init

Bindings for core::init namespace

pyrosetta.rosetta.core.init.check_deprecated_flags() → None

Check for deprecated flags specified by the user and output error messages if necessary

C++: core::init::check_deprecated_flags() –> void

pyrosetta.rosetta.core.init.check_score_function_sanity(*args, **kwargs)

Overloaded function.

1. check_score_function_sanity(options: pyrosetta.rosetta.utility.options.OptionCollection, scorefxn_key: str) -> bool
2. check_score_function_sanity(options: pyrosetta.rosetta.utility.options.OptionCollection, scorefxn_key: str, throw_exception: bool) -> bool

Check if a score function is requested with incompatible option flags

Will return true if scorefunction is “sane” and false if not. If throw_exception is true, will raise an exception instead of returning false.

C++: core::init::check_score_function_sanity(const class utility::options::OptionCollection &, const class std::basic_string<char> &, bool) –> bool

pyrosetta.rosetta.core.init.determine_random_number_seed(settings: pyrosetta.rosetta.core.init.RandomGeneratorSettings) → int

Figure out what seed to use based on a variety of settings stored in the

RandomGeneratorSettings object.

In MPI mode, this function uses MPI_Bcast calls, and that these calls require that all MPI nodes reach this function, or deadlock will occur. This deadlock can be avoided if the settings’ mpi_bcast_seed_from_node0_ boolean is set to false.

C++: core::init::determine_random_number_seed(const class core::init::RandomGeneratorSettings &) –> int

pyrosetta.rosetta.core.init.init(args: pyrosetta.rosetta.utility.vector1_std_string) → None

wrapper for core system Init

C++: core::init::init(const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> void

pyrosetta.rosetta.core.init.init_beta_correction(options: pyrosetta.rosetta.utility.options.OptionCollection) → None

Initialize the _most recent_ beta score function (-beta)

C++: core::init::init_beta_correction(class utility::options::OptionCollection &) –> void

pyrosetta.rosetta.core.init.init_beta_july15_correction(options: pyrosetta.rosetta.utility.options.OptionCollection) → None

Initialize the -beta_july15 score function

C++: core::init::init_beta_july15_correction(class utility::options::OptionCollection &) –> void

pyrosetta.rosetta.core.init.init_beta_nov16_correction(options: pyrosetta.rosetta.utility.options.OptionCollection) → None

Initialize the -beta_nov16 score function

C++: core::init::init_beta_nov16_correction(class utility::options::OptionCollection &) –> void

pyrosetta.rosetta.core.init.init_correct_correction(options: pyrosetta.rosetta.utility.options.OptionCollection) → None

Initialize the -correct correction

C++: core::init::init_correct_correction(class utility::options::OptionCollection &) –> void

pyrosetta.rosetta.core.init.init_crystal_refinement_correction(options: pyrosetta.rosetta.utility.options.OptionCollection) → None

Initialize the crystal refinement correction

C++: core::init::init_crystal_refinement_correction(class utility::options::OptionCollection &) –> void

pyrosetta.rosetta.core.init.init_dna_correction(options: pyrosetta.rosetta.utility.options.OptionCollection) → None

Apply some DNA-specific mods that are still in testing phase; only if -corrections::newdna present

C++: core::init::init_dna_correction(class utility::options::OptionCollection &) –> void

pyrosetta.rosetta.core.init.init_facts_correction(options: pyrosetta.rosetta.utility.options.OptionCollection) → None

Initialize the FACTS correction

C++: core::init::init_facts_correction(class utility::options::OptionCollection &) –> void

pyrosetta.rosetta.core.init.init_hbond_sp2_correction(options: pyrosetta.rosetta.utility.options.OptionCollection) → None

Initialize the hbond Sp2 correction

Deprecated as Talaris2013 becomes default.

C++: core::init::init_hbond_sp2_correction(class utility::options::OptionCollection &) –> void

pyrosetta.rosetta.core.init.init_nonideal_correction(options: pyrosetta.rosetta.utility.options.OptionCollection) → None

Initialize nonideal bond geometry correction

C++: core::init::init_nonideal_correction(class utility::options::OptionCollection &) –> void

pyrosetta.rosetta.core.init.init_paths() → None

Setup basic search paths

C++: core::init::init_paths() –> void

pyrosetta.rosetta.core.init.init_profiling() → None

Profiling measures execution performance

C++: core::init::init_profiling() –> void

pyrosetta.rosetta.core.init.init_random_generators(start_seed: int, RGtype: str) → None

Given a particular seed, initialize random generator systems (and send debug io to tracer with seed/mode info).

C++: core::init::init_random_generators(int, const class std::basic_string<char> &) –> void

pyrosetta.rosetta.core.init.init_random_number_generators() → None

Initalize random number generators from the command line

C++: core::init::init_random_number_generators() –> void

pyrosetta.rosetta.core.init.init_resources() → None

Set up system resources

C++: core::init::init_resources() –> void

pyrosetta.rosetta.core.init.init_restore_score12prime(options: pyrosetta.rosetta.utility.options.OptionCollection) → None

restore the the score function to the Score12prime version

C++: core::init::init_restore_score12prime(class utility::options::OptionCollection &) –> void

pyrosetta.rosetta.core.init.init_revert_to_pre_talaris_2013_mistake(options: pyrosetta.rosetta.utility.options.OptionCollection) → None

Initialize the “revert to before Talaris2013” mistake

C++: core::init::init_revert_to_pre_talaris_2013_mistake(class utility::options::OptionCollection &) –> void

pyrosetta.rosetta.core.init.init_revert_to_talaris(options: pyrosetta.rosetta.utility.options.OptionCollection) → None

Initialize the revert-to-Talaris2014

C++: core::init::init_revert_to_talaris(class utility::options::OptionCollection &) –> void

pyrosetta.rosetta.core.init.init_score_function_corrections(options: pyrosetta.rosetta.utility.options.OptionCollection) → None

Initialize the latest and greatest score function parameters

C++: core::init::init_score_function_corrections(class utility::options::OptionCollection &) –> void

pyrosetta.rosetta.core.init.init_shapovalov_lib_fixes_enable_correction(options: pyrosetta.rosetta.utility.options.OptionCollection) → None

Initialize the -shapovalov_lib_fixes_enable correction

C++: core::init::init_shapovalov_lib_fixes_enable_correction(class utility::options::OptionCollection &) –> void

pyrosetta.rosetta.core.init.init_source_revision() → None

Choose to output source version control information?

C++: core::init::init_source_revision() –> void

pyrosetta.rosetta.core.init.init_spades_score_function_correction(options: pyrosetta.rosetta.utility.options.OptionCollection) → None

Alter the water/water and water/non-water solvation potential if the score:water_hybrid_sf flag is

on the command line

C++: core::init::init_spades_score_function_correction(class utility::options::OptionCollection &) –> void

pyrosetta.rosetta.core.init.init_tracers() → None

Tracers control output to std::cout and std::cerr

C++: core::init::init_tracers() –> void

pyrosetta.rosetta.core.init.locate_rosetta_database() → None

Locate rosetta_database

C++: core::init::locate_rosetta_database() –> void

pyrosetta.rosetta.core.init.random_delay() → None

Choose to randomly delay execution to desyncronize parallel execution

C++: core::init::random_delay() –> void

pyrosetta.rosetta.core.init.revert_to_pre_talaris_2013_defaults(options: pyrosetta.rosetta.utility.options.OptionCollection) → None

Reset a set of flags to their pre-talaris behavior

C++: core::init::revert_to_pre_talaris_2013_defaults(class utility::options::OptionCollection &) –> void