pyrosetta_help.blueprint_maker package
Module contents
- class pyrosetta_help.blueprint_maker.Blueprinter(seq: str, ss: str | None = None)[source]
Bases:
BlueprinterInit
,BlueprinterSubscripted
,BlueprinterCommon
,BlueprinterExpected
,Remodel
,BlueCopier
Make a blueprint file for Rosetta Remodel and load it into the options (
.set(fn)
). The rows property is a list of lists, this is what the operations manipulate. Where each row is something like [20, ‘G’, ‘.’] subscript assignment allows the 4th field to be altered. The SS is based on the pose..from_pose(pose)
initialises it from pose, while the reg. init is from sequence and ss.
Whereas
.del_span(10, 29)
deletes a span.wobble_span(100, 105)
wobbles a span (NATAA).mutate(5, 'W')
mutates resi i to aa.insert(3, 'PIKAA W')
or.insert(3, ['PIKAA W', 'PIKAA A'])
inserts.
a more flexible approach is using subscripts and slices:
>>> blue = Blueprinter.from_pose(pose) >>> blue[10:14] = 'NATAA' # preceding loop >>> del blue[15:20] >>> blue[20:25] = 'NATAA' # following loop >>> blue[22] = 'PIKAA W'
blue.set(bluprint_filename)
remember that if remodelmover is already initialised to call
rm.register_options()
About the subscript setter, there are three (weird) things to note:
A star will be convered into the native amino acid. PIKAA F*CK on a glutamine, will result in PIKAA FECK
The ranges are human style: deletion of resi 10-15 means that 6 residues are missing, including 15. Where normally in python 10:15 is 5, 15 is excluded.
The value is a string but there are no safegards or checks, even if there are a limited amount of possibilities and it would be really nice seeing if the non-canonical for EMPTY NC XAA
- class ResInfo(number: int, chain: str, icode: str = ' ', segmentID: str = ' ')
Bases:
object
- __init__(number: int, chain: str, icode: str = ' ', segmentID: str = ' ')
- classmethod get(index: int)
- pdb_info = None
pdb_info: pyrosetta.rosetta.core.pose.PDBInfo
- set(index: int, pdb_info: PDBInfo | None = None)