bcl

Bindings for core::chemical::bcl namespace

class pyrosetta.rosetta.core.chemical.bcl.BCLFragmentHandler

Bases: pybind11_object

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.core.chemical.bcl.BCLFragmentHandler) -> None

2. __init__(self: pyrosetta.rosetta.core.chemical.bcl.BCLFragmentHandler, arg0: pyrosetta.rosetta.core.chemical.bcl.BCLFragmentHandler) -> None

_pybind11_conduit_v1_()

assign(self: pyrosetta.rosetta.core.chemical.bcl.BCLFragmentHandler, : pyrosetta.rosetta.core.chemical.bcl.BCLFragmentHandler) → pyrosetta.rosetta.core.chemical.bcl.BCLFragmentHandler

C++: core::chemical::bcl::BCLFragmentHandler::operator=(const class core::chemical::bcl::BCLFragmentHandler &) –> class core::chemical::bcl::BCLFragmentHandler &

get_index_to_vd(self: pyrosetta.rosetta.core.chemical.bcl.BCLFragmentHandler) → pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t

Get how the most recently created ResidueType corresponds to the underlying fragment.

C++: core::chemical::bcl::BCLFragmentHandler::get_index_to_vd() const –> const class core::chemical::AtomRefMapping<unsigned long, void *> &

get_nbr(self: pyrosetta.rosetta.core.chemical.bcl.BCLFragmentHandler) → int

Get the atom used as the neighbor atom when restype is generated

C++: core::chemical::bcl::BCLFragmentHandler::get_nbr() const –> unsigned long

get_rosetta_restype(self: pyrosetta.rosetta.core.chemical.bcl.BCLFragmentHandler) → pyrosetta.rosetta.core.chemical.MutableResidueType

Return a Rosetta molecule as a MutableResidueType

C++: core::chemical::bcl::BCLFragmentHandler::get_rosetta_restype() const –> class std::shared_ptr<const class core::chemical::MutableResidueType>

get_vd_to_index(self: pyrosetta.rosetta.core.chemical.bcl.BCLFragmentHandler) → pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t

Get mapping of restype vertex descriptors to indices of the bcl fragments

C++: core::chemical::bcl::BCLFragmentHandler::get_vd_to_index() const –> const class core::chemical::AtomRefMapping<void *, unsigned long> &

set_nbr(self: pyrosetta.rosetta.core.chemical.bcl.BCLFragmentHandler, nbr: int) → None

Which atom in the fragment to use as the neighbor atom when the a restype is generated.

C++: core::chemical::bcl::BCLFragmentHandler::set_nbr(unsigned long) –> void

set_rosetta_restype(self: pyrosetta.rosetta.core.chemical.bcl.BCLFragmentHandler, restype: pyrosetta.rosetta.core.chemical.MutableResidueType) → None

Set the Rosetta molecule

C++: core::chemical::bcl::BCLFragmentHandler::set_rosetta_restype(class std::shared_ptr<const class core::chemical::MutableResidueType>) –> void

pyrosetta.rosetta.core.chemical.bcl.initialize_bcl_main() → None

Initialize core components of the bcl apps/apps.cpp

e.g. GetExecutablePath, etc.

C++: core::chemical::bcl::initialize_bcl_main() –> void

pyrosetta.rosetta.core.chemical.bcl.initialize_bcl_random(seed: int) → None

Initialize the BCL random number generator.

Note that seed is an int to match the seed generated in core/init.cc

C++: core::chemical::bcl::initialize_bcl_random(const int) –> void

pyrosetta.rosetta.core.chemical.bcl.initialize_bcl_tracers() → None

Initialize the BCL output levels with the Rosetta commandline settings

You can set the global BCL output by controlling the “BCL” tracer.

C++: core::chemical::bcl::initialize_bcl_tracers() –> void

pyrosetta.rosetta.core.chemical.bcl.locate_bcl() → None

Locate the BCL executable path within /main/source/externals/bcl

Required that we find the BCL submodule executable path so that we can set paths to the rotamer library and model directories; this is based obviously on the locate_database() function in init.cc with some extra logic and minor additional differences

C++: core::chemical::bcl::locate_bcl() –> void

pyrosetta.rosetta.core.chemical.bcl.require_bcl() → None

Utility function to print BCL usage details and then utility_exit

C++: core::chemical::bcl::require_bcl() –> void