

read_score_headers(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line: str, enames: pyrosetta.rosetta.utility.vector1_std_string, container: core::io::silent::SilentFileData) → None

C++: core::io::silent::SilentStruct::read_score_headers(const std::string &, class utility::vector1<std::string, class std::allocator<std::string > > &, class core::io::silent::SilentFileData &) –> void

read_sequence(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line: str) → bool

C++: core::io::silent::SilentStruct::read_sequence(const std::string &) –> bool

rename_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

C++: core::io::silent::SilentStruct::rename_energies() –> void

residue_numbers_into_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: core::io::silent::SilentStruct::residue_numbers_into_pose(class core::pose::Pose &) const –> void

scoreline_prefix(*args, **kwargs)

Overloaded function.

1. scoreline_prefix(self: pyrosetta.rosetta.core.io.silent.SilentStruct, prefix: str) -> None

C++: core::io::silent::SilentStruct::scoreline_prefix(const std::string &) –> void

2. scoreline_prefix(self: pyrosetta.rosetta.core.io.silent.SilentStruct) -> str

C++: core::io::silent::SilentStruct::scoreline_prefix() const –> std::string

sequence(*args, **kwargs)

Overloaded function.

1. sequence(self: pyrosetta.rosetta.core.io.silent.SilentStruct) -> pyrosetta.rosetta.core.sequence.AnnotatedSequence

returns the sequence associated with this SilentStruct.

C++: core::io::silent::SilentStruct::sequence() const –> const class core::sequence::AnnotatedSequence &

2. sequence(self: pyrosetta.rosetta.core.io.silent.SilentStruct, sequence: pyrosetta.rosetta.core.sequence.AnnotatedSequence) -> None

sets the sequence for this SilentStruct.

C++: core::io::silent::SilentStruct::sequence(const class core::sequence::AnnotatedSequence &) –> void

set_chains(self: pyrosetta.rosetta.core.io.silent.SilentStruct, chains: pyrosetta.rosetta.utility.vector1_char) → None

C++: core::io::silent::SilentStruct::set_chains(const class utility::vector1<char, class std::allocator<char> > &) –> void

set_decoy_tag(self: pyrosetta.rosetta.core.io.silent.SilentStruct, tag: str) → None

set the tag associate with this SilentStruct

C++: core::io::silent::SilentStruct::set_decoy_tag(const std::string &) –> void

set_force_bitflip(self: pyrosetta.rosetta.core.io.silent.SilentStruct, setting: bool) → None

Sets whether conversion from big-endian to little-endian (or the converse) should be forced

when a binary silent structure is initialized from lines.

C++: core::io::silent::SilentStruct::set_force_bitflip(const bool) –> void

set_full_model_parameters(self: pyrosetta.rosetta.core.io.silent.SilentStruct, setting: core::pose::full_model_info::FullModelParameters) → None

C++: core::io::silent::SilentStruct::set_full_model_parameters(class std::shared_ptr<const class core::pose::full_model_info::FullModelParameters>) –> void

set_residue_numbers(self: pyrosetta.rosetta.core.io.silent.SilentStruct, residue_numbers: pyrosetta.rosetta.utility.vector1_int) → None

C++: core::io::silent::SilentStruct::set_residue_numbers(const class utility::vector1<int, class std::allocator<int> > &) –> void

set_segment_IDs(self: pyrosetta.rosetta.core.io.silent.SilentStruct, segids: pyrosetta.rosetta.utility.vector1_std_string) → None

C++: core::io::silent::SilentStruct::set_segment_IDs(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_tag_from_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

Sets the tag from the Pose DataCache.

C++: core::io::silent::SilentStruct::set_tag_from_pose(const class core::pose::Pose &) –> void

set_valid_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct, valid: pyrosetta.rosetta.utility.vector1_std_string) → None

C++: core::io::silent::SilentStruct::set_valid_energies(class utility::vector1<std::string, class std::allocator<std::string > >) –> void

silent_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct, new_se: pyrosetta.rosetta.utility.vector1_core_io_silent_SilentEnergy) → None

sets the silent_energies for this SilentStruct.

C++: core::io::silent::SilentStruct::silent_energies(const class utility::vector1<class core::io::silent::SilentEnergy, class std::allocator<class core::io::silent::SilentEnergy> > &) –> void

sort_silent_scores(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

sort all the silent energies by their name.

C++: core::io::silent::SilentStruct::sort_silent_scores() –> void

class pyrosetta.rosetta.core.io.silent.ScoreFileSilentStructCreator

Bases: SilentStructCreator

creator for the ScoreFileSilentStruct class

assign(self: pyrosetta.rosetta.core.io.silent.ScoreFileSilentStructCreator, : pyrosetta.rosetta.core.io.silent.ScoreFileSilentStructCreator) → pyrosetta.rosetta.core.io.silent.ScoreFileSilentStructCreator

C++: core::io::silent::ScoreFileSilentStructCreator::operator=(const class core::io::silent::ScoreFileSilentStructCreator &) –> class core::io::silent::ScoreFileSilentStructCreator &

create_silent_struct(self: pyrosetta.rosetta.core.io.silent.ScoreFileSilentStructCreator, : pyrosetta.rosetta.core.io.silent.SilentFileOptions) → pyrosetta.rosetta.core.io.silent.SilentStruct

C++: core::io::silent::ScoreFileSilentStructCreator::create_silent_struct(const class core::io::silent::SilentFileOptions &) const –> class std::shared_ptr<class core::io::silent::SilentStruct>

keyname(self: pyrosetta.rosetta.core.io.silent.ScoreFileSilentStructCreator) → str

C++: core::io::silent::ScoreFileSilentStructCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct

Bases: SilentStruct

add_comment(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str, value: str) → None

add a named comment to this SilentStruct object.

Similar to methods for playing with energies, but mapping is string => string rather than string => Real.

C++: core::io::silent::SilentStruct::add_comment(std::string, std::string) –> void

add_energy(*args, **kwargs)

Overloaded function.

1. add_energy(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str, value: float) -> None

2. add_energy(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str, value: float, weight: float) -> None

add a score of a given name and value to this SilentStruct.

Takes an optional weight that defaults to 1.0.

C++: core::io::silent::SilentStruct::add_energy(const std::string &, double, double) –> void

add_jump(self: pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct, jump: pyrosetta.rosetta.core.kinematics.Jump) → None

C++: core::io::silent::ScoreJumpFileSilentStruct::add_jump(class core::kinematics::Jump) –> void

add_other_struct(self: pyrosetta.rosetta.core.io.silent.SilentStruct, silent_struct: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

C++: core::io::silent::SilentStruct::add_other_struct(class std::shared_ptr<class core::io::silent::SilentStruct>) –> void

add_parent_remark(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str, value: str) → None

C++: core::io::silent::SilentStruct::add_parent_remark(const std::string &, const std::string &) –> void

add_string_value(*args, **kwargs)

Overloaded function.

1. add_string_value(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str, value: str) -> None

2. add_string_value(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str, value: str, index: int) -> None

add a non-floating point score of a given name and value to this

SilentStruct.

C++: core::io::silent::SilentStruct::add_string_value(const std::string &, const std::string &, const int) –> void

add_submotif_info_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line_stream: pyrosetta.rosetta.std.istream) → None

C++: core::io::silent::SilentStruct::add_submotif_info_from_line(std::istream &) –> void

assign(self: pyrosetta.rosetta.core.io.silent.SilentStruct, : pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.core.io.silent.SilentStruct

C++: core::io::silent::SilentStruct::operator=(const class core::io::silent::SilentStruct &) –> class core::io::silent::SilentStruct &

clear_comments(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

C++: core::io::silent::SilentStruct::clear_comments() –> void

clear_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

Clear all of the energies in the SilentStruct. Doesn’t just

zero the energies, it entirely removes all knowledge of all energies from this SilentStruct.

C++: core::io::silent::SilentStruct::clear_energies() –> void

clone(self: pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct) → pyrosetta.rosetta.core.io.silent.SilentStruct

C++: core::io::silent::ScoreJumpFileSilentStruct::clone() const –> class std::shared_ptr<class core::io::silent::SilentStruct>

comment_from_line(*args, **kwargs)

Overloaded function.

1. comment_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line: str) -> None

C++: core::io::silent::SilentStruct::comment_from_line(const std::string &) –> void

2. comment_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line: str, include_silentfile_comments: bool) -> None

Creates and adds a comment from an input REMARK line

Input comment line, of the format “REMARK key value [value]*”

If true, ‘REMARK XXX SILENTFILE’ lines will be added to comments.

C++: core::io::silent::SilentStruct::comment_from_line(const std::string &, const bool) –> void

copy_scores(self: pyrosetta.rosetta.core.io.silent.SilentStruct, src_ss: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

Copy the score information in the given SilentStruct into

this SilentStruct.

C++: core::io::silent::SilentStruct::copy_scores(const class core::io::silent::SilentStruct &) –> void

decoy_tag(*args, **kwargs)

Overloaded function.

1. decoy_tag(self: pyrosetta.rosetta.core.io.silent.SilentStruct) -> str

returns the tag associated with this SilentStruct.

C++: core::io::silent::SilentStruct::decoy_tag() const –> std::string

2. decoy_tag(self: pyrosetta.rosetta.core.io.silent.SilentStruct, tag: str) -> None

sets the tag associated with this SilentStruct.

C++: core::io::silent::SilentStruct::decoy_tag(const std::string &) –> void

energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.utility.vector1_core_io_silent_SilentEnergy

Returns the vector of SilentEnergy objects associated with

this SilentStruct object.

C++: core::io::silent::SilentStruct::energies() const –> class utility::vector1<class core::io::silent::SilentEnergy, class std::allocator<class core::io::silent::SilentEnergy> >

energies_from_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

Initialize this SilentStruct’s energies from the given Pose.

This sets energies, energy weights, and the output widths for the energies.

C++: core::io::silent::SilentStruct::energies_from_pose(const class core::pose::Pose &) –> void

energies_into_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

Put the energy information from this SilentStruct into the

pose. Energies that correspond to a ScoreType are put into the pose.energies().total_energies() EnergyMap, all other energies are put into the ARBITRARY_FLOAT_DATA map in the pose DataCache. Also sets the scorefxn_weights in the Energies object using the information from this SilentStruct.

C++: core::io::silent::SilentStruct::energies_into_pose(class core::pose::Pose &) const –> void

energy_names(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → core::io::silent::EnergyNames

Returns the EnergyNames that this SilentStruct contains.

C++: core::io::silent::SilentStruct::energy_names() const –> class core::io::silent::EnergyNames

erase_comment(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str) → None

C++: core::io::silent::SilentStruct::erase_comment(const std::string &) –> void

figure_out_residue_numbers_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line_stream: pyrosetta.rosetta.std.istream) → None

C++: core::io::silent::SilentStruct::figure_out_residue_numbers_from_line(std::istream &) –> void

figure_out_segment_ids_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line_stream: pyrosetta.rosetta.std.istream) → None

C++: core::io::silent::SilentStruct::figure_out_segment_ids_from_line(std::istream &) –> void

fill_other_struct_list(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: core::io::silent::SilentStruct::fill_other_struct_list(const class core::pose::Pose &) –> void

fill_pose(*args, **kwargs)

Overloaded function.

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

2. fill_pose(self: pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct, pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, metapatches: bool) -> None

Configure the conformation of the given Pose with the

conformational data within this ScoreJumpFileSilentStruct. Calls pose.clear() and rebuilds Pose from scratch using the / user-specified residue types.

C++: core::io::silent::ScoreJumpFileSilentStruct::fill_pose(class core::pose::Pose &, const class core::chemical::ResidueTypeSet &, const bool) const –> void

fill_struct(self: pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct, pose: pyrosetta.rosetta.core.pose.Pose, tag: str) → None

opposite of fill_pose

C++: core::io::silent::ScoreJumpFileSilentStruct::fill_struct(const class core::pose::Pose &, const std::string &) –> void

fill_struct_with_residue_numbers(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: core::io::silent::SilentStruct::fill_struct_with_residue_numbers(const class core::pose::Pose &) –> void

fill_struct_with_submotif_info_list(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: core::io::silent::SilentStruct::fill_struct_with_submotif_info_list(const class core::pose::Pose &) –> void

finish_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

calls optH if command line requests optH.

must be called by derived classes.

C++: core::io::silent::SilentStruct::finish_pose(class core::pose::Pose &) const –> void

fold_tree(*args, **kwargs)

Overloaded function.

1. fold_tree(self: pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct, f: pyrosetta.rosetta.core.kinematics.FoldTree) -> None

C++: core::io::silent::ScoreJumpFileSilentStruct::fold_tree(const class core::kinematics::FoldTree &) –> void

2. fold_tree(self: pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct) -> pyrosetta.rosetta.core.kinematics.FoldTree

C++: core::io::silent::ScoreJumpFileSilentStruct::fold_tree() const –> const class core::kinematics::FoldTree &

force_bitflip(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → bool

Gets whether conversion from big-endian to little-endian (or the converse) should be forced

when a binary silent structure is initialized from lines.

C++: core::io::silent::SilentStruct::force_bitflip() const –> bool

full_model_info_into_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: core::io::silent::SilentStruct::full_model_info_into_pose(class core::pose::Pose &) const –> void

full_model_parameters(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → core::pose::full_model_info::FullModelParameters

C++: core::io::silent::SilentStruct::full_model_parameters() const –> class std::shared_ptr<const class core::pose::full_model_info::FullModelParameters>

get_CA_xyz(self: pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct) → pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t

returns the positions of the CA atoms in this ScoreJumpFileSilentStruct.

Useful for RMS calculations.

C++: core::io::silent::ScoreJumpFileSilentStruct::get_CA_xyz() const –> class ObjexxFCL::FArray2D<double>

get_all_comments(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.std.map_std_string_std_string

C++: core::io::silent::SilentStruct::get_all_comments() const –> class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > >

get_comment(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str) → str

C++: core::io::silent::SilentStruct::get_comment(const std::string &) const –> std::string

get_debug_rmsd(self: pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct) → float

calculates the RMSD between the C-alpha atoms of a Pose built from the torsions in this

ScoreJumpFileSilentStruct and the C-alpha atoms from this ScoreJumpFileSilentStruct.

C++: core::io::silent::ScoreJumpFileSilentStruct::get_debug_rmsd() –> double

get_energy(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str) → float

Returns the energy associated with the given scorename if this

SilentStruct has an energy for that scorename. Otherwise returns 0.

C++: core::io::silent::SilentStruct::get_energy(const std::string &) const –> double

get_parent_remark(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str) → str

C++: core::io::silent::SilentStruct::get_parent_remark(const std::string &) const –> std::string

get_parent_remark_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line: str) → None

C++: core::io::silent::SilentStruct::get_parent_remark_from_line(const std::string &) –> void

get_self_ptr(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.core.io.silent.SilentStruct

C++: core::io::silent::SilentStruct::get_self_ptr() –> class std::shared_ptr<class core::io::silent::SilentStruct>

get_silent_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.utility.vector1_core_io_silent_SilentEnergy

C++: core::io::silent::SilentStruct::get_silent_energies() –> class utility::vector1<class core::io::silent::SilentEnergy, class std::allocator<class core::io::silent::SilentEnergy> >

get_silent_energy(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str) → pyrosetta.rosetta.core.io.silent.SilentEnergy

Returns the SilentEnergy associated with this scorename.

C++: core::io::silent::SilentStruct::get_silent_energy(const std::string &) const –> const class core::io::silent::SilentEnergy &

get_string_value(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str) → str

Returns the energy associated with the given scorename if this

SilentStruct has an energy for that scorename. Otherwise returns 0.

C++: core::io::silent::SilentStruct::get_string_value(const std::string &) const –> const std::string &

has_comment(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str) → bool

C++: core::io::silent::SilentStruct::has_comment(const std::string &) const –> bool

has_energy(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str) → bool

returns true if this SilentStruct has an energy for the given

scorename, returns false otherwise.

C++: core::io::silent::SilentStruct::has_energy(const std::string &) const –> bool

has_parent_remark(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str) → bool

C++: core::io::silent::SilentStruct::has_parent_remark(const std::string &) const –> bool

init_from_lines(self: pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct, lines: pyrosetta.rosetta.utility.vector1_std_string, container: pyrosetta.rosetta.core.io.silent.SilentFileData) → bool

Tells this ScoreJumpFileSilentStruct object to initialize itself from the given set of lines.

Only initializes energies.

C++: core::io::silent::ScoreJumpFileSilentStruct::init_from_lines(const class utility::vector1<std::string, class std::allocator<std::string > > &, class core::io::silent::SilentFileData &) –> bool

jump(self: pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct, jump_num: int) → pyrosetta.rosetta.core.kinematics.RT

C++: core::io::silent::ScoreJumpFileSilentStruct::jump(unsigned long) const –> const class core::kinematics::RT &

mem_footprint(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → int

C++: core::io::silent::SilentStruct::mem_footprint() const –> unsigned long

nonconst_other_struct_list(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_io_silent_SilentStruct_t

C++: core::io::silent::SilentStruct::nonconst_other_struct_list() –> class utility::vector1<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &

nres(*args, **kwargs)

Overloaded function.

1. nres(self: pyrosetta.rosetta.core.io.silent.SilentStruct) -> int

returns the number of residues contained by this

SilentStruct.

C++: core::io::silent::SilentStruct::nres() const –> unsigned long

2. nres(self: pyrosetta.rosetta.core.io.silent.SilentStruct, nres: int) -> None

returns the number of residues in this SilentStruct.

C++: core::io::silent::SilentStruct::nres(unsigned long) –> void

one_letter_sequence(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → str

strip […] comment from seqeunce_ and return pure

one-letter sequence

C++: core::io::silent::SilentStruct::one_letter_sequence() const –> std::string

options(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.core.io.silent.SilentFileOptions

C++: core::io::silent::SilentStruct::options() const –> const class core::io::silent::SilentFileOptions &

other_struct_list(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_io_silent_SilentStruct_t

C++: core::io::silent::SilentStruct::other_struct_list() const –> const class utility::vector1<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &

parse_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct, input: pyrosetta.rosetta.std.istream, energy_names: pyrosetta.rosetta.utility.vector1_std_string) → None

C++: core::io::silent::SilentStruct::parse_energies(std::istream &, const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

precision(*args, **kwargs)

Overloaded function.

1. precision(self: pyrosetta.rosetta.core.io.silent.SilentStruct, precision: int) -> None

C++: core::io::silent::SilentStruct::precision(unsigned long) –> void

2. precision(self: pyrosetta.rosetta.core.io.silent.SilentStruct) -> int

C++: core::io::silent::SilentStruct::precision() const –> unsigned long

print_comments(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None

print the comments in this SilentStruct.

C++: core::io::silent::SilentStruct::print_comments(std::ostream &) const –> void

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

Prints the conformation information within this ScoreJumpFileSilentStruct

to the given std::ostream.

C++: core::io::silent::ScoreJumpFileSilentStruct::print_conformation(std::ostream &) const –> void

print_header(self: pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct, out: pyrosetta.rosetta.std.ostream) → None

Prints the header information within this ScoreJumpFileSilentStruct

to the given std::ostream.

C++: core::io::silent::ScoreJumpFileSilentStruct::print_header(std::ostream &) const –> void

print_parent_remarks(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None

C++: core::io::silent::SilentStruct::print_parent_remarks(std::ostream &) const –> void

print_residue_numbers(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None

print the resnum in this SilentStruct, if filled.

C++: core::io::silent::SilentStruct::print_residue_numbers(std::ostream &) const –> void

print_score_header(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None

only print SCORE: header line

C++: core::io::silent::SilentStruct::print_score_header(std::ostream &) const –> void

print_scores(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None

print out a SCORE line to the given ozstream.

C++: core::io::silent::SilentStruct::print_scores(std::ostream &) const –> void

print_submotif_info(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None

print the submotif_info in this SilentStruct, if filled.

C++: core::io::silent::SilentStruct::print_submotif_info(std::ostream &) const –> void

read_score_headers(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line: str, enames: pyrosetta.rosetta.utility.vector1_std_string, container: core::io::silent::SilentFileData) → None

C++: core::io::silent::SilentStruct::read_score_headers(const std::string &, class utility::vector1<std::string, class std::allocator<std::string > > &, class core::io::silent::SilentFileData &) –> void

read_sequence(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line: str) → bool

C++: core::io::silent::SilentStruct::read_sequence(const std::string &) –> bool

rename_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

C++: core::io::silent::SilentStruct::rename_energies() –> void

residue_numbers_into_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: core::io::silent::SilentStruct::residue_numbers_into_pose(class core::pose::Pose &) const –> void

scoreline_prefix(*args, **kwargs)

Overloaded function.

1. scoreline_prefix(self: pyrosetta.rosetta.core.io.silent.SilentStruct, prefix: str) -> None

C++: core::io::silent::SilentStruct::scoreline_prefix(const std::string &) –> void

2. scoreline_prefix(self: pyrosetta.rosetta.core.io.silent.SilentStruct) -> str

C++: core::io::silent::SilentStruct::scoreline_prefix() const –> std::string

sequence(*args, **kwargs)

Overloaded function.

1. sequence(self: pyrosetta.rosetta.core.io.silent.SilentStruct) -> pyrosetta.rosetta.core.sequence.AnnotatedSequence

returns the sequence associated with this SilentStruct.

C++: core::io::silent::SilentStruct::sequence() const –> const class core::sequence::AnnotatedSequence &

2. sequence(self: pyrosetta.rosetta.core.io.silent.SilentStruct, sequence: pyrosetta.rosetta.core.sequence.AnnotatedSequence) -> None

sets the sequence for this SilentStruct.

C++: core::io::silent::SilentStruct::sequence(const class core::sequence::AnnotatedSequence &) –> void

set_chains(self: pyrosetta.rosetta.core.io.silent.SilentStruct, chains: pyrosetta.rosetta.utility.vector1_char) → None

C++: core::io::silent::SilentStruct::set_chains(const class utility::vector1<char, class std::allocator<char> > &) –> void

set_decoy_tag(self: pyrosetta.rosetta.core.io.silent.SilentStruct, tag: str) → None

set the tag associate with this SilentStruct

C++: core::io::silent::SilentStruct::set_decoy_tag(const std::string &) –> void

set_force_bitflip(self: pyrosetta.rosetta.core.io.silent.SilentStruct, setting: bool) → None

Sets whether conversion from big-endian to little-endian (or the converse) should be forced

when a binary silent structure is initialized from lines.

C++: core::io::silent::SilentStruct::set_force_bitflip(const bool) –> void

set_full_model_parameters(self: pyrosetta.rosetta.core.io.silent.SilentStruct, setting: core::pose::full_model_info::FullModelParameters) → None

C++: core::io::silent::SilentStruct::set_full_model_parameters(class std::shared_ptr<const class core::pose::full_model_info::FullModelParameters>) –> void

set_residue_numbers(self: pyrosetta.rosetta.core.io.silent.SilentStruct, residue_numbers: pyrosetta.rosetta.utility.vector1_int) → None

C++: core::io::silent::SilentStruct::set_residue_numbers(const class utility::vector1<int, class std::allocator<int> > &) –> void

set_segment_IDs(self: pyrosetta.rosetta.core.io.silent.SilentStruct, segids: pyrosetta.rosetta.utility.vector1_std_string) → None

C++: core::io::silent::SilentStruct::set_segment_IDs(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_tag_from_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

Sets the tag from the Pose DataCache.

C++: core::io::silent::SilentStruct::set_tag_from_pose(const class core::pose::Pose &) –> void

set_valid_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct, valid: pyrosetta.rosetta.utility.vector1_std_string) → None

C++: core::io::silent::SilentStruct::set_valid_energies(class utility::vector1<std::string, class std::allocator<std::string > >) –> void

shared_from_this(self: pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct) → pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct

C++: core::io::silent::ScoreJumpFileSilentStruct::shared_from_this() –> class std::shared_ptr<class core::io::silent::ScoreJumpFileSilentStruct>

silent_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct, new_se: pyrosetta.rosetta.utility.vector1_core_io_silent_SilentEnergy) → None

sets the silent_energies for this SilentStruct.

C++: core::io::silent::SilentStruct::silent_energies(const class utility::vector1<class core::io::silent::SilentEnergy, class std::allocator<class core::io::silent::SilentEnergy> > &) –> void

sort_silent_scores(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

sort all the silent energies by their name.

C++: core::io::silent::SilentStruct::sort_silent_scores() –> void

class pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStructCreator

Bases: SilentStructCreator

creator for the ScoreJumpFileSilentStruct class

assign(self: pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStructCreator, : pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStructCreator) → pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStructCreator

C++: core::io::silent::ScoreJumpFileSilentStructCreator::operator=(const class core::io::silent::ScoreJumpFileSilentStructCreator &) –> class core::io::silent::ScoreJumpFileSilentStructCreator &

create_silent_struct(self: pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStructCreator, : pyrosetta.rosetta.core.io.silent.SilentFileOptions) → pyrosetta.rosetta.core.io.silent.SilentStruct

C++: core::io::silent::ScoreJumpFileSilentStructCreator::create_silent_struct(const class core::io::silent::SilentFileOptions &) const –> class std::shared_ptr<class core::io::silent::SilentStruct>

keyname(self: pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStructCreator) → str

C++: core::io::silent::ScoreJumpFileSilentStructCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.io.silent.SharedSilentData

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.io.silent.SharedSilentData, : pyrosetta.rosetta.core.io.silent.SharedSilentData) → pyrosetta.rosetta.core.io.silent.SharedSilentData

C++: core::io::silent::SharedSilentData::operator=(const class core::io::silent::SharedSilentData &) –> class core::io::silent::SharedSilentData &

class pyrosetta.rosetta.core.io.silent.SharedSilentDataType

Bases: pybind11_object

Members:

energynames

simplesequencedata

energynames = <SharedSilentDataType.energynames: 1>

property name

simplesequencedata = <SharedSilentDataType.simplesequencedata: 2>

property value

class pyrosetta.rosetta.core.io.silent.SilentEnergy

Bases: pybind11_object

Helper class for silent-file classes to keep track of energy information.

assign(self: pyrosetta.rosetta.core.io.silent.SilentEnergy, : pyrosetta.rosetta.core.io.silent.SilentEnergy) → pyrosetta.rosetta.core.io.silent.SilentEnergy

C++: core::io::silent::SilentEnergy::operator=(const class core::io::silent::SilentEnergy &) –> class core::io::silent::SilentEnergy &

name(*args, **kwargs)

Overloaded function.

1. name(self: pyrosetta.rosetta.core.io.silent.SilentEnergy) -> str

C++: core::io::silent::SilentEnergy::name() const –> const std::string &

2. name(self: pyrosetta.rosetta.core.io.silent.SilentEnergy, new_name: str) -> None

C++: core::io::silent::SilentEnergy::name(const std::string &) –> void

string_value(self: pyrosetta.rosetta.core.io.silent.SilentEnergy) → str

C++: core::io::silent::SilentEnergy::string_value() const –> const std::string &

value(*args, **kwargs)

Overloaded function.

1. value(self: pyrosetta.rosetta.core.io.silent.SilentEnergy) -> float

C++: core::io::silent::SilentEnergy::value() const –> double

2. value(self: pyrosetta.rosetta.core.io.silent.SilentEnergy, new_value: float) -> None

C++: core::io::silent::SilentEnergy::value(const double &) –> void

3. value(self: pyrosetta.rosetta.core.io.silent.SilentEnergy, new_string_value: str) -> None

C++: core::io::silent::SilentEnergy::value(const std::string &) –> void

weight(*args, **kwargs)

Overloaded function.

1. weight(self: pyrosetta.rosetta.core.io.silent.SilentEnergy) -> float

C++: core::io::silent::SilentEnergy::weight() const –> double

2. weight(self: pyrosetta.rosetta.core.io.silent.SilentEnergy, new_weight: float) -> None

C++: core::io::silent::SilentEnergy::weight(const double &) –> void

width(*args, **kwargs)

Overloaded function.

1. width(self: pyrosetta.rosetta.core.io.silent.SilentEnergy) -> int

C++: core::io::silent::SilentEnergy::width() const –> int

2. width(self: pyrosetta.rosetta.core.io.silent.SilentEnergy, new_width: int) -> None

C++: core::io::silent::SilentEnergy::width(const int &) –> void

class pyrosetta.rosetta.core.io.silent.SilentFileData

Bases: pybind11_object

Abstract base class for classes that read and write different types of silent-files. Silent-files can contain SilentStruct objects which are expected, to be uniquely identified by some sort of string-based tag inside the file.

_read_file(*args, **kwargs)

Overloaded function.

1. _read_file(self: pyrosetta.rosetta.core.io.silent.SilentFileData, filename: str) -> bool

2. _read_file(self: pyrosetta.rosetta.core.io.silent.SilentFileData, filename: str, throw_exception_on_bad_structs: bool) -> bool

Read in the SilentStruct objects contained in the given filename.

this version returns with a boolean to tell you about success

C++: core::io::silent::SilentFileData::_read_file(const std::string &, bool) –> bool

3. _read_file(self: pyrosetta.rosetta.core.io.silent.SilentFileData, filename: str, tags: pyrosetta.rosetta.utility.vector1_std_string) -> bool

4. _read_file(self: pyrosetta.rosetta.core.io.silent.SilentFileData, filename: str, tags: pyrosetta.rosetta.utility.vector1_std_string, throw_exception_on_bad_structs: bool) -> bool

Read in the SilentStruct objects contained in the given filename.

Ignore any SilentStruct with a tag not in the tags vector. returns with a boolean to tell about success

C++: core::io::silent::SilentFileData::_read_file(const std::string &, const class utility::vector1<std::string, class std::allocator<std::string > > &, bool) –> bool

_write_silent_struct(*args, **kwargs)

Overloaded function.

1. _write_silent_struct(self: pyrosetta.rosetta.core.io.silent.SilentFileData, s: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) -> bool

2. _write_silent_struct(self: pyrosetta.rosetta.core.io.silent.SilentFileData, s: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream, bWriteScoreOnly: bool) -> bool

Write the given silent-struct, including the header, to the given

ostream.

C++: core::io::silent::SilentFileData::_write_silent_struct(class core::io::silent::SilentStruct &, std::ostream &, bool) const –> bool

add_as_other_struct_if_relevant(self: pyrosetta.rosetta.core.io.silent.SilentFileData, new_struct: pyrosetta.rosetta.core.io.silent.SilentStruct) → bool

In stepwise modeling, sometimes poses carry refs to ‘other poses’

C++: core::io::silent::SilentFileData::add_as_other_struct_if_relevant(const class std::shared_ptr<class core::io::silent::SilentStruct> &) –> bool

add_structure(*args, **kwargs)

Overloaded function.

1. add_structure(self: pyrosetta.rosetta.core.io.silent.SilentFileData, new_struct: pyrosetta.rosetta.core.io.silent.SilentStruct) -> None

Adds a SilentStructOP to the structure_map_. If the SilentStruct’s

tag already exists in the structure_map_, a new tag is assigned. Careful with this method, as it stores an owning pointer. If you change the SilentStruct later, it will change your already stored structures.

C++: core::io::silent::SilentFileData::add_structure(const class std::shared_ptr<class core::io::silent::SilentStruct> &) –> void

2. add_structure(self: pyrosetta.rosetta.core.io.silent.SilentFileData, new_struct: pyrosetta.rosetta.core.io.silent.SilentStruct) -> None

Saves a copy of the silent struct. This method is:

• SAFE! in the sense that it actually copies the SilentStruct object, not

just the pointer to the object. - SLOW! in the sense that copying the object takes a small amount of time.

C++: core::io::silent::SilentFileData::add_structure(const class core::io::silent::SilentStruct &) –> void

add_structure_replace_tag_if_necessary(self: pyrosetta.rosetta.core.io.silent.SilentFileData, new_struct: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

C++: core::io::silent::SilentFileData::add_structure_replace_tag_if_necessary(class std::shared_ptr<class core::io::silent::SilentStruct> &) –> void

assign(self: pyrosetta.rosetta.core.io.silent.SilentFileData, : pyrosetta.rosetta.core.io.silent.SilentFileData) → pyrosetta.rosetta.core.io.silent.SilentFileData

C++: core::io::silent::SilentFileData::operator=(const class core::io::silent::SilentFileData &) –> class core::io::silent::SilentFileData &

begin(self: pyrosetta.rosetta.core.io.silent.SilentFileData) → core::io::silent::SilentFileData::iterator

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

C++: core::io::silent::SilentFileData::begin() –> class core::io::silent::SilentFileData::iterator

clear(self: pyrosetta.rosetta.core.io.silent.SilentFileData) → None

Clears all of the data associated with this object.

C++: core::io::silent::SilentFileData::clear() –> void

clear_shared_silent_data(self: pyrosetta.rosetta.core.io.silent.SilentFileData) → None

Clears all of the data associated with this object.

C++: core::io::silent::SilentFileData::clear_shared_silent_data() –> void

clear_structure_map(self: pyrosetta.rosetta.core.io.silent.SilentFileData) → None

Remove all of the SilentStruct objects from this object.

C++: core::io::silent::SilentFileData::clear_structure_map() –> void

comment_line(self: pyrosetta.rosetta.core.io.silent.SilentFileData, line: str) → None

Adds a comment-line that will be printed in write_all method.

Comment lines are simply lines in the silent-file that begin with the # character, and are printed in the write_all method.

C++: core::io::silent::SilentFileData::comment_line(const std::string &) –> void

comment_lines(self: pyrosetta.rosetta.core.io.silent.SilentFileData) → pyrosetta.rosetta.utility.vector1_std_string

Returns a vector1 of the comment lines read in from

a silent-file. Comment lines are any lines in the silent-file beginning with a # character.

C++: core::io::silent::SilentFileData::comment_lines() –> class utility::vector1<std::string, class std::allocator<std::string > >

class const_iterator

Bases: pybind11_object

const_iterator class for SilentFileData container.

arrow(self: pyrosetta.rosetta.core.io.silent.SilentFileData.const_iterator) → pyrosetta.rosetta.core.io.silent.SilentStruct

C++: core::io::silent::SilentFileData::const_iterator::operator->() const –> class std::shared_ptr<class core::io::silent::SilentStruct>

dereference(self: pyrosetta.rosetta.core.io.silent.SilentFileData.const_iterator) → pyrosetta.rosetta.core.io.silent.SilentStruct

C++: core::io::silent::SilentFileData::const_iterator::operator*() const –> class std::shared_ptr<class core::io::silent::SilentStruct>

pre_decrement(self: pyrosetta.rosetta.core.io.silent.SilentFileData.const_iterator) → pyrosetta.rosetta.core.io.silent.SilentFileData.const_iterator

C++: core::io::silent::SilentFileData::const_iterator::operator–() –> class core::io::silent::SilentFileData::const_iterator &

pre_increment(self: pyrosetta.rosetta.core.io.silent.SilentFileData.const_iterator) → pyrosetta.rosetta.core.io.silent.SilentFileData.const_iterator

C++: core::io::silent::SilentFileData::const_iterator::operator++() –> class core::io::silent::SilentFileData::const_iterator &

create_SilentStructOP(self: pyrosetta.rosetta.core.io.silent.SilentFileData) → pyrosetta.rosetta.core.io.silent.SilentStruct

C++: core::io::silent::SilentFileData::create_SilentStructOP() –> class std::shared_ptr<class core::io::silent::SilentStruct>

end(self: pyrosetta.rosetta.core.io.silent.SilentFileData) → core::io::silent::SilentFileData::iterator

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

C++: core::io::silent::SilentFileData::end() –> class core::io::silent::SilentFileData::iterator

filename(self: pyrosetta.rosetta.core.io.silent.SilentFileData) → str

Gets the filename that this SilentFileData object will

write to (i.e. OUTPUT filename).

C++: core::io::silent::SilentFileData::filename() const –> const std::string &

get_iterator_for_tag(self: pyrosetta.rosetta.core.io.silent.SilentFileData, tag: str) → core::io::silent::SilentFileData::iterator

C++: core::io::silent::SilentFileData::get_iterator_for_tag(const std::string &) –> class core::io::silent::SilentFileData::iterator

get_resnum(self: pyrosetta.rosetta.core.io.silent.SilentFileData, filename: str) → Tuple[pyrosetta.rosetta.utility.vector1_int, pyrosetta.rosetta.utility.vector1_char, pyrosetta.rosetta.utility.vector1_std_string]

C++: core::io::silent::SilentFileData::get_resnum(const std::string &) –> class std::tuple<class utility::vector1<int, class std::allocator<int> >, class utility::vector1<char, class std::allocator<char> >, class utility::vector1<std::string, class std::allocator<std::string > > >

get_sequence(self: pyrosetta.rosetta.core.io.silent.SilentFileData, filename: str) → str

C++: core::io::silent::SilentFileData::get_sequence(const std::string &) –> std::string

get_shared_silent_data(self: pyrosetta.rosetta.core.io.silent.SilentFileData, ssdt: pyrosetta.rosetta.core.io.silent.SharedSilentDataType) → pyrosetta.rosetta.core.io.silent.SharedSilentData

SharedSilentData methods

C++: core::io::silent::SilentFileData::get_shared_silent_data(enum core::io::silent::SharedSilentDataType) const –> class std::shared_ptr<class core::io::silent::SharedSilentData>

get_structure(self: pyrosetta.rosetta.core.io.silent.SilentFileData, tag: str) → pyrosetta.rosetta.core.io.silent.SilentStruct

Return a SilentStruct referred to by the given tag. Assumes that

we have checked the tag!!

C++: core::io::silent::SilentFileData::get_structure(const std::string &) const –> const class core::io::silent::SilentStruct &

has_shared_silent_data(self: pyrosetta.rosetta.core.io.silent.SilentFileData, ssdt: pyrosetta.rosetta.core.io.silent.SharedSilentDataType) → bool

C++: core::io::silent::SilentFileData::has_shared_silent_data(enum core::io::silent::SharedSilentDataType) const –> bool

has_tag(self: pyrosetta.rosetta.core.io.silent.SilentFileData, tag: str) → bool

Returns true if we have a SilentStruct matching the given tag,

false otherwise.

C++: core::io::silent::SilentFileData::has_tag(const std::string &) const –> bool

input_filename(self: pyrosetta.rosetta.core.io.silent.SilentFileData) → str

Get the filename that this SilentFileData object was

initialized FROM (i.e. INPUT filename).

C++: core::io::silent::SilentFileData::input_filename() const –> const std::string &

class iterator

Bases: pybind11_object

Iterator class for SilentFileData container.

arrow(self: pyrosetta.rosetta.core.io.silent.SilentFileData.iterator) → pyrosetta.rosetta.core.io.silent.SilentStruct

C++: core::io::silent::SilentFileData::iterator::operator->() const –> class std::shared_ptr<class core::io::silent::SilentStruct>

assign(self: pyrosetta.rosetta.core.io.silent.SilentFileData.iterator, : pyrosetta.rosetta.core.io.silent.SilentFileData.iterator) → pyrosetta.rosetta.core.io.silent.SilentFileData.iterator

C++: core::io::silent::SilentFileData::iterator::operator=(const class core::io::silent::SilentFileData::iterator &) –> class core::io::silent::SilentFileData::iterator &

dereference(self: pyrosetta.rosetta.core.io.silent.SilentFileData.iterator) → pyrosetta.rosetta.core.io.silent.SilentStruct

C++: core::io::silent::SilentFileData::iterator::operator*() const –> class std::shared_ptr<class core::io::silent::SilentStruct>

pre_decrement(self: pyrosetta.rosetta.core.io.silent.SilentFileData.iterator) → pyrosetta.rosetta.core.io.silent.SilentFileData.iterator

C++: core::io::silent::SilentFileData::iterator::operator–() –> class core::io::silent::SilentFileData::iterator &

pre_increment(self: pyrosetta.rosetta.core.io.silent.SilentFileData.iterator) → pyrosetta.rosetta.core.io.silent.SilentFileData.iterator

C++: core::io::silent::SilentFileData::iterator::operator++() –> class core::io::silent::SilentFileData::iterator &

matched_tags(self: pyrosetta.rosetta.core.io.silent.SilentFileData, expression: str, mode: str, tags_in_file: pyrosetta.rosetta.utility.vector1_std_string) → bool

return mode=first,last,all matched tags – currently matching ‘expression*’ to tags in file, boost::regexp possible later

C++: core::io::silent::SilentFileData::matched_tags(const std::string &, const std::string &, class utility::vector1<std::string, class std::allocator<std::string > > &) const –> bool

nres(self: pyrosetta.rosetta.core.io.silent.SilentFileData) → 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::silent::SilentFileData::nres() const –> int

order_by_energy(self: pyrosetta.rosetta.core.io.silent.SilentFileData) → None

Orders silent structs by energy.

C++: core::io::silent::SilentFileData::order_by_energy() –> void

push_back(self: pyrosetta.rosetta.core.io.silent.SilentFileData, new_struct: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

push_back to provide compatibility with other std containers.

C++: core::io::silent::SilentFileData::push_back(const class std::shared_ptr<class core::io::silent::SilentStruct> &) –> void

read_file(*args, **kwargs)

Overloaded function.

1. read_file(self: pyrosetta.rosetta.core.io.silent.SilentFileData, filename: str) -> bool

Read in the SilentStruct objects contained in the given filename.

this version will throw an exception if things go wrong (boolean return value is thus always true)

C++: core::io::silent::SilentFileData::read_file(const std::string &) –> bool

2. read_file(self: pyrosetta.rosetta.core.io.silent.SilentFileData, filename: str, tags: pyrosetta.rosetta.utility.vector1_std_string) -> bool

Read in the SilentStruct objects contained in the given filename.

Ignore any SilentStruct with a tag not in the tags vector. throw an exception if things go wrong (returned boolean always true)

C++: core::io::silent::SilentFileData::read_file(const std::string &, const class utility::vector1<std::string, class std::allocator<std::string > > &) –> bool

read_stream(*args, **kwargs)

Overloaded function.

1. read_stream(self: pyrosetta.rosetta.core.io.silent.SilentFileData, data: pyrosetta.rosetta.std.istream, tags: pyrosetta.rosetta.utility.vector1_std_string, throw_exception_on_bad_structs: bool) -> bool

2. read_stream(self: pyrosetta.rosetta.core.io.silent.SilentFileData, data: pyrosetta.rosetta.std.istream, tags: pyrosetta.rosetta.utility.vector1_std_string, throw_exception_on_bad_structs: bool, filename: str) -> bool

C++: core::io::silent::SilentFileData::read_stream(std::istream &, const class utility::vector1<std::string, class std::allocator<std::string > > &, bool, std::string) –> bool

read_tags_fast(*args, **kwargs)

Overloaded function.

1. read_tags_fast(self: pyrosetta.rosetta.core.io.silent.SilentFileData, 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::silent::SilentFileData::read_tags_fast(const std::string &) const –> class utility::vector1<std::string, class std::allocator<std::string > >

2. read_tags_fast(self: pyrosetta.rosetta.core.io.silent.SilentFileData, filename: str, : pyrosetta.rosetta.utility.vector1_std_string) -> bool

quickly read a list of tags from a silent-input file. Only checks

lines beginning with SCORE: strings.

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

renumber_all_decoys(self: pyrosetta.rosetta.core.io.silent.SilentFileData) → None

renumber all of the decoys in this SilentFileData object. This

obliterates decoy tag associated with every SilentStruct object, and tries to sensibly number the decoys with similar and increasingly numbered decoy tags.

C++: core::io::silent::SilentFileData::renumber_all_decoys() –> void

reverse_score_filter(self: pyrosetta.rosetta.core.io.silent.SilentFileData, score_fraction: float) → None

C++: core::io::silent::SilentFileData::reverse_score_filter(const double) –> void

score_filter(self: pyrosetta.rosetta.core.io.silent.SilentFileData, score_fraction: float) → None

Removes the worst ( 1 - score_fraction ) percent of the decoys by

score. The value of score_fraction should be between 0 and 1.0.

C++: core::io::silent::SilentFileData::score_filter(const double) –> void

set_filename(self: pyrosetta.rosetta.core.io.silent.SilentFileData, filename: str) → None

Sets the filename that this SilentFileData object will

write to.

C++: core::io::silent::SilentFileData::set_filename(std::string) –> void

set_record_source(self: pyrosetta.rosetta.core.io.silent.SilentFileData, new_mode: bool) → None

C++: core::io::silent::SilentFileData::set_record_source(const bool &) –> void

set_shared_silent_data(self: pyrosetta.rosetta.core.io.silent.SilentFileData, ssdt: pyrosetta.rosetta.core.io.silent.SharedSilentDataType, ssd_op: pyrosetta.rosetta.core.io.silent.SharedSilentData) → None

C++: core::io::silent::SilentFileData::set_shared_silent_data(enum core::io::silent::SharedSilentDataType, class std::shared_ptr<class core::io::silent::SharedSilentData>) const –> void

set_verbose(self: pyrosetta.rosetta.core.io.silent.SilentFileData, setting: bool) → None

Sets the filename that this SilentFileData object will

write to.

C++: core::io::silent::SilentFileData::set_verbose(const bool) –> void

size(self: pyrosetta.rosetta.core.io.silent.SilentFileData) → int

Returns the number of structures contained in this container.

C++: core::io::silent::SilentFileData::size() const –> unsigned long

store_argv_in_file(*args, **kwargs)

Overloaded function.

1. store_argv_in_file(self: pyrosetta.rosetta.core.io.silent.SilentFileData) -> bool

Returns true if this silent-file plans on storing

option.get_argv() as a comment in the silent-file, false otherwise.

C++: core::io::silent::SilentFileData::store_argv_in_file() const –> bool

2. store_argv_in_file(self: pyrosetta.rosetta.core.io.silent.SilentFileData, new_setting: bool) -> None

Sets a boolean variable governing if this silent-file

plans on storing option.get_argv() as a comment in the silent-file.

C++: core::io::silent::SilentFileData::store_argv_in_file(bool) –> void

strict_column_mode(*args, **kwargs)

Overloaded function.

1. strict_column_mode(self: pyrosetta.rosetta.core.io.silent.SilentFileData) -> bool

Returns a boolean indicating whether or not the strict_column_mode

is turned on when printing scores.

If strict_column_mode() is true, then the first SilentStruct printed to this SilentFileData object sets the EnergyNames that will be printed for all other SilentStruct objects. Extra EnergyNames in subsequent SilentStruct objects are ignored. If new objects are missing energies that should be printed in strict_column_mode, missing energy values are set to zero. In !strict_column_mode(), when each SilentStruct is printed, a new SCORE: header is printed if energies differ from last printed SilentStruct.

C++: core::io::silent::SilentFileData::strict_column_mode() const –> bool

2. strict_column_mode(self: pyrosetta.rosetta.core.io.silent.SilentFileData, new_mode: bool) -> None

Sets value for strict column mode. See strict_column_mode() for

more information.

C++: core::io::silent::SilentFileData::strict_column_mode(bool) –> void

structure_list(self: pyrosetta.rosetta.core.io.silent.SilentFileData) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_io_silent_SilentStruct_t

Function to access the vector of silent structure owning pointers

ordered as they were in the input file.

C++: core::io::silent::SilentFileData::structure_list() –> class utility::vector1<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > >

tags(self: pyrosetta.rosetta.core.io.silent.SilentFileData) → pyrosetta.rosetta.utility.vector1_std_string

Return all tags in this container.

C++: core::io::silent::SilentFileData::tags() const –> class utility::vector1<std::string, class std::allocator<std::string > >

write_all(*args, **kwargs)

Overloaded function.

1. write_all(self: pyrosetta.rosetta.core.io.silent.SilentFileData, filename: str) -> None

2. write_all(self: pyrosetta.rosetta.core.io.silent.SilentFileData, filename: str, bWriteScoreOnly: bool) -> None

write all SilentStruct objects in the structure_map_ to the given

filename.

C++: core::io::silent::SilentFileData::write_all(const std::string &, bool) const –> void

write_comment(self: pyrosetta.rosetta.core.io.silent.SilentFileData, out: pyrosetta.rosetta.std.ostream, line: str) → None

Write a comment to the given output stream.

C++: core::io::silent::SilentFileData::write_comment(std::ostream &, const std::string &) const –> void

write_silent_struct(*args, **kwargs)

Overloaded function.

1. write_silent_struct(self: pyrosetta.rosetta.core.io.silent.SilentFileData, s: pyrosetta.rosetta.core.io.silent.SilentStruct, filename: str) -> bool

2. write_silent_struct(self: pyrosetta.rosetta.core.io.silent.SilentFileData, s: pyrosetta.rosetta.core.io.silent.SilentStruct, filename: str, bWriteScoreOnly: bool) -> bool

Write the given silent-struct to the given outfile.

C++: core::io::silent::SilentFileData::write_silent_struct(class core::io::silent::SilentStruct &, const std::string &, bool) const –> bool

3. write_silent_struct(self: pyrosetta.rosetta.core.io.silent.SilentFileData, s: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) -> bool

4. write_silent_struct(self: pyrosetta.rosetta.core.io.silent.SilentFileData, s: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream, bWriteScoreOnly: bool) -> bool

Write the given silent-struct, minus the header, to the given

ostream.

C++: core::io::silent::SilentFileData::write_silent_struct(class core::io::silent::SilentStruct &, std::ostream &, bool) const –> bool

class pyrosetta.rosetta.core.io.silent.SilentFileHeaderLine

Bases: pybind11_object

Enum for the types of lines that a silent file can have in its header section.

Some silent file types (e.g. BinarySilentFiles) are initialized from their header data.

Vikram K. Mulligan (vmullig.edu)

Members:

SFHEADER_SEQUENCE_LINE

SFHEADER_SCORE_TYPE_LINE

SFHEADER_SCORE_LINE

SFHEADER_SCORE_LINE = <SilentFileHeaderLine.SFHEADER_SCORE_LINE: 3>

SFHEADER_SCORE_TYPE_LINE = <SilentFileHeaderLine.SFHEADER_SCORE_TYPE_LINE: 2>

SFHEADER_SEQUENCE_LINE = <SilentFileHeaderLine.SFHEADER_SEQUENCE_LINE: 1>

property name

property value

class pyrosetta.rosetta.core.io.silent.SilentFileOptions

Bases: pybind11_object

static append_attributes_for_tag_parsing(xsd: utility::tag::XMLSchemaDefinition, attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None

C++: core::io::silent::SilentFileOptions::append_attributes_for_tag_parsing(class utility::tag::XMLSchemaDefinition &, class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

assign(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions, : pyrosetta.rosetta.core.io.silent.SilentFileOptions) → pyrosetta.rosetta.core.io.silent.SilentFileOptions

C++: core::io::silent::SilentFileOptions::operator=(const class core::io::silent::SilentFileOptions &) –> class core::io::silent::SilentFileOptions &

binary_output(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions) → bool

C++: core::io::silent::SilentFileOptions::binary_output() const –> bool

force_silent_bitflip_on_read(*args, **kwargs)

Overloaded function.

1. force_silent_bitflip_on_read(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions) -> bool

C++: core::io::silent::SilentFileOptions::force_silent_bitflip_on_read() const –> bool

2. force_silent_bitflip_on_read(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions, setting: bool) -> None

C++: core::io::silent::SilentFileOptions::force_silent_bitflip_on_read(bool) –> void

force_silent_bitflip_on_read_set(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions) → bool

C++: core::io::silent::SilentFileOptions::force_silent_bitflip_on_read_set() const –> bool

in_fullatom(*args, **kwargs)

Overloaded function.

1. in_fullatom(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions) -> bool

C++: core::io::silent::SilentFileOptions::in_fullatom() const –> bool

2. in_fullatom(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions, setting: bool) -> None

C++: core::io::silent::SilentFileOptions::in_fullatom(bool) –> void

in_silent_score_prefix(*args, **kwargs)

Overloaded function.

1. in_silent_score_prefix(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions) -> str

C++: core::io::silent::SilentFileOptions::in_silent_score_prefix() const –> std::string

2. in_silent_score_prefix(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions, setting: str) -> None

C++: core::io::silent::SilentFileOptions::in_silent_score_prefix(std::string) –> void

in_silent_scores_wanted(*args, **kwargs)

Overloaded function.

1. in_silent_scores_wanted(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions) -> pyrosetta.rosetta.utility.vector1_std_string

C++: core::io::silent::SilentFileOptions::in_silent_scores_wanted() const –> class utility::vector1<std::string, class std::allocator<std::string > >

2. in_silent_scores_wanted(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions, setting: pyrosetta.rosetta.utility.vector1_std_string) -> None

C++: core::io::silent::SilentFileOptions::in_silent_scores_wanted(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

in_silent_scores_wanted_set(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions) → bool

C++: core::io::silent::SilentFileOptions::in_silent_scores_wanted_set() const –> bool

in_silent_struct_type(*args, **kwargs)

Overloaded function.

1. in_silent_struct_type(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions) -> str

C++: core::io::silent::SilentFileOptions::in_silent_struct_type() const –> std::string

2. in_silent_struct_type(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions, setting: str) -> None

C++: core::io::silent::SilentFileOptions::in_silent_struct_type(std::string) –> void

in_silent_struct_type_set(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions) → bool

C++: core::io::silent::SilentFileOptions::in_silent_struct_type_set() const –> bool

keep_input_scores(*args, **kwargs)

Overloaded function.

1. keep_input_scores(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions) -> bool

C++: core::io::silent::SilentFileOptions::keep_input_scores() const –> bool

2. keep_input_scores(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions, setting: bool) -> None

C++: core::io::silent::SilentFileOptions::keep_input_scores(bool) –> void

static list_read_options(read_options: pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t) → None

C++: core::io::silent::SilentFileOptions::list_read_options(class std::list<class utility::keys::VariantKey<class utility::options::OptionKey>, class std::allocator<class utility::keys::VariantKey<class utility::options::OptionKey> > > &) –> void

out_silent_struct_type(*args, **kwargs)

Overloaded function.

1. out_silent_struct_type(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions) -> str

C++: core::io::silent::SilentFileOptions::out_silent_struct_type() const –> std::string

2. out_silent_struct_type(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions, setting: str) -> None

C++: core::io::silent::SilentFileOptions::out_silent_struct_type(std::string) –> void

out_silent_struct_type_set(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions) → bool

C++: core::io::silent::SilentFileOptions::out_silent_struct_type_set() const –> bool

out_user_tag(*args, **kwargs)

Overloaded function.

1. out_user_tag(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions) -> str

C++: core::io::silent::SilentFileOptions::out_user_tag() const –> std::string

2. out_user_tag(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions, setting: str) -> None

C++: core::io::silent::SilentFileOptions::out_user_tag(std::string) –> void

out_user_tag_set(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions) → bool

C++: core::io::silent::SilentFileOptions::out_user_tag_set() const –> bool

out_weight_silent_scores(*args, **kwargs)

Overloaded function.

1. out_weight_silent_scores(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions) -> bool

C++: core::io::silent::SilentFileOptions::out_weight_silent_scores() const –> bool

2. out_weight_silent_scores(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions, setting: bool) -> None

C++: core::io::silent::SilentFileOptions::out_weight_silent_scores(bool) –> void

print_all_score_headers(*args, **kwargs)

Overloaded function.

1. print_all_score_headers(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions) -> bool

C++: core::io::silent::SilentFileOptions::print_all_score_headers() const –> bool

2. print_all_score_headers(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions, setting: bool) -> None

C++: core::io::silent::SilentFileOptions::print_all_score_headers(bool) –> void

read_from_global_options(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions) → None

C++: core::io::silent::SilentFileOptions::read_from_global_options() –> void

read_from_options(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions, options: pyrosetta.rosetta.utility.options.OptionCollection) → None

C++: core::io::silent::SilentFileOptions::read_from_options(const class utility::options::OptionCollection &) –> void

read_from_tag(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions, tag: utility::tag::Tag) → None

C++: core::io::silent::SilentFileOptions::read_from_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

read_through_errors(*args, **kwargs)

Overloaded function.

1. read_through_errors(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions) -> bool

C++: core::io::silent::SilentFileOptions::read_through_errors() const –> bool

2. read_through_errors(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions, setting: bool) -> None

C++: core::io::silent::SilentFileOptions::read_through_errors(bool) –> void

select_random(*args, **kwargs)

Overloaded function.

1. select_random(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions) -> int

C++: core::io::silent::SilentFileOptions::select_random() const –> int

2. select_random(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions, setting: int) -> None

C++: core::io::silent::SilentFileOptions::select_random(int) –> void

select_random_set(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions) → bool

C++: core::io::silent::SilentFileOptions::select_random_set() const –> bool

select_range_len(*args, **kwargs)

Overloaded function.

1. select_range_len(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions) -> int

C++: core::io::silent::SilentFileOptions::select_range_len() const –> int

2. select_range_len(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions, setting: int) -> None

C++: core::io::silent::SilentFileOptions::select_range_len(int) –> void

select_range_mul(*args, **kwargs)

Overloaded function.

1. select_range_mul(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions) -> int

C++: core::io::silent::SilentFileOptions::select_range_mul() const –> int

2. select_range_mul(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions, setting: int) -> None

C++: core::io::silent::SilentFileOptions::select_range_mul(int) –> void

select_range_start(*args, **kwargs)

Overloaded function.

1. select_range_start(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions) -> int

C++: core::io::silent::SilentFileOptions::select_range_start() const –> int

2. select_range_start(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions, setting: int) -> None

C++: core::io::silent::SilentFileOptions::select_range_start(int) –> void

set_binary_output(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions, setting: bool) → None

C++: core::io::silent::SilentFileOptions::set_binary_output(bool) –> void

write_failures(*args, **kwargs)

Overloaded function.

1. write_failures(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions) -> bool

C++: core::io::silent::SilentFileOptions::write_failures() const –> bool

2. write_failures(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions, setting: bool) -> None

C++: core::io::silent::SilentFileOptions::write_failures(bool) –> void

write_failures_set(self: pyrosetta.rosetta.core.io.silent.SilentFileOptions) → bool

C++: core::io::silent::SilentFileOptions::write_failures_set() const –> bool

class pyrosetta.rosetta.core.io.silent.SilentStruct

Bases: pybind11_object

add_comment(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str, value: str) → None

add a named comment to this SilentStruct object.

Similar to methods for playing with energies, but mapping is string => string rather than string => Real.

C++: core::io::silent::SilentStruct::add_comment(std::string, std::string) –> void

add_energy(*args, **kwargs)

Overloaded function.

1. add_energy(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str, value: float) -> None

2. add_energy(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str, value: float, weight: float) -> None

add a score of a given name and value to this SilentStruct.

Takes an optional weight that defaults to 1.0.

C++: core::io::silent::SilentStruct::add_energy(const std::string &, double, double) –> void

add_other_struct(self: pyrosetta.rosetta.core.io.silent.SilentStruct, silent_struct: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

C++: core::io::silent::SilentStruct::add_other_struct(class std::shared_ptr<class core::io::silent::SilentStruct>) –> void

add_parent_remark(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str, value: str) → None

C++: core::io::silent::SilentStruct::add_parent_remark(const std::string &, const std::string &) –> void

add_string_value(*args, **kwargs)

Overloaded function.

1. add_string_value(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str, value: str) -> None

2. add_string_value(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str, value: str, index: int) -> None

add a non-floating point score of a given name and value to this

SilentStruct.

C++: core::io::silent::SilentStruct::add_string_value(const std::string &, const std::string &, const int) –> void

add_submotif_info_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line_stream: pyrosetta.rosetta.std.istream) → None

C++: core::io::silent::SilentStruct::add_submotif_info_from_line(std::istream &) –> void

assign(self: pyrosetta.rosetta.core.io.silent.SilentStruct, : pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.core.io.silent.SilentStruct

C++: core::io::silent::SilentStruct::operator=(const class core::io::silent::SilentStruct &) –> class core::io::silent::SilentStruct &

clear_comments(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

C++: core::io::silent::SilentStruct::clear_comments() –> void

clear_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

Clear all of the energies in the SilentStruct. Doesn’t just

zero the energies, it entirely removes all knowledge of all energies from this SilentStruct.

C++: core::io::silent::SilentStruct::clear_energies() –> void

clone(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.core.io.silent.SilentStruct

C++: core::io::silent::SilentStruct::clone() const –> class std::shared_ptr<class core::io::silent::SilentStruct>

comment_from_line(*args, **kwargs)

Overloaded function.

1. comment_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line: str) -> None

C++: core::io::silent::SilentStruct::comment_from_line(const std::string &) –> void

2. comment_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line: str, include_silentfile_comments: bool) -> None

Creates and adds a comment from an input REMARK line

Input comment line, of the format “REMARK key value [value]*”

If true, ‘REMARK XXX SILENTFILE’ lines will be added to comments.

C++: core::io::silent::SilentStruct::comment_from_line(const std::string &, const bool) –> void

copy_scores(self: pyrosetta.rosetta.core.io.silent.SilentStruct, src_ss: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

Copy the score information in the given SilentStruct into

this SilentStruct.

C++: core::io::silent::SilentStruct::copy_scores(const class core::io::silent::SilentStruct &) –> void

decoy_tag(*args, **kwargs)

Overloaded function.

1. decoy_tag(self: pyrosetta.rosetta.core.io.silent.SilentStruct) -> str

returns the tag associated with this SilentStruct.

C++: core::io::silent::SilentStruct::decoy_tag() const –> std::string

2. decoy_tag(self: pyrosetta.rosetta.core.io.silent.SilentStruct, tag: str) -> None

sets the tag associated with this SilentStruct.

C++: core::io::silent::SilentStruct::decoy_tag(const std::string &) –> void

energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.utility.vector1_core_io_silent_SilentEnergy

Returns the vector of SilentEnergy objects associated with

this SilentStruct object.

C++: core::io::silent::SilentStruct::energies() const –> class utility::vector1<class core::io::silent::SilentEnergy, class std::allocator<class core::io::silent::SilentEnergy> >

energies_from_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

Initialize this SilentStruct’s energies from the given Pose.

This sets energies, energy weights, and the output widths for the energies.

C++: core::io::silent::SilentStruct::energies_from_pose(const class core::pose::Pose &) –> void

energies_into_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

Put the energy information from this SilentStruct into the

pose. Energies that correspond to a ScoreType are put into the pose.energies().total_energies() EnergyMap, all other energies are put into the ARBITRARY_FLOAT_DATA map in the pose DataCache. Also sets the scorefxn_weights in the Energies object using the information from this SilentStruct.

C++: core::io::silent::SilentStruct::energies_into_pose(class core::pose::Pose &) const –> void

energy_names(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → core::io::silent::EnergyNames

Returns the EnergyNames that this SilentStruct contains.

C++: core::io::silent::SilentStruct::energy_names() const –> class core::io::silent::EnergyNames

erase_comment(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str) → None

C++: core::io::silent::SilentStruct::erase_comment(const std::string &) –> void

figure_out_residue_numbers_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line_stream: pyrosetta.rosetta.std.istream) → None

C++: core::io::silent::SilentStruct::figure_out_residue_numbers_from_line(std::istream &) –> void

figure_out_segment_ids_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line_stream: pyrosetta.rosetta.std.istream) → None

C++: core::io::silent::SilentStruct::figure_out_segment_ids_from_line(std::istream &) –> void

fill_other_struct_list(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: core::io::silent::SilentStruct::fill_other_struct_list(const class core::pose::Pose &) –> void

fill_pose(*args, **kwargs)

Overloaded function.

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

2. fill_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose, metapatches: bool) -> None

C++: core::io::silent::SilentStruct::fill_pose(class core::pose::Pose &, const bool) const –> void

3. fill_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) -> None

4. fill_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, metapatches: bool) -> None

non-virtual interface that takes a ResidueTypeSetCOP (instead of a const & to one)

and invokes the virtual method that takes the const &.

C++: core::io::silent::SilentStruct::fill_pose(class core::pose::Pose &, class std::shared_ptr<const class core::chemical::ResidueTypeSet>, const bool) const –> void

5. fill_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) -> None

6. fill_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, metapatches: bool) -> None

Fill a Pose with the conformation information in this

SilentStruct and the ResidueTypeSet provided by the caller. This is a virtual method which should be implemented by classes derived from SilentStruct.

C++: core::io::silent::SilentStruct::fill_pose(class core::pose::Pose &, const class core::chemical::ResidueTypeSet &, const bool) const –> void

fill_struct(*args, **kwargs)

Overloaded function.

1. fill_struct(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) -> None

2. fill_struct(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose, tag: str) -> None

opposite of fill_pose – superclass provides

functionality used by most SilentStruct types, and is optionally called at the beginning of the subclass’s fill_struct method. As of this writing, used only by protein SilentStructs

C++: core::io::silent::SilentStruct::fill_struct(const class core::pose::Pose &, const std::string &) –> void

fill_struct_with_residue_numbers(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: core::io::silent::SilentStruct::fill_struct_with_residue_numbers(const class core::pose::Pose &) –> void

fill_struct_with_submotif_info_list(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: core::io::silent::SilentStruct::fill_struct_with_submotif_info_list(const class core::pose::Pose &) –> void

finish_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

calls optH if command line requests optH.

must be called by derived classes.

C++: core::io::silent::SilentStruct::finish_pose(class core::pose::Pose &) const –> void

force_bitflip(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → bool

Gets whether conversion from big-endian to little-endian (or the converse) should be forced

when a binary silent structure is initialized from lines.

C++: core::io::silent::SilentStruct::force_bitflip() const –> bool

full_model_info_into_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: core::io::silent::SilentStruct::full_model_info_into_pose(class core::pose::Pose &) const –> void

full_model_parameters(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → core::pose::full_model_info::FullModelParameters

C++: core::io::silent::SilentStruct::full_model_parameters() const –> class std::shared_ptr<const class core::pose::full_model_info::FullModelParameters>

get_CA_xyz(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t

returns the positions of the CA atoms in this

ProteinSilentStruct. Useful for RMS calculations.

C++: core::io::silent::SilentStruct::get_CA_xyz() const –> class ObjexxFCL::FArray2D<double>

get_all_comments(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.std.map_std_string_std_string

C++: core::io::silent::SilentStruct::get_all_comments() const –> class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > >

get_comment(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str) → str

C++: core::io::silent::SilentStruct::get_comment(const std::string &) const –> std::string

get_debug_rmsd(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → float

Do some sort of comparison between the actual RMSD of this

silent-struct and the cached coordinates. Used for SilentStruct objects that are rebuild from torsions or other reduced representations of data.

C++: core::io::silent::SilentStruct::get_debug_rmsd() –> double

get_energy(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str) → float

Returns the energy associated with the given scorename if this

SilentStruct has an energy for that scorename. Otherwise returns 0.

C++: core::io::silent::SilentStruct::get_energy(const std::string &) const –> double

get_parent_remark(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str) → str

C++: core::io::silent::SilentStruct::get_parent_remark(const std::string &) const –> std::string

get_parent_remark_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line: str) → None

C++: core::io::silent::SilentStruct::get_parent_remark_from_line(const std::string &) –> void

get_self_ptr(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.core.io.silent.SilentStruct

C++: core::io::silent::SilentStruct::get_self_ptr() –> class std::shared_ptr<class core::io::silent::SilentStruct>

get_silent_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.utility.vector1_core_io_silent_SilentEnergy

C++: core::io::silent::SilentStruct::get_silent_energies() –> class utility::vector1<class core::io::silent::SilentEnergy, class std::allocator<class core::io::silent::SilentEnergy> >

get_silent_energy(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str) → pyrosetta.rosetta.core.io.silent.SilentEnergy

Returns the SilentEnergy associated with this scorename.

C++: core::io::silent::SilentStruct::get_silent_energy(const std::string &) const –> const class core::io::silent::SilentEnergy &

get_string_value(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str) → str

Returns the energy associated with the given scorename if this

SilentStruct has an energy for that scorename. Otherwise returns 0.

C++: core::io::silent::SilentStruct::get_string_value(const std::string &) const –> const std::string &

has_comment(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str) → bool

C++: core::io::silent::SilentStruct::has_comment(const std::string &) const –> bool

has_energy(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str) → bool

returns true if this SilentStruct has an energy for the given

scorename, returns false otherwise.

C++: core::io::silent::SilentStruct::has_energy(const std::string &) const –> bool

has_parent_remark(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str) → bool

C++: core::io::silent::SilentStruct::has_parent_remark(const std::string &) const –> bool

init_from_lines(self: pyrosetta.rosetta.core.io.silent.SilentStruct, lines: pyrosetta.rosetta.utility.vector1_std_string, container: core::io::silent::SilentFileData) → bool

Create a new SilentStruct object from the provided set of

lines. This abstract method should be overwritten by derived classes. Returns false if the init_from_lines routine encounters a problem with the lines provided.

C++: core::io::silent::SilentStruct::init_from_lines(const class utility::vector1<std::string, class std::allocator<std::string > > &, class core::io::silent::SilentFileData &) –> bool

mem_footprint(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → int

C++: core::io::silent::SilentStruct::mem_footprint() const –> unsigned long

nonconst_other_struct_list(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_io_silent_SilentStruct_t

C++: core::io::silent::SilentStruct::nonconst_other_struct_list() –> class utility::vector1<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &

nres(*args, **kwargs)

Overloaded function.

1. nres(self: pyrosetta.rosetta.core.io.silent.SilentStruct) -> int

returns the number of residues contained by this

SilentStruct.

C++: core::io::silent::SilentStruct::nres() const –> unsigned long

2. nres(self: pyrosetta.rosetta.core.io.silent.SilentStruct, nres: int) -> None

returns the number of residues in this SilentStruct.

C++: core::io::silent::SilentStruct::nres(unsigned long) –> void

one_letter_sequence(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → str

strip […] comment from seqeunce_ and return pure

one-letter sequence

C++: core::io::silent::SilentStruct::one_letter_sequence() const –> std::string

options(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.core.io.silent.SilentFileOptions

C++: core::io::silent::SilentStruct::options() const –> const class core::io::silent::SilentFileOptions &

other_struct_list(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_io_silent_SilentStruct_t

C++: core::io::silent::SilentStruct::other_struct_list() const –> const class utility::vector1<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &

parse_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct, input: pyrosetta.rosetta.std.istream, energy_names: pyrosetta.rosetta.utility.vector1_std_string) → None

C++: core::io::silent::SilentStruct::parse_energies(std::istream &, const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

precision(*args, **kwargs)

Overloaded function.

1. precision(self: pyrosetta.rosetta.core.io.silent.SilentStruct, precision: int) -> None

C++: core::io::silent::SilentStruct::precision(unsigned long) –> void

2. precision(self: pyrosetta.rosetta.core.io.silent.SilentStruct) -> int

C++: core::io::silent::SilentStruct::precision() const –> unsigned long

print_comments(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None

print the comments in this SilentStruct.

C++: core::io::silent::SilentStruct::print_comments(std::ostream &) const –> void

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

print the conformation information in SilentStruct to out.

C++: core::io::silent::SilentStruct::print_conformation(std::ostream &) const –> void

print_header(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → 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::silent::SilentStruct::print_header(std::ostream &) const –> void

print_parent_remarks(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None

C++: core::io::silent::SilentStruct::print_parent_remarks(std::ostream &) const –> void

print_residue_numbers(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None

print the resnum in this SilentStruct, if filled.

C++: core::io::silent::SilentStruct::print_residue_numbers(std::ostream &) const –> void

print_score_header(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None

only print SCORE: header line

C++: core::io::silent::SilentStruct::print_score_header(std::ostream &) const –> void

print_scores(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None

print out a SCORE line to the given ozstream.

C++: core::io::silent::SilentStruct::print_scores(std::ostream &) const –> void

print_submotif_info(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None

print the submotif_info in this SilentStruct, if filled.

C++: core::io::silent::SilentStruct::print_submotif_info(std::ostream &) const –> void

read_score_headers(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line: str, enames: pyrosetta.rosetta.utility.vector1_std_string, container: core::io::silent::SilentFileData) → None

C++: core::io::silent::SilentStruct::read_score_headers(const std::string &, class utility::vector1<std::string, class std::allocator<std::string > > &, class core::io::silent::SilentFileData &) –> void

read_sequence(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line: str) → bool

C++: core::io::silent::SilentStruct::read_sequence(const std::string &) –> bool

rename_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

C++: core::io::silent::SilentStruct::rename_energies() –> void

residue_numbers_into_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: core::io::silent::SilentStruct::residue_numbers_into_pose(class core::pose::Pose &) const –> void

scoreline_prefix(*args, **kwargs)

Overloaded function.

1. scoreline_prefix(self: pyrosetta.rosetta.core.io.silent.SilentStruct, prefix: str) -> None

C++: core::io::silent::SilentStruct::scoreline_prefix(const std::string &) –> void

2. scoreline_prefix(self: pyrosetta.rosetta.core.io.silent.SilentStruct) -> str

C++: core::io::silent::SilentStruct::scoreline_prefix() const –> std::string

sequence(*args, **kwargs)

Overloaded function.

1. sequence(self: pyrosetta.rosetta.core.io.silent.SilentStruct) -> pyrosetta.rosetta.core.sequence.AnnotatedSequence

returns the sequence associated with this SilentStruct.

C++: core::io::silent::SilentStruct::sequence() const –> const class core::sequence::AnnotatedSequence &

2. sequence(self: pyrosetta.rosetta.core.io.silent.SilentStruct, sequence: pyrosetta.rosetta.core.sequence.AnnotatedSequence) -> None

sets the sequence for this SilentStruct.

C++: core::io::silent::SilentStruct::sequence(const class core::sequence::AnnotatedSequence &) –> void

set_chains(self: pyrosetta.rosetta.core.io.silent.SilentStruct, chains: pyrosetta.rosetta.utility.vector1_char) → None

C++: core::io::silent::SilentStruct::set_chains(const class utility::vector1<char, class std::allocator<char> > &) –> void

set_decoy_tag(self: pyrosetta.rosetta.core.io.silent.SilentStruct, tag: str) → None

set the tag associate with this SilentStruct

C++: core::io::silent::SilentStruct::set_decoy_tag(const std::string &) –> void

set_force_bitflip(self: pyrosetta.rosetta.core.io.silent.SilentStruct, setting: bool) → None

Sets whether conversion from big-endian to little-endian (or the converse) should be forced

when a binary silent structure is initialized from lines.

C++: core::io::silent::SilentStruct::set_force_bitflip(const bool) –> void

set_full_model_parameters(self: pyrosetta.rosetta.core.io.silent.SilentStruct, setting: core::pose::full_model_info::FullModelParameters) → None

C++: core::io::silent::SilentStruct::set_full_model_parameters(class std::shared_ptr<const class core::pose::full_model_info::FullModelParameters>) –> void

set_residue_numbers(self: pyrosetta.rosetta.core.io.silent.SilentStruct, residue_numbers: pyrosetta.rosetta.utility.vector1_int) → None

C++: core::io::silent::SilentStruct::set_residue_numbers(const class utility::vector1<int, class std::allocator<int> > &) –> void

set_segment_IDs(self: pyrosetta.rosetta.core.io.silent.SilentStruct, segids: pyrosetta.rosetta.utility.vector1_std_string) → None

C++: core::io::silent::SilentStruct::set_segment_IDs(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_tag_from_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None

Sets the tag from the Pose DataCache.

C++: core::io::silent::SilentStruct::set_tag_from_pose(const class core::pose::Pose &) –> void

set_valid_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct, valid: pyrosetta.rosetta.utility.vector1_std_string) → None

C++: core::io::silent::SilentStruct::set_valid_energies(class utility::vector1<std::string, class std::allocator<std::string > >) –> void

silent_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct, new_se: pyrosetta.rosetta.utility.vector1_core_io_silent_SilentEnergy) → None

sets the silent_energies for this SilentStruct.

C++: core::io::silent::SilentStruct::silent_energies(const class utility::vector1<class core::io::silent::SilentEnergy, class std::allocator<class core::io::silent::SilentEnergy> > &) –> void

sort_silent_scores(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

sort all the silent energies by their name.

C++: core::io::silent::SilentStruct::sort_silent_scores() –> void

class pyrosetta.rosetta.core.io.silent.SilentStructCreator

Bases: pybind11_object

Abstract base class for a Mover factory; the Creator class is responsible for creating a particular mover class.

assign(self: pyrosetta.rosetta.core.io.silent.SilentStructCreator, : pyrosetta.rosetta.core.io.silent.SilentStructCreator) → pyrosetta.rosetta.core.io.silent.SilentStructCreator

C++: core::io::silent::SilentStructCreator::operator=(const class core::io::silent::SilentStructCreator &) –> class core::io::silent::SilentStructCreator &

create_silent_struct(self: pyrosetta.rosetta.core.io.silent.SilentStructCreator, : pyrosetta.rosetta.core.io.silent.SilentFileOptions) → pyrosetta.rosetta.core.io.silent.SilentStruct

C++: core::io::silent::SilentStructCreator::create_silent_struct(const class core::io::silent::SilentFileOptions &) const –> class std::shared_ptr<class core::io::silent::SilentStruct>

keyname(self: pyrosetta.rosetta.core.io.silent.SilentStructCreator) → str

C++: core::io::silent::SilentStructCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.io.silent.SilentStructFactory

Bases: SingletonBase_core_io_silent_SilentStructFactory_t

factory_register(self: pyrosetta.rosetta.core.io.silent.SilentStructFactory, creator: pyrosetta.rosetta.core.io.silent.SilentStructCreator) → None

C++: core::io::silent::SilentStructFactory::factory_register(class std::shared_ptr<const class core::io::silent::SilentStructCreator>) –> void

get_creator(self: pyrosetta.rosetta.core.io.silent.SilentStructFactory, type_name: str) → pyrosetta.rosetta.core.io.silent.SilentStructCreator

C++: core::io::silent::SilentStructFactory::get_creator(const std::string &) –> class std::shared_ptr<const class core::io::silent::SilentStructCreator>

static get_instance() → core::io::silent::SilentStructFactory

C++: utility::SingletonBase<core::io::silent::SilentStructFactory>::get_instance() –> class core::io::silent::SilentStructFactory *

get_silent_struct(self: pyrosetta.rosetta.core.io.silent.SilentStructFactory, type_name: str, : pyrosetta.rosetta.core.io.silent.SilentFileOptions) → pyrosetta.rosetta.core.io.silent.SilentStruct

C++: core::io::silent::SilentStructFactory::get_silent_struct(const std::string &, const class core::io::silent::SilentFileOptions &) –> class std::shared_ptr<class core::io::silent::SilentStruct>

get_silent_struct_in(self: pyrosetta.rosetta.core.io.silent.SilentStructFactory, : pyrosetta.rosetta.core.io.silent.SilentFileOptions) → pyrosetta.rosetta.core.io.silent.SilentStruct

C++: core::io::silent::SilentStructFactory::get_silent_struct_in(const class core::io::silent::SilentFileOptions &) –> class std::shared_ptr<class core::io::silent::SilentStruct>

get_silent_struct_out(*args, **kwargs)

Overloaded function.

1. get_silent_struct_out(self: pyrosetta.rosetta.core.io.silent.SilentStructFactory, : pyrosetta.rosetta.core.io.silent.SilentFileOptions) -> pyrosetta.rosetta.core.io.silent.SilentStruct

C++: core::io::silent::SilentStructFactory::get_silent_struct_out(const class core::io::silent::SilentFileOptions &) –> class std::shared_ptr<class core::io::silent::SilentStruct>

2. get_silent_struct_out(self: pyrosetta.rosetta.core.io.silent.SilentStructFactory, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.io.silent.SilentFileOptions) -> pyrosetta.rosetta.core.io.silent.SilentStruct

C++: core::io::silent::SilentStructFactory::get_silent_struct_out(const class core::pose::Pose &, const class core::io::silent::SilentFileOptions &) –> class std::shared_ptr<class core::io::silent::SilentStruct>

get_ss_names(self: pyrosetta.rosetta.core.io.silent.SilentStructFactory) → pyrosetta.rosetta.utility.vector1_std_string

C++: core::io::silent::SilentStructFactory::get_ss_names() const –> class utility::vector1<std::string, class std::allocator<std::string > >

has_silent_struct_type(self: pyrosetta.rosetta.core.io.silent.SilentStructFactory, type_name: str) → bool

test if the specified silent struct type name is associated with a registered silent struct type.

C++: core::io::silent::SilentStructFactory::has_silent_struct_type(const std::string &) –> bool

show_available_silent_struct_types(self: pyrosetta.rosetta.core.io.silent.SilentStructFactory, out: pyrosetta.rosetta.std.ostream) → None

pretty print a list of the available silent struct types.

C++: core::io::silent::SilentStructFactory::show_available_silent_struct_types(std::ostream &) –> void

class pyrosetta.rosetta.core.io.silent.SimpleSequenceData

Bases: SharedSilentData

assign(self: pyrosetta.rosetta.core.io.silent.SimpleSequenceData, : pyrosetta.rosetta.core.io.silent.SimpleSequenceData) → pyrosetta.rosetta.core.io.silent.SimpleSequenceData

C++: core::io::silent::SimpleSequenceData::operator=(const class core::io::silent::SimpleSequenceData &) –> class core::io::silent::SimpleSequenceData &

sequence(self: pyrosetta.rosetta.core.io.silent.SimpleSequenceData) → str

C++: core::io::silent::SimpleSequenceData::sequence() –> std::string

set_sequence(self: pyrosetta.rosetta.core.io.silent.SimpleSequenceData, sequence: str) → None

C++: core::io::silent::SimpleSequenceData::set_sequence(std::string) –> void

pyrosetta.rosetta.core.io.silent.figure_out_residue_numbers_from_line(line_stream: pyrosetta.rosetta.std.istream, residue_numbers: pyrosetta.rosetta.utility.vector1_int, chains: pyrosetta.rosetta.utility.vector1_char, segids: pyrosetta.rosetta.utility.vector1_std_string) → None

needed for reading out RESNUM lines from silent files

C++: core::io::silent::figure_out_residue_numbers_from_line(std::istream &, class utility::vector1<int, class std::allocator<int> > &, class utility::vector1<char, class std::allocator<char> > &, class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

pyrosetta.rosetta.core.io.silent.get_outfile_name_with_tag(silent_file: str, tag: str) → str

Changes blah.out to blah_LORES.out (if tag is “_LORES”)

C++: core::io::silent::get_outfile_name_with_tag(const std::string &, const std::string &) –> std::string

pyrosetta.rosetta.core.io.silent.gzip() → None

gzip all of the files in -out::file::silent().

C++: core::io::silent::gzip() –> void

pyrosetta.rosetta.core.io.silent.initialize_tag_is_done(silent_file: str) → pyrosetta.rosetta.std.map_std_string_bool

figures out which decoys are already stored in silent file.

C++: core::io::silent::initialize_tag_is_done(const std::string &) –> class std::map<std::string, bool, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, bool> > >

pyrosetta.rosetta.core.io.silent.remove_silent_file_if_it_exists(silent_file: str) → None

used with -overwrite flag

C++: core::io::silent::remove_silent_file_if_it_exists(const std::string &) –> void