pyrosetta¶
- pyrosetta._rosetta_database_from_env()¶
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.
- pyrosetta._is_interactive()¶
Determine if in an interactive context.
See: https://stackoverflow.com/questions/2356399/tell-if-python-is-in-interactive-mode
- pyrosetta.init(options='-ex1 -ex2aro', extra_options='', set_logging_handler=None, notebook=None, silent=False)¶
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
- pyrosetta._version_string()¶
- pyrosetta._build_signature()¶
- pyrosetta.version()¶
- pyrosetta._vector_extend_func(vec, othervec)¶
- pyrosetta.Vector1(list_in)¶
Creates a Vector1 object, deducing type from the given list.
- pyrosetta.Set(list_in)¶
Creates a std::set object, deducing type from the given list.
- pyrosetta.generate_nonstandard_residue_set(pose, params_list)¶
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()
- pyrosetta.standard_task_factory()¶
- pyrosetta.standard_packer_task(pose)¶
- class pyrosetta.CD(base, first, last, methods)¶
Bases:
tuple- _asdict()¶
Return a new dict which maps field names to their values.
- _field_defaults = {}¶
- _fields = ('base', 'first', 'last', 'methods')¶
- classmethod _make(iterable)¶
Make a new CD object from a sequence or iterable
- _replace(**kwds)¶
Return a new CD object replacing specified fields with new values
- base¶
Alias for field number 0
- count(value, /)¶
Return number of occurrences of value.
- first¶
Alias for field number 1
- index(value, start=0, stop=9223372036854775807, /)¶
Return first index of value.
Raises ValueError if the value is not present.
- last¶
Alias for field number 2
- methods¶
Alias for field number 3
- pyrosetta.defineEnergyMethodCreator(class_, scoreType)¶