cyclic_peptide_predict

Bindings for protocols::cyclic_peptide_predict namespace

class pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type

Bases: pybind11_builtins.pybind11_object

An enum for the cyclization type.

If additional values are added, please add them to the SimpleCycpepPredictApplication::get_cyclization_name_from_type() function.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(*args, **kwargs)

Overloaded function.

  1. __eq__(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type, arg0: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type) -> bool
  2. __eq__(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type, arg0: int) -> bool
__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getstate__(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type) → tuple
__gt__

Return self>value.

__hash__(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type) → int
__init__(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type, arg0: int) → None
__init_subclass__()

This method is called when a class is subclassed.

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

__int__(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type) → int
__le__

Return self<=value.

__lt__

Return self<value.

__ne__(*args, **kwargs)

Overloaded function.

  1. __ne__(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type, arg0: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type) -> bool
  2. __ne__(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type, arg0: int) -> bool
__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type) → str
__setattr__

Implement setattr(self, name, value).

__setstate__(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type, arg0: tuple) → None
__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

class pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication

Bases: pybind11_builtins.pybind11_object

Application-level code for simple_cycpep_predict application.

Also called by the BOINC minirosetta app.

Vikram K. Mulligan, Baker laboratory (vmullig.edu)

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

  1. __init__(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication) -> None

doc

  1. __init__(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, allow_file_read: bool) -> None
  2. __init__(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, arg0: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication) -> None
__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, : pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication) → pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::operator=(const class protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication &) –> class protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication &

disable_cis_pro_sampling(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication) → None

Set cis proline sampling OFF.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::disable_cis_pro_sampling() –> void

disable_total_energy_cutoff(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication) → None

Sets use_total_energy_cutoff_ to ‘false’.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::disable_total_energy_cutoff() –> void

get_cyclization_name_from_type(type: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type) → str

Given a cyclization name string, return its type enum.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::get_cyclization_name_from_type(const enum protocols::cyclic_peptide_predict::SCPA_cyclization_type) –> std::string

get_cyclization_type_from_name(name: str) → pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type

Given a cyclization type enum, return its name string.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::get_cyclization_type_from_name(const class std::basic_string<char> &) –> enum protocols::cyclic_peptide_predict::SCPA_cyclization_type

initialize_from_options(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication) → None

Initialize the application.

Initializes using the option system.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::initialize_from_options() –> void

register_options() → None

Register the set of options that this application uses (for the help menu).

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::register_options() –> void

run(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication) → None

Actually run the application.

The initialize_from_options() function must be called before calling this. (Called by default constructor.)

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::run() const –> void

set_D_alpha_compfile_contents(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, contents_in: str) → None

Allows external code to set the file contents for the D-alpha aa_composition file.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_D_alpha_compfile_contents(const class std::basic_string<char> &) –> void

set_D_beta_compfile_contents(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, contents_in: str) → None

Allows external code to set the file contents for the D-beta aa_composition file.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_D_beta_compfile_contents(const class std::basic_string<char> &) –> void

set_L_alpha_compfile_contents(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, contents_in: str) → None

Allows external code to set the file contents for the L-alpha aa_composition file.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_L_alpha_compfile_contents(const class std::basic_string<char> &) –> void

set_L_beta_compfile_contents(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, contents_in: str) → None

Allows external code to set the file contents for the L-beta aa_composition file.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_L_beta_compfile_contents(const class std::basic_string<char> &) –> void

set_abba_bins_binfile_contents(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, contents_in: str) → None
Allows external code to set the ABBA bin parameters without having to read the
bin params file directly from disk.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_abba_bins_binfile_contents(const class std::basic_string<char> &) –> void

set_allowed_residues_by_position(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, allowed_canonicals: pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_string_std_allocator_std_string_t, allowed_noncanonicals: pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_string_std_allocator_std_string_t) → None
Allows external code to set the allowed residues by position, so that this needn’t be read directly
from disk.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_allowed_residues_by_position(const class std::map<unsigned long, class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > > > > &, const class std::map<unsigned long, class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > > > > &) –> void

set_already_completed_job_count(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, count_in: int) → None

Set the number of jobs that this process has already completed.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_already_completed_job_count(const unsigned long) –> void

set_angle_length_relax_rounds(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, rounds_in: int) → None
Set the number of rounds of relaxation with flexible
bond angles and bond lengths.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_angle_length_relax_rounds(const unsigned long) –> void

set_angle_relax_rounds(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, rounds_in: int) → None
Set the number of rounds of relaxation with flexible
bond angles.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_angle_relax_rounds(const unsigned long) –> void

set_cartesian_relax_rounds(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, rounds_in: int) → None

Set the number of rounds of Cartesian relaxation.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_cartesian_relax_rounds(const unsigned long) –> void

set_cyclization_type(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, type_in: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type) → None

Set the cyclization type.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_cyclization_type(const enum protocols::cyclic_peptide_predict::SCPA_cyclization_type) –> void

set_my_rank(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, rank_in: int) → None

If called by MPI code, the rank of the current process can be stored here.

Used for output of job summaries.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_my_rank(const int) –> void

set_native(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, native: pyrosetta.rosetta.core.pose.Pose) → None
Allows external code to provide a native, so that the SimpleCycpepPredictApplication doesn’t have to read
directly from disk.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_native(class std::shared_ptr<const class core::pose::Pose>) –> void

set_nstruct(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, nstruct_in: int) → None
Allows external code to override the number of structures that this should generate (otherwise
set by options system.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_nstruct(const unsigned long) –> void

set_sample_cis_pro_frequency(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, freq_in: float) → None

Set the frequency with which we sample cis proline.

Implicitly sets sample_cis_pro_ to “true” if freq_in is not 0.0, “false” if it is.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_sample_cis_pro_frequency(const double &) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, sfxn_in: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

Sets the default scorefunction to use.

The scorefunction is cloned. The high-hbond version is constructed from this one. If necessary, the aa_composition score term will be turned on in that one; it needn’t be turned on in this one.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

set_sequence(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, seq: str) → None
Allows external code to provide a sequence, so that the SimpleCycpepPredictApplication doesn’t have to read
directly from disk.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_sequence(const class std::basic_string<char> &) –> void

set_suppress_checkpoints(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, suppress_checkpoints: bool) → None

Allows external code to suppress checkpointing, to prevent direct file I/O from disk.

Useful on Blue Gene.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_suppress_checkpoints(const bool) –> void

set_total_energy_cutoff(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, value_in: float) → None

Set the total energy cutoff.

Also sets use_total_energy_cutoff_ to ‘true’.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_total_energy_cutoff(const double &) –> void

set_use_rama_prepro_for_sampling(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, setting: bool) → None

Set whether we’re using RamaPrePro tables for sampling.

Setting this to “false” lets us use classic rama tables. True by default.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_use_rama_prepro_for_sampling(const bool) –> void

class pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary

Bases: pybind11_builtins.pybind11_object

A class for summarizing the result of an MPI-mode job run with the SimpleCycpepPredictApplication.

Vikram K. Mulligan, Baker laboratory (vmullig.edu)

MPI_ranks_handling_message(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary) → pyrosetta.rosetta.utility.vector1_int

Get the list of procs that transmitted this JobResultsSummary.

Whenever a proc sends it to someone else, the receiving proc appends the sender’s rank here. This allows the emperor node to address an output request to the correct proc.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication_MPI_JobResultsSummary::MPI_ranks_handling_message() const –> const class utility::vector1<int, class std::allocator<int> > &

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

  1. __init__(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary) -> None
  2. __init__(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary, originating_node_MPI_rank: int, jobindex_on_originating_node: int, pose_energy: float, rmsd: float, hbonds: int, cis_peptide_bonds: int) -> None
__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

add_MPI_rank_handling_message(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary, new_proc: int) → None

Add a proc that handled this message to the list of procs that transmitted this JobResultsSummary.

Whenever a proc sends it to someone else, the receiving proc appends the sender’s rank here. This allows the emperor node to address an output request to the correct proc.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication_MPI_JobResultsSummary::add_MPI_rank_handling_message(const int) –> void

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary, : pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary) → pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication_MPI_JobResultsSummary::operator=(const class protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication_MPI_JobResultsSummary &) –> class protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication_MPI_JobResultsSummary &

cis_peptide_bonds(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary) → int

Get the number of cis-peptide bonds of the pose generated by this job.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication_MPI_JobResultsSummary::cis_peptide_bonds() const –> unsigned long

hbonds(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary) → int

Get the number of hbonds of the pose generated by this job.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication_MPI_JobResultsSummary::hbonds() const –> unsigned long

jobindex_on_originating_node(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary) → int

Get the local index of the job on the node on which it was carried out.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication_MPI_JobResultsSummary::jobindex_on_originating_node() const –> unsigned long

originating_node_MPI_rank(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary) → int

Get the MPI rank of the process that initially carried out this job.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication_MPI_JobResultsSummary::originating_node_MPI_rank() const –> int

pose_energy(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary) → float

Get the energy of the pose generated by this job.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication_MPI_JobResultsSummary::pose_energy() const –> const double &

rmsd(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary) → float

Get the RMSD of the pose generated by this job to native.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication_MPI_JobResultsSummary::rmsd() const –> const double &

set_cis_peptide_bonds(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary, val: int) → None

Set the number of cis-peptide bonds of the pose generated by this job.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication_MPI_JobResultsSummary::set_cis_peptide_bonds(const unsigned long) –> void

set_hbonds(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary, val: int) → None

Set the number of hbonds of the pose generated by this job.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication_MPI_JobResultsSummary::set_hbonds(const unsigned long) –> void

set_jobindex_on_originating_node(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary, index: int) → None

Set the local index of the job on the node on which it was carried out.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication_MPI_JobResultsSummary::set_jobindex_on_originating_node(const unsigned long) –> void

set_originating_node_MPI_rank(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary, rank: int) → None

Set the MPI rank of the process that initially carried out this job.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication_MPI_JobResultsSummary::set_originating_node_MPI_rank(const int) –> void

set_pose_energy(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary, val: float) → None

Set the energy of the pose generated by this job.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication_MPI_JobResultsSummary::set_pose_energy(const double &) –> void

set_rmsd(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary, val: float) → None

Set the RMSD of the pose generated by this job to native.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication_MPI_JobResultsSummary::set_rmsd(const double &) –> void

show(self: pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary, out: pyrosetta.rosetta.std.ostream) → None

Print a summary of this object to a stream.

C++: protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication_MPI_JobResultsSummary::show(class std::basic_ostream<char> &) const –> void

pyrosetta.rosetta.protocols.cyclic_peptide_predict.is_canonical(resname: str) → bool
Given a residue name, return true if this is one of the 20
canonical amino acids, false otherwise.

C++: protocols::cyclic_peptide_predict::is_canonical(const class std::basic_string<char> &) –> bool

pyrosetta.rosetta.protocols.cyclic_peptide_predict.read_file_into_string(output_string: str, filename: str, from_database: bool) → None

Given an ASCII file name, read the contents into a string. If from_database is true, the read is from the database.

The string that will be filled with the file contents. Overwritten by this operation.

The name of the file to read. If from_database is true, this is a relative database path.

If true, the file is assumed to be in the database. If false, the path is relative the execution directory, or is absolute.

C++: protocols::cyclic_peptide_predict::read_file_into_string(class std::basic_string<char> &, const class std::basic_string<char> &, const bool) –> void

pyrosetta.rosetta.protocols.cyclic_peptide_predict.read_peptide_design_file(filename: str, allowed_canonicals_by_position: pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_string_std_allocator_std_string_t, allowed_noncanonicals_by_position: pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_string_std_allocator_std_string_t) → None
Given a filename, read and parse the file, returning a list of canonical residues allowed at each position

and a list of noncanonicals allowed at each position.

This does the actual file read. It is NOT THREADSAFE. The file format is a series of lines with the pattern: residue_index residuetype_1_fullname residuetype_2_fullname residuetype_3_fullname … Anything after a pound sign should be ignored. A line with DEFAULT in place of the resiude index should be interpreted as providing default values, which should be stored as map key 0.

The file name from which we’ll read.

A map of [position->vector of strings of full names] listing the allowed canonical residue types at each position. Reset and populated by this function. Key 0 indicates default settings applied anywhere that lacks a map key.

A map of [position->vector of strings of full names] listing the allowed noncanonical residue types at each position. Reset and populated by this function. Key 0 indicates default settings applied anywhere that lacks a map key.

C++: protocols::cyclic_peptide_predict::read_peptide_design_file(const class std::basic_string<char> &, class std::map<unsigned long, class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > > > > &, class std::map<unsigned long, class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > > > > &) –> void