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Rosetta
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Namespaces | |
| bindings | |
| distributed | |
| io | |
| logging_support | |
| mpi | |
| network | |
| numeric | |
| protocols | |
| PyMOLRosettaServer | |
| teaching | |
| tests | |
| toolbox | |
| utility | |
Classes | |
| class | PyRosettaException |
| Exception handling. More... | |
| class | PythonPyExitCallback |
| class | EnergyMethod |
Functions | |
| def | _rosetta_database_from_env () |
| def | _is_interactive () |
| def | init (options='-ex1 -ex2aro', extra_options='', set_logging_handler=None, notebook=None, silent=False) |
| def | _version_string () |
| def | version () |
| def | _vector_extend_func (vec, othervec) |
| Vector compatibility: Adding 'extend' to all utility.vector* functions. More... | |
| def | Vector1 (list_in) |
| def | Set (list_in) |
| def | generate_nonstandard_residue_set (pose, params_list) |
| New methods. More... | |
| def | standard_task_factory () |
| def | standard_packer_task (pose) |
| def | defineEnergyMethodCreator (class_, scoreType) |
Variables | |
| vector1_string | |
| list_std_shared_ptr_core_pack_task_operation_TaskOperation_std_allocator_std_shared_ptr_core_pack_task_operation_TaskOperation_t | |
| vector_std_vector_double_std_allocator_double_t | |
| set_std_string_std_less_std_string_std_allocator_std_string_t | |
| logger = logging.getLogger("pyrosetta.rosetta") | |
| extend | |
| list | _mem_EnergyMethods_ = [] |
| Decorator generation for custom PyRosetta energy methods. More... | |
| list | _mem_EnergyCreators_ = [] |
| CD = namedtuple("CD", "base first last methods") | |
| list | _ScoreTypesRegistryByType_ |
| dictionary | ScoreTypesRegistry = {} |
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private |
Determine if in an interactive context. See: https://stackoverflow.com/questions/2356399/tell-if-python-is-in-interactive-mode
Referenced by init(), and pyrosetta.distributed.maybe_init().
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Read rosetta database directory from environment or standard install locations. Database resolution proceeds by first searching the current installation for a 'database' or 'rosetta_database' path. If not found the search then continues to the users's home dir, cygwin, and osx standard installation locations. Returns database path if found, else None.
Referenced by init().
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Vector compatibility: Adding 'extend' to all utility.vector* functions.
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References join().
Referenced by pyrosetta.distributed.cluster.converters._parse_pyrosetta_build(), and version().
| def pyrosetta.defineEnergyMethodCreator | ( | class_, | |
| scoreType | |||
| ) |
| def pyrosetta.generate_nonstandard_residue_set | ( | pose, | |
| params_list | |||
| ) |
New methods.
Places the ResidueTypes corresponding to a list of .params filenames into a given pose
.params files must be generated beforehand. Typically, one would obtain a
molfile (.mdl) generated from the xyz coordinates of a residue, small
molecule, or ion. The script molfile_to_params.py can be used to convert
to a Rosetta-readable .params file. It can be found in the /test/tools
folder of your PyRosetta installation or downloaded from the Rosetta
Commons.
Example:
params = ["penicillin.params", "amoxicillin.params"]
pose = Pose()
generate_nonstandard_residue_set(pose, params)
pose_from_file(pose, "TEM-1_with_substrates.pdb")
See also:
ResidueTypeSet
Vector1()
pose_from_file()
References Vector1().
| def pyrosetta.init | ( | options = '-ex1 -ex2aro', |
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extra_options = '', |
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set_logging_handler = None, |
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notebook = None, |
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silent = False |
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| ) |
Initialize Rosetta. Includes core data and global options.
options string with default Rosetta command-line options args.
(default: '-ex1 -ex2aro')
kwargs -
extra_options - Extra command line options to pass rosetta init.
(default None)
set_logging_handler - Route rosetta tracing through logging logger 'rosetta':
None - Set handler if interactive, otherwise not.
False - Write logs via c++-level filehandles.
"interactive" - Register python log handling and make visible if not.
"logging" - Register python log handling, do not update logging config.
True - Register python log handling, make visible if logging isn't configured.
Examples:
init() # uses default flags
init(extra_options='-pH') # adds flags to supplement the default
init('-pH -database /home/me/pyrosetta/rosetta_database') # overrides default flags - be sure to include the dB last
References _is_interactive(), _rosetta_database_from_env(), pyrosetta.protocols.h5_fragment_store_provider.init_H5FragmentStoreProvider(), pyrosetta.protocols.h5_structure_store_provider.init_H5StructureStoreProvider(), print(), and version().
Referenced by pyrosetta.toolbox.load_ligand.add_cid_to_database(), pyrosetta.tests.distributed.cluster.skip_cloudpickle_version.main(), pyrosetta.distributed.maybe_init(), pyrosetta.mpi.mpi_init(), pyrosetta.tests.bindings.core.test_pose.TestPoseCacheAccessor.setUpClass(), test.T010_LoadPDB.LoadPDBTest.setUpClass(), and test.T300_PyJobDistributor.TestPyJobDistributor.setUpClass().
| def pyrosetta.Set | ( | list_in | ) |
Creates a std::set object, deducing type from the given list.
References all, str(), and predPRE.t.
Referenced by operator>>().
| def pyrosetta.standard_packer_task | ( | pose | ) |
References standard_task_factory().
Referenced by pyrosetta.toolbox.mutants.mutate_residue(), demo.D090_Ala_scan.mutate_residue(), demo.D050_Packer_task.packer_task(), demo.D070_Refinement.sample_refinement(), pyrosetta.tests.distributed.cluster.test_reproducibility.TestReproducibilityMulti.test_reproducibility_from_reproduce(), pyrosetta.tests.distributed.cluster.test_reproducibility.TestReproducibility.test_reproducibility_packer_nstruct(), pyrosetta.tests.distributed.cluster.test_reproducibility.TestReproducibilityMulti.test_reproducibility_packer_nstruct_multi(), pyrosetta.tests.distributed.cluster.test_reproducibility.TestReproducibilityMulti.test_reproducibility_packer_nstruct_multi_decoy_ids(), and pyrosetta.tests.distributed.cluster.test_reproducibility.TestReproducibility.test_reproducibility_packer_separate().
| def pyrosetta.standard_task_factory | ( | ) |
Referenced by demo.D090_Ala_scan.calc_binding_energy(), and standard_packer_task().
| def pyrosetta.Vector1 | ( | list_in | ) |
Creates a Vector1 object, deducing type from the given list.
References all, str(), and predPRE.t.
Referenced by generate_nonstandard_residue_set(), pyrosetta.toolbox.mutants.mutate_residue(), pyrosetta.toolbox.load_ligand.pose_from_params(), demo.D110_DNA_interface.sample_dna_interface(), demo.D100_Docking.sample_docking(), demo.D120_Ligand_interface.sample_ligand_interface(), and demo.D090_Ala_scan.scanning().
| def pyrosetta.version | ( | ) |
References _version_string(), and binder.split().
Referenced by pyrosetta.utility.get_package_version(), init(), and test.T010_LoadPDB.LoadPDBTest.setUpClass().
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private |
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private |
Decorator generation for custom PyRosetta energy methods.
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private |
| pyrosetta.CD = namedtuple("CD", "base first last methods") |
| pyrosetta.extend |
| pyrosetta.list_std_shared_ptr_core_pack_task_operation_TaskOperation_std_allocator_std_shared_ptr_core_pack_task_operation_TaskOperation_t |
| pyrosetta.logger = logging.getLogger("pyrosetta.rosetta") |
| dictionary pyrosetta.ScoreTypesRegistry = {} |
| pyrosetta.set_std_string_std_less_std_string_std_allocator_std_string_t |
| pyrosetta.vector1_string |
| pyrosetta.vector_std_vector_double_std_allocator_double_t |
1.9.1