MELT/Step2_DesignPyrosetta.py at main · izzetbiophysicist/MELT · GitHub

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#imports from pyrosetta
from mimetypes import init
from operator import pos
from pyrosetta import *
from pyrosetta.teaching import *
#from IPython.display import Image
#Core Includes
from rosetta.core.kinematics import MoveMap
from rosetta.core.kinematics import FoldTree
from rosetta.core.pack.task import TaskFactory
from rosetta.core.pack.task import operation
from rosetta.core.simple_metrics import metrics
from rosetta.core.select import residue_selector as selections
from rosetta.core import select
from rosetta.core.select.movemap import *
from rosetta.protocols import minimization_packing as pack_min
from rosetta.protocols import relax as rel
from rosetta.protocols.antibody.residue_selector import CDRResidueSelector
from rosetta.protocols.antibody import *
from rosetta.protocols.loops import *
from rosetta.protocols.relax import FastRelax
from pyrosetta.rosetta.protocols.docking import setup_foldtree
from pyrosetta.rosetta.protocols import *
from pyrosetta.rosetta.protocols.docking import setup_foldtree


import pandas as pd
import os
import random
import math

pyrosetta.init()

## Loads Pose and score
pose_controle = pose_from_pdb("desloc_7_plus.pdb")
scorefxn = pyrosetta.create_score_function("ref2015_cart.wts")
scorefxn(pose_controle)


def pack_relax(pose, scorefxn):
    """
    Perform a fast relaxation protocol on the given pose using PyRosetta's FastRelax.

    Parameters:
    - pose: PyRosetta Pose object
    - scorefxn: Score function to evaluate the energy of the structure

    Returns:
    None
    """
    tf = TaskFactory()
    tf.push_back(operation.InitializeFromCommandline())
    tf.push_back(operation.RestrictToRepacking())
    # Set up a MoveMapFactory
    mmf = pyrosetta.rosetta.core.select.movemap.MoveMapFactory()
    mmf.all_bb(setting=True)
    mmf.all_bondangles(setting=True)
    mmf.all_bondlengths(setting=True)
    mmf.all_chi(setting=True)
    mmf.all_jumps(setting=True)
    mmf.set_cartesian(setting=True)

    ## Print informations about structure before apply fast relax
    # display_pose = pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover()
    # display_pose.tasks(tf)
    # display_pose.movemap_factory(mmf)
    # display_pose.apply(pose)

    fr = pyrosetta.rosetta.protocols.relax.FastRelax(scorefxn_in=scorefxn, standard_repeats=1)
    fr.cartesian(True)
    fr.set_task_factory(tf)
    fr.set_movemap_factory(mmf)
    fr.min_type("lbfgs_armijo_nonmonotone")
    fr.apply(pose)
    return

def design(pose, scorefxn, chain):
    chain_D = pyrosetta.rosetta.core.pose.get_resnums_for_chain(pose, chain)
    chain_D = list(chain_D)

    mut_posi = pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector()
    mut_posi.set_index(str(chain_D[0])+"-"+str(chain_D[-1]))

    #### Print selected residues for mut posi
    print(pyrosetta.rosetta.core.select.get_residues_from_subset(mut_posi.apply(pose)))

    # Select Neighbor Position
    nbr_selector = pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector()
    nbr_selector.set_focus_selector(mut_posi)
    nbr_selector.set_include_focus_in_subset(True)
    print(pyrosetta.rosetta.core.select.get_residues_from_subset(nbr_selector.apply(pose)))

    # Select No Design Area
    not_design = pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector(mut_posi)
    #### Print residues to NOT design
    #print(pyrosetta.rosetta.core.select.get_residues_from_subset(not_design.apply(pose)))

    # The task factory accepts all the task operations
    tf = pyrosetta.rosetta.core.pack.task.TaskFactory()

    # These are pretty standard
    tf.push_back(pyrosetta.rosetta.core.pack.task.operation.InitializeFromCommandline())
    tf.push_back(pyrosetta.rosetta.core.pack.task.operation.IncludeCurrent())
    tf.push_back(pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides())

    # Disable Packing
    prevent_repacking_rlt = pyrosetta.rosetta.core.pack.task.operation.PreventRepackingRLT()
    prevent_subset_repacking = pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset(prevent_repacking_rlt, nbr_selector, True )
    tf.push_back(prevent_subset_repacking)

    # Disable design
    tf.push_back(pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset(
        pyrosetta.rosetta.core.pack.task.operation.RestrictToRepackingRLT(),not_design))

    # Enable design
    aa_to_design = pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAASRLT()
    aa_to_design.aas_to_keep("ACDEFHIKLMNQRGPSTVWY")
    tf.push_back(pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset(aa_to_design, mut_posi))

    # Create Packer
    packer = pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover(scorefxn)
    packer.task_factory(tf)

    mmf = pyrosetta.rosetta.core.select.movemap.MoveMapFactory()
    mmf.all_bb(setting=True)
    mmf.all_bondangles(setting=True)
    mmf.all_bondlengths(setting=True)
    mmf.all_chi(setting=True)
    mmf.all_jumps(setting=True)
    mmf.set_cartesian(setting=True)
    #### Apply fastrelax to pose
    fr = pyrosetta.rosetta.protocols.relax.FastRelax(scorefxn_in=scorefxn, standard_repeats=1)
    fr.cartesian(True)
    fr.set_task_factory(tf)
    fr.set_movemap_factory(mmf)
    fr.min_type("lbfgs_armijo_nonmonotone")
    packer.apply(pose)
    fr.apply(pose)
    return(pose)


pack_relax(pose_controle, scorefxn)
pose_controle.dump_pdb("desloc_7_relaxed.pdb")
design(pose_controle, scorefxn, "A")
pose_controle.dump_pdb("desloc_7_relaxed_designed.pdb")