pyrosetta

• bindings
• io
• logging_support
• method_bindings
• mpi
• teaching
• toolbox
• util

class pyrosetta.CD(**entries)

Bases: object

Class to represent named tuples.

class pyrosetta.EnergyMethod(scoreName=None, scoreType=None, version=1)

Bases: object

Decorator function for custom EnergyMethods in PyRosetta.

pyrosetta.Set(list_in)

Creates a std::set object, deducing type from the given list.

pyrosetta.Vector1(list_in)

Creates a Vector1 object, deducing type from the given list.

pyrosetta._is_interactive()

Determine if in an interactive context.

See: https://stackoverflow.com/questions/2356399/tell-if-python-is-in-interactive-mode

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.dump_atom_pair_energy_table(sfxn, score_type, residue_1, residue_2, output_filename)

Usage: dump_atom_pair_energy_table(sfxn, score_type, residue_1, residue_2, output_filename)

Description: dumps a csv formatted table (saved as “output_filename”) of all pairwise atom pair energies for the complete list of atoms contained by residue_1 and residue_2 using a specified score_type in the provided sfxn.

pyrosetta.dump_residue_pair_energies(res, pose, sfxn, score_type, output_filename)

Usage: dump_residue_pair_energies(res, pose, sfxn, score_type, output_filename)

Description: dumps a csv formatted table (saved as “output_filename”) of the interactions of a single residue (res) with all other residues in the specified pose using a specified score_type in the provided sfxn.

pyrosetta.etable_atom_pair_energies(res1, atom_index_1, res2, atom_index_2, sfxn)

Usage: lj_atr, lj_rep, solv=etable_atom_pair_energies(res1, atom_index_1, res2, atom_index_2, sfxn)

Description: given a pair of atoms (specified using a pair of residue objects and atom indices) and scorefunction, use the precomputed ‘etable’ to return LJ attractive, LJ repulsive, and LK solvation energies

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.init(options='-ex1 -ex2aro', extra_options='', set_logging_handler=None, notebook=None)

Initialize Rosetta. Includes core data and global options.

options string with default Rosetta command-line options args.

(default: ‘-ex1 -ex2aro’)

kargs -

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.output_scorefile(pose, pdb_name, current_name, scorefilepath, scorefxn, nstruct, native_pose=None, additional_decoy_info=None)

Moved from PyJobDistributor (Jared Adolf-Bryfogle) Creates a scorefile if none exists, or appends the current one. Calculates and writes CA_rmsd if native pose is given, as well as any additional decoy info

pyrosetta.print_atom_pair_energy_table(sfxn, score_type, residue_1, residue_2, threshold)

Usage: print_atom_pair_energy_table(sfxn, score_type, residue_1, residue_2, threshold)

Description: outputs a formatted table to the commandline of all pairwise atom pair energies for the complete list of atoms contained by residue_1 and residue_2 using a specified score_type in the provided sfxn. Only interactions with an absolute value energy above the threshold are printed

pyrosetta.print_residue_pair_energies(res, pose, sfxn, score_type, threshold)

Usage: print_residue_pair_energies(res, pose, sfxn, score_type, threshold)

Description: outputs a formatted table to the commandline of the interactions of a single residue (res) with all other residues in the specified pose using a specified score_type in the provided sfxn. Only interactions with an absolute value energy above the threshold are printed

pyrosetta.rrange(n)

Return an iterator from 1 to n inclusive