PyRosetta Initiation

Basic Initiation

from pyrosetta import *
init 
# pyrosetta.rosetta.init() # We can pass in Rosetta commandlines here
#import pyrosetta
#pyrosetta.init

Multithreading

init(extra_options="-multithreading:total_threads 8 -multithreading:interaction_graph_threads 4") 
# `8` and `4` is the numbers of threads as an example
'''
init(-multithreading -total_threads <int>)
'''

Enabling Extra χ Sampling

init(-ex1 -ex2)

Linear Memory Interaction Graph

For speed, the Packer uses an “Interaction Graph” to cache the residue interaction energies. (See packing-options for command line options to control the packer.) Depending on the protocol you’re using, maintaining this interaction graph can account for a considerable amount of time and memory. As such, different interaction graphs (IG) are available.

• The default interaction graph (the Pairwise Decomposable Interaction Graph) is good for general repacking applications.
• For design, the Linear Memory Interaction Graph (-linmem_ig) reduces both the memory and runtime over the default interaction graph
• The Lazy Interaction Graph (-lazy_ig) is in all cases faster than the Linear Memory Interaction Graph, but at the cost of more memory usage.
• The Double Lazy Interaction Graph (-double_lazy_ig) is only useful for multistate design.

-linmem_ig behaves as a boolean. If the flag is passed, it activates use of LinearMemoryInteractionGraph (as it should). The value passed to the flag is supposed to control how much memory is used in the linmem_ig, but it does not; it is hardcoded (I think to an effective value of 10).

init(-linmem_ig 10)

Mute/Unmute outputs from Tracer channel

All output messages have channel + priority level assign to them. User can dynamically, in run time specify command line options to mute/unmute specific/all channels and to change level of output.

init(-mute core.select.residue_selector.SecondaryStructureSelector) 
# Mute specified Tracer channels; specify 'all' to mute all channels.

init(-unmute core.select.residue_selector.SecondaryStructureSelector)
# Unmute specified Tracer channels; specify 'all' to mute all channels.

Resources

https://docs.rosettacommons.org/docs/latest/full-options-list