# mixin classes are private
from ._init import BlueprinterInit as _Init
from ._common import BlueprinterCommon as _Common
from ._subscripted import BlueprinterSubscripted as _Subscripted
from ._expected import BlueprinterExpected as _Expected
from ._remodel import Remodel as _Remodel
from ._pdb_info import BlueCopier as _Copier
# public
from ._pdb_info import ResInfo
[docs]class Blueprinter(_Init, _Subscripted, _Common, _Expected, _Remodel, _Copier):
"""
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`
"""
ResInfo = ResInfo
# ========= init ===========================
# from BlueprinterInit
# adding init and classmethods
# ========= subscripted ===========================
# from BlueprinterSubscripted
# adds subscription methods
# === common operations =============================================
# from BlueprinterCommon
# adds some common tasks
# === expected =============================================
# from BlueprinterExpected
# adds expected_seq dynamic property