FoldTree的不连续性¶

# 初始化pyrosetta，使用pyrosetta必须要做的一件事情
from pyrosetta import init, pose_from_pdb, pose_from_sequence
init()

#首先读取data文件中的PDB：1V74文件
pose = pose_from_pdb('./data/1v74.pdb')

# 输出该pose的FoldTree
print("PDB:1V74: ",pose.fold_tree())
print(f"The size of the foldtree (number of edges) is {pose.fold_tree().size()}") #Foldtree 的尺寸（edge的个数）
print(f"The number of the jump is {pose.fold_tree().num_jump()}") #Foldtree 的jump点的个数

from pyrosetta.rosetta.core.kinematics import FoldTree
# 完整定义试试:
ft = FoldTree() #设置一个空的foldtree对象
ft.add_edge(start=1, stop=107, label=-1)
ft.add_edge(start=108, stop=194, label=-1)
ft.add_edge(start=1, stop=108, label=1)  # add jump
ft.check_fold_tree()  # 检查foldtree的有效性;
print(ft)

from pyrosetta.rosetta.core.kinematics import FoldTree
# 完整定义试试:
ft = FoldTree() #设置一个空的foldtree对象
ft.add_edge(start=1, stop=107, label=-1)
ft.add_edge(start=1, stop=108, label=1)  # add jump
ft.add_edge(start=108, stop=194, label=-1)
ft.check_fold_tree()  # 检查foldtree的有效性;

# 答案
from pyrosetta.rosetta.core.kinematics import FoldTree
# 完整定义试试:
ft = FoldTree() #设置一个空的foldtree对象

# 正确答案:
ft.add_edge(start=1, stop=107, label=-1)
ft.add_edge(start=107, stop=108, label=1)  # add jump1
ft.add_edge(start=108, stop=157, label=-1)
ft.add_edge(start=88, stop=158, label=2)  # add jump2
ft.add_edge(start=158, stop=194, label=-1)
ft.check_fold_tree()  # 检查foldtree的有效性;

# demo for add a cutpoint
cutpoint_pose = pose_from_sequence('AAAAAAAAAA')
pose_foldtree = cutpoint_pose.fold_tree()
print(pose_foldtree)

#看对应pose中cutpoint的属性
print(f"The FoldTree of the Pose: {cutpoint_pose.fold_tree()}")
print(f"The number of the cutpoint in Pose is : {cutpoint_pose.fold_tree().num_cutpoint()}") #说明Pose的cutpoint只有一个
print(f"The cutpoint in Pose is : {cutpoint_pose.fold_tree().cutpoint(1)}") #说明Pose中的断点在5号残基处

# set phi3
cutpoint_pose.dump_pdb('./data/cutpoint_raw.pdb')
cutpoint_pose.set_phi(7, 69)
cutpoint_pose.set_psi(7, 60)
cutpoint_pose.dump_pdb('./data/cutpoint_pertuber.pdb')

# demo for add a cutpoint
cutpoint_pose = pose_from_sequence('AAAAAAAAAA')
pose_foldtree = cutpoint_pose.fold_tree()
pose_foldtree.new_jump(jump_pos1=5, jump_pos2=10, cutpoint=5)

#看对应pose中cutpoint的属性
print(f"The FoldTree of the Pose: {cutpoint_pose.fold_tree()}")
print(f"The number of the cutpoint in Pose is : {cutpoint_pose.fold_tree().num_cutpoint()}") #说明Pose的cutpoint只有一个
print(f"The cutpoint in Pose is : {cutpoint_pose.fold_tree().cutpoint(1)}") #说明Pose中的断点在5号残基处

from pyrosetta.rosetta.protocols.docking import setup_foldtree
from pyrosetta.rosetta.utility import vector1_int
# Docking FoldTree
#首先读取data文件中的PDB：1V74文件
pose = pose_from_pdb('./data/1v74.pdb')
print(pose.pdb_info())

# 默认设置可以在刚体中移动的jumps为1
movable_jumps_v = vector1_int()
movable_jumps_v.append(1)

# 设置foldtree
setup_foldtree(pose, partner_chainID='A_B', movable_jumps=movable_jumps_v)

print(pose.fold_tree())

# 创建序列Pose
pose = pose_from_sequence('AAAAAAAAAAAAAAAAAAAAAAAAAAA')
print(pose.pdb_info())

from pyrosetta.rosetta.protocols.loops import Loops, Loop, fold_tree_from_loops

# define loops;
loop_fold_tree = FoldTree()
loops = Loops()
loop = Loop(10, 20, 15)  # start_res, end_res, cut_res
loops.add_loop(loop)

# setup loop modelling foldtree;
fold_tree_from_loops(pose, loops, loop_fold_tree)
print(loop_fold_tree)
pose.fold_tree(loop_fold_tree)