Notebook

Pose Operation¶

@Author: 吴炜坤

@email：weikun.wu@xtalpi.com weikunwu@163.com

Pose中储存了非常多的信息，同时还提供了接口可以让用户方便的对其中的信息进行修改（采样）。本章节将着重介绍Pose的基本操作方式。

In [1]:

# 首先依然是从PDB中读入Pose
from pyrosetta import init, pose_from_pdb
init()
pose = pose_from_pdb('./data/4R80.clean.pdb')

PyRosetta-4 2021 [Rosetta PyRosetta4.conda.mac.cxx11thread.serialization.python37.Release 2021.31+release.c7009b3115c22daa9efe2805d9d1ebba08426a54 2021-08-07T10:04:12] retrieved from: http://www.pyrosetta.org
(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.
core.init: {0} Checking for fconfig files in pwd and ./rosetta/flags
core.init: {0} Rosetta version: PyRosetta4.conda.mac.cxx11thread.serialization.python37.Release r292 2021.31+release.c7009b3115c c7009b3115c22daa9efe2805d9d1ebba08426a54 http://www.pyrosetta.org 2021-08-07T10:04:12
core.init: {0} command: PyRosetta -ex1 -ex2aro -database /opt/miniconda3/lib/python3.7/site-packages/pyrosetta/database
basic.random.init_random_generator: {0} 'RNG device' seed mode, using '/dev/urandom', seed=-1249606663 seed_offset=0 real_seed=-1249606663 thread_index=0
basic.random.init_random_generator: {0} RandomGenerator:init: Normal mode, seed=-1249606663 RG_type=mt19937
core.chemical.GlobalResidueTypeSet: {0} Finished initializing fa_standard residue type set.  Created 983 residue types
core.chemical.GlobalResidueTypeSet: {0} Total time to initialize 0.695115 seconds.
core.import_pose.import_pose: {0} File './data/4R80.clean.pdb' automatically determined to be of type PDB
core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OXT on residue SER:CtermProteinFull 76
core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OXT on residue SER:CtermProteinFull 152

一、 Pose的创建和复制¶

前几节中提及过，pose是一个容器，理所当然我们可以创建一个空的容器，里面什么都不放。
很多时候，我们需要创建空的Pose对象，便于保存当前pose的实例化状态，可作为可回溯点或初始状态，方便反复调用。

In [2]:

# 通过创建一个新的Pose
from pyrosetta import Pose
copy_pose1 = Pose()
copy_pose2 = None

此处通过两种方法，将已有的Pose信息放入新的容器里，一种是通过assign函数复制，一种是通过python赋值符号来赋值。

In [3]:

# 方法1：通过assign复制新的构象
copy_pose1.assign(pose)

# 方法2：通过python的直接赋值符号
copy_pose2 = pose

print(copy_pose1)
print('\n')
print(copy_pose2)

PDB file name: ./data/4R80.clean.pdb
Total residues: 152
Sequence: PSEEEEKRRAKQVAKEKILEQNPSSKVQVRRVQKQGNTIRVELEITENGKKTNITVEVEKQGNTFTVKRITETVGSPSEEEEKRRAKQVAKEKILEQNPSSKVQVRRVQKQGNTIRVELEITENGKKTNITVEVEKQGNTFTVKRITETVGS
Fold tree:
FOLD_TREE  EDGE 1 76 -1  EDGE 1 77 1  EDGE 77 152 -1 


PDB file name: ./data/4R80.clean.pdb
Total residues: 152
Sequence: PSEEEEKRRAKQVAKEKILEQNPSSKVQVRRVQKQGNTIRVELEITENGKKTNITVEVEKQGNTFTVKRITETVGSPSEEEEKRRAKQVAKEKILEQNPSSKVQVRRVQKQGNTIRVELEITENGKKTNITVEVEKQGNTFTVKRITETVGS
Fold tree:
FOLD_TREE  EDGE 1 76 -1  EDGE 1 77 1  EDGE 77 152 -1

可见，两种方式“看”起来里面都有了新的pose信息。但真的如此么？

In [4]:

# 尝试调整初始pose中的24号氨基酸phi值:
pose.set_phi(24, 170.0)

# 查看对starting_pose以及starting_pose2的影响:
print(f'copy_pose1 24 residue phi:{copy_pose1.phi(24)}')
print(f'copy_pose2 24 residue phi:{copy_pose2.phi(24)}')

copy_pose1 24 residue phi:-91.24043946940483
copy_pose2 24 residue phi:170.0

结果表明:

copy_pose2是用过python直接赋值的Pose并没有复制，而只是pose的一个"超链接"符，并没有进行"复制"的操作。
copy_pose1通过assign的复制，原始的pose的任何调整都没有对copy_pose1造成任何的影响，可见其独立性。

二、链与氨基酸操作¶

先前章节中描述的都是对蛋白质的几何空间做参数的调整，而并不涉及到拓扑结构的改变。在PyRosetta中，对蛋白的结构域进行修改本质上就是对氨基酸的插入和删除。

2.1 Pose中链的顺序交换¶

In [5]:

# 链交换, 注意链号会变成AB.
from pyrosetta.rosetta.protocols.simple_moves import SwitchChainOrderMover
exchange_pose = pose_from_pdb('./data/6LZ9_H_L.pdb')
print(exchange_pose.pdb_info())

core.import_pose.import_pose: {0} File './data/6LZ9_H_L.pdb' automatically determined to be of type PDB
core.conformation.Conformation: {0} Found disulfide between residues 21 94
core.conformation.Conformation: {0} current variant for 21 CYS
core.conformation.Conformation: {0} current variant for 94 CYS
core.conformation.Conformation: {0} current variant for 21 CYD
core.conformation.Conformation: {0} current variant for 94 CYD
core.conformation.Conformation: {0} Found disulfide between residues 141 206
core.conformation.Conformation: {0} current variant for 141 CYS
core.conformation.Conformation: {0} current variant for 206 CYS
core.conformation.Conformation: {0} current variant for 141 CYD
core.conformation.Conformation: {0} current variant for 206 CYD
PDB file name: ./data/6LZ9_H_L.pdb
 Pose Range  Chain    PDB Range  |   #Residues         #Atoms

0001 -- 0081    H 0002  -- 0082  |   0081 residues;    01283 atoms
0082 -- 0082    H 0082A -- 0082A |   0001 residues;    00011 atoms
0083 -- 0083    H 0082B -- 0082B |   0001 residues;    00011 atoms
0084 -- 0084    H 0082C -- 0082C |   0001 residues;    00019 atoms
0085 -- 0102    H 0083  -- 0100  |   0018 residues;    00271 atoms
0103 -- 0103    H 0100A -- 0100A |   0001 residues;    00010 atoms
0104 -- 0104    H 0100B -- 0100B |   0001 residues;    00021 atoms
0105 -- 0105    H 0100C -- 0100C |   0001 residues;    00021 atoms
0106 -- 0106    H 0100D -- 0100D |   0001 residues;    00010 atoms
0107 -- 0107    H 0100E -- 0100E |   0001 residues;    00017 atoms
0108 -- 0119    H 0101  -- 0112  |   0012 residues;    00171 atoms
0120 -- 0223    L 0002  -- 0105  |   0104 residues;    01588 atoms
                           TOTAL |   0223 residues;    03433 atoms

In [6]:

switch_chains = SwitchChainOrderMover()
switch_chains.chain_order("LH")
switch_chains.apply(exchange_pose)
print(exchange_pose.pdb_info())

core.scoring.ScoreFunctionFactory: {0} SCOREFUNCTION: ref2015
core.scoring.etable: {0} Starting energy table calculation
core.scoring.etable: {0} smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: {0} smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: {0} smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: {0} Finished calculating energy tables.
basic.io.database: {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv
basic.io.database: {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv
basic.io.database: {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv
basic.io.database: {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv
basic.io.database: {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv
basic.io.database: {0} Database file opened: scoring/score_functions/rama/fd/all.ramaProb
basic.io.database: {0} Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb
basic.io.database: {0} Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt
basic.io.database: {0} Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt
basic.io.database: {0} Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt
basic.io.database: {0} Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt
basic.io.database: {0} Database file opened: scoring/score_functions/P_AA_pp/P_AA
basic.io.database: {0} Database file opened: scoring/score_functions/P_AA_pp/P_AA_n
core.scoring.P_AA: {0} shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.
basic.io.database: {0} Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop
protocols.simple_moves.SwitchChainOrderMover: {0} Number of chains in pose: 2
protocols.simple_moves.SwitchChainOrderMover: {0} Now at chain: 2
protocols.simple_moves.SwitchChainOrderMover: {0} Now at chain: 1
core.conformation.Conformation: {0} Found disulfide between residues 22 87
core.conformation.Conformation: {0} current variant for 22 CYD
core.conformation.Conformation: {0} current variant for 87 CYD
core.conformation.Conformation: {0} current variant for 22 CYD
core.conformation.Conformation: {0} current variant for 87 CYD
core.conformation.Conformation: {0} Found disulfide between residues 125 198
core.conformation.Conformation: {0} current variant for 125 CYD
core.conformation.Conformation: {0} current variant for 198 CYD
core.conformation.Conformation: {0} current variant for 125 CYD
core.conformation.Conformation: {0} current variant for 198 CYD
basic.io.database: {0} Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: {0} Read 40 countpair representative atoms
core.pack.dunbrack.RotamerLibrary: {0} shapovalov_lib_fixes_enable option is true.
core.pack.dunbrack.RotamerLibrary: {0} shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.
core.pack.dunbrack.RotamerLibrary: {0} Binary rotamer library selected: /opt/miniconda3/lib/python3.7/site-packages/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin
core.pack.dunbrack.RotamerLibrary: {0} Using Dunbrack library binary file '/opt/miniconda3/lib/python3.7/site-packages/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.
core.pack.dunbrack.RotamerLibrary: {0} Dunbrack 2010 library took 0.181558 seconds to load from binary
protocols.simple_moves.SwitchChainOrderMover: {0} New pose's foldtree FOLD_TREE  EDGE 1 104 -1  EDGE 1 105 1  EDGE 105 223 -1
PDB file name: 
 Pose Range  Chain    PDB Range  |   #Residues         #Atoms

0001 -- 0104    A 0001  -- 0104  |   0104 residues;    01588 atoms
0105 -- 0223    B 0105  -- 0223  |   0119 residues;    01845 atoms
                           TOTAL |   0223 residues;    03433 atoms

注意，这种方法虽然可以进行链交换，但是其中的PDB_info被强制更新为A链和B链了，如果需要保留原有的PDB信息系统，就不应该用这种快捷修改的方式！

2.2 Pose中链的删除¶

Pose中的链是可以被整条删除的。（反之也可以添加）

In [7]:

# 链删除
from pyrosetta.rosetta.protocols.simple_moves import DeleteChainMover
delete_chain = DeleteChainMover()
delete_chain.chain_num(1)
delete_chain.apply(pose)
print(pose.pdb_info())

protocols.simple_moves.DeleteChainMover: {0} Removing chain 1 from pose with 2 chains
PDB file name: ./data/4R80.clean.pdb
 Pose Range  Chain    PDB Range  |   #Residues         #Atoms

0001 -- 0076    B 0001  -- 0076  |   0076 residues;    01251 atoms
                           TOTAL |   0076 residues;    01251 atoms

可见A链已经在Pose中消失，而B链还存在。

2.3 Pose中链的索引分离¶

尽管pose的氨基酸编号是忽略多肽链的分隔的，pose中的链依然是根据多肽链的物理结构进行编号的，同理也是从1开始编号。如一个蛋白中有2条链A和B，那么链编号结果即为1和2。其中A对应1号链，B对应2号链，与PDB的链顺序有关（当然A链的顺序如果在后面，那么B链就是1号链）。 Pose类中许多的方法可以很方便对链的增减进行操作, 以下2个举例进行说明:

In [8]:

# 将Pose按照链的数量进行切割
pose = pose_from_pdb('./data/6LZ9_H_L.pdb')
pose_list = pose.split_by_chain()
pose_list

core.import_pose.import_pose: {0} File './data/6LZ9_H_L.pdb' automatically determined to be of type PDB
core.conformation.Conformation: {0} Found disulfide between residues 21 94
core.conformation.Conformation: {0} current variant for 21 CYS
core.conformation.Conformation: {0} current variant for 94 CYS
core.conformation.Conformation: {0} current variant for 21 CYD
core.conformation.Conformation: {0} current variant for 94 CYD
core.conformation.Conformation: {0} Found disulfide between residues 141 206
core.conformation.Conformation: {0} current variant for 141 CYS
core.conformation.Conformation: {0} current variant for 206 CYS
core.conformation.Conformation: {0} current variant for 141 CYD
core.conformation.Conformation: {0} current variant for 206 CYD
core.conformation.Conformation: {0} Found disulfide between residues 21 94
core.conformation.Conformation: {0} current variant for 21 CYD
core.conformation.Conformation: {0} current variant for 94 CYD
core.conformation.Conformation: {0} current variant for 21 CYD
core.conformation.Conformation: {0} current variant for 94 CYD
core.conformation.Conformation: {0} Found disulfide between residues 22 87
core.conformation.Conformation: {0} current variant for 22 CYD
core.conformation.Conformation: {0} current variant for 87 CYD
core.conformation.Conformation: {0} current variant for 22 CYD
core.conformation.Conformation: {0} current variant for 87 CYD

Out[8]:

vector1_std_shared_ptr_core_pose_Pose_t[0x7ff14f8106a8, 0x7ff14e6a6a18]

此处的pose_list中存放了2个数据，说明链已经被切割成2个独立的pose对象了。

通过python的索引，可以获得具体的pose:

In [9]:

# 获取只含有第一个链的pose
chain1_pose = pose.split_by_chain()[1]  # 直接切片索引链号。
chain2_pose = pose.split_by_chain()[2]  # 直接切片索引链号。

# check
print(chain1_pose.pdb_info())
print(chain2_pose.pdb_info())

core.conformation.Conformation: {0} Found disulfide between residues 21 94
core.conformation.Conformation: {0} current variant for 21 CYD
core.conformation.Conformation: {0} current variant for 94 CYD
core.conformation.Conformation: {0} current variant for 21 CYD
core.conformation.Conformation: {0} current variant for 94 CYD
core.conformation.Conformation: {0} Found disulfide between residues 22 87
core.conformation.Conformation: {0} current variant for 22 CYD
core.conformation.Conformation: {0} current variant for 87 CYD
core.conformation.Conformation: {0} current variant for 22 CYD
core.conformation.Conformation: {0} current variant for 87 CYD
core.conformation.Conformation: {0} Found disulfide between residues 21 94
core.conformation.Conformation: {0} current variant for 21 CYD
core.conformation.Conformation: {0} current variant for 94 CYD
core.conformation.Conformation: {0} current variant for 21 CYD
core.conformation.Conformation: {0} current variant for 94 CYD
core.conformation.Conformation: {0} Found disulfide between residues 22 87
core.conformation.Conformation: {0} current variant for 22 CYD
core.conformation.Conformation: {0} current variant for 87 CYD
core.conformation.Conformation: {0} current variant for 22 CYD
core.conformation.Conformation: {0} current variant for 87 CYD
PDB file name: ./data/6LZ9_H_L.pdb
 Pose Range  Chain    PDB Range  |   #Residues         #Atoms

0001 -- 0081    H 0002  -- 0082  |   0081 residues;    01283 atoms
0082 -- 0082    H 0082A -- 0082A |   0001 residues;    00011 atoms
0083 -- 0083    H 0082B -- 0082B |   0001 residues;    00011 atoms
0084 -- 0084    H 0082C -- 0082C |   0001 residues;    00019 atoms
0085 -- 0102    H 0083  -- 0100  |   0018 residues;    00271 atoms
0103 -- 0103    H 0100A -- 0100A |   0001 residues;    00010 atoms
0104 -- 0104    H 0100B -- 0100B |   0001 residues;    00021 atoms
0105 -- 0105    H 0100C -- 0100C |   0001 residues;    00021 atoms
0106 -- 0106    H 0100D -- 0100D |   0001 residues;    00010 atoms
0107 -- 0107    H 0100E -- 0100E |   0001 residues;    00017 atoms
0108 -- 0119    H 0101  -- 0112  |   0012 residues;    00171 atoms
                           TOTAL |   0119 residues;    01845 atoms

PDB file name: ./data/6LZ9_H_L.pdb
 Pose Range  Chain    PDB Range  |   #Residues         #Atoms

0001 -- 0104    L 0002  -- 0105  |   0104 residues;    01588 atoms
                           TOTAL |   0104 residues;    01588 atoms

2.4 Pose链的合并或延伸¶

除了索引操作，用户还可以通过一些简单的方式把链合并到一个pose中，此处使用append_pose_to_pose函数就可以达到目的。但需要注意，pose中的氨基酸、链的数量变化后，都需要对PDBinfo进行更新。否则PDBinfo的信息与Pose信息不对称。

添加新的链

In [10]:

# 将chain2加载到chain1 pose的最后一个氨基酸的后面。
chain1_pose_last_residue = chain1_pose.total_residue()
chain1_pose.append_pose_by_jump(chain2_pose, jump_anchor_residue=chain1_pose_last_residue)
chain1_pose.update_residue_neighbors()
chain1_pose.update_pose_chains_from_pdb_chains()
chain1_pose.conformation().detect_disulfides()

core.conformation.Conformation: {0} Found disulfide between residues 21 94
core.conformation.Conformation: {0} current variant for 21 CYD
core.conformation.Conformation: {0} current variant for 94 CYD
core.conformation.Conformation: {0} current variant for 21 CYD
core.conformation.Conformation: {0} current variant for 94 CYD
core.conformation.Conformation: {0} Found disulfide between residues 141 206
core.conformation.Conformation: {0} current variant for 141 CYD
core.conformation.Conformation: {0} current variant for 206 CYD
core.conformation.Conformation: {0} current variant for 141 CYD
core.conformation.Conformation: {0} current variant for 206 CYD

In [11]:

print(chain1_pose.pdb_info())

# 检查Pose的PDB_info是否是奇怪的:
print(f'PDBinfo是否需要被更新:{chain1_pose.pdb_info().obsolete()}')

PDB file name: ./data/6LZ9_H_L.pdb
 Pose Range  Chain    PDB Range  |   #Residues         #Atoms

0001 -- 0081    H 0002  -- 0082  |   0081 residues;    01283 atoms
0082 -- 0082    H 0082A -- 0082A |   0001 residues;    00011 atoms
0083 -- 0083    H 0082B -- 0082B |   0001 residues;    00011 atoms
0084 -- 0084    H 0082C -- 0082C |   0001 residues;    00019 atoms
0085 -- 0102    H 0083  -- 0100  |   0018 residues;    00271 atoms
0103 -- 0103    H 0100A -- 0100A |   0001 residues;    00010 atoms
0104 -- 0104    H 0100B -- 0100B |   0001 residues;    00021 atoms
0105 -- 0105    H 0100C -- 0100C |   0001 residues;    00021 atoms
0106 -- 0106    H 0100D -- 0100D |   0001 residues;    00010 atoms
0107 -- 0107    H 0100E -- 0100E |   0001 residues;    00017 atoms
0108 -- 0119    H 0101  -- 0112  |   0012 residues;    00171 atoms
0120 -- 0223    L 0002  -- 0105  |   0104 residues;    01588 atoms
                           TOTAL |   0223 residues;    03433 atoms

PDBinfo是否需要被更新:True

In [12]:

# update pdbinfo; 别忘了更新pdbinfo;
from pyrosetta.rosetta.core.pose import renumber_pdbinfo_based_on_conf_chains
renumber_pdbinfo_based_on_conf_chains(chain1_pose)
print(f'PDBinfo是否需要被更新:{chain1_pose.pdb_info().obsolete()}')

PDBinfo是否需要被更新:False

In [13]:

# 如果你非常确定，新的pose中不会有PDB的编号冲突等问题。可以直接修改obsolete的检查结果:
chain1_pose.pdb_info().obsolete(False)

合并为一条多肽链的case

In [14]:

# 链的延伸; 合并成一条链的意思;
from pyrosetta.rosetta.core.pose import append_pose_to_pose
pose = pose_from_pdb('./data/6LZ9_H_L.pdb')
chain1_pose = pose.split_by_chain()[1]
chain2_pose = pose.split_by_chain()[2]

new_chain = False
combine_pose = Pose()
combine_pose.assign(chain1_pose)
append_pose_to_pose(combine_pose, chain2_pose, new_chain)

# update pdbinfo; 别忘了更新pdbinfo;
renumber_pdbinfo_based_on_conf_chains(combine_pose)

print(f'append之后的chain1_pose中的氨基酸总数:{combine_pose.total_residue()}')
combine_pose.sequence()
print(f'append之后chain的总数:{combine_pose.num_chains()}')
print(combine_pose.pdb_info())

core.import_pose.import_pose: {0} File './data/6LZ9_H_L.pdb' automatically determined to be of type PDB
core.conformation.Conformation: {0} Found disulfide between residues 21 94
core.conformation.Conformation: {0} current variant for 21 CYS
core.conformation.Conformation: {0} current variant for 94 CYS
core.conformation.Conformation: {0} current variant for 21 CYD
core.conformation.Conformation: {0} current variant for 94 CYD
core.conformation.Conformation: {0} Found disulfide between residues 141 206
core.conformation.Conformation: {0} current variant for 141 CYS
core.conformation.Conformation: {0} current variant for 206 CYS
core.conformation.Conformation: {0} current variant for 141 CYD
core.conformation.Conformation: {0} current variant for 206 CYD
core.conformation.Conformation: {0} Found disulfide between residues 21 94
core.conformation.Conformation: {0} current variant for 21 CYD
core.conformation.Conformation: {0} current variant for 94 CYD
core.conformation.Conformation: {0} current variant for 21 CYD
core.conformation.Conformation: {0} current variant for 94 CYD
core.conformation.Conformation: {0} Found disulfide between residues 22 87
core.conformation.Conformation: {0} current variant for 22 CYD
core.conformation.Conformation: {0} current variant for 87 CYD
core.conformation.Conformation: {0} current variant for 22 CYD
core.conformation.Conformation: {0} current variant for 87 CYD
core.conformation.Conformation: {0} Found disulfide between residues 21 94
core.conformation.Conformation: {0} current variant for 21 CYD
core.conformation.Conformation: {0} current variant for 94 CYD
core.conformation.Conformation: {0} current variant for 21 CYD
core.conformation.Conformation: {0} current variant for 94 CYD
core.conformation.Conformation: {0} Found disulfide between residues 22 87
core.conformation.Conformation: {0} current variant for 22 CYD
core.conformation.Conformation: {0} current variant for 87 CYD
core.conformation.Conformation: {0} current variant for 22 CYD
core.conformation.Conformation: {0} current variant for 87 CYD
append之后的chain1_pose中的氨基酸总数:223
append之后chain的总数:1
PDB file name: ./data/6LZ9_H_L.pdb
 Pose Range  Chain    PDB Range  |   #Residues         #Atoms

0001 -- 0223    H 0002  -- 0224  |   0223 residues;    03433 atoms
                           TOTAL |   0223 residues;    03433 atoms

2.5 Pose中删除Region区域¶

In [15]:

pose = pose_from_pdb('./data/4R80.clean.pdb')
print('删除前的PDB_info:')
print(pose.pdb_info())
from pyrosetta.rosetta.protocols.grafting import delete_region
delete_region_mover = delete_region(pose, 1, 50)  # 此处是pose number;

# update pdbinfo; 别忘了更新pdbinfo;
renumber_pdbinfo_based_on_conf_chains(pose)

# 打印查看信息, 一整个区域都被删除【比一个个氨基酸删除快得多】:
print('删除后的PDB_info:')
print(pose.pdb_info())

core.import_pose.import_pose: {0} File './data/4R80.clean.pdb' automatically determined to be of type PDB
core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OXT on residue SER:CtermProteinFull 76
core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OXT on residue SER:CtermProteinFull 152
删除前的PDB_info:
PDB file name: ./data/4R80.clean.pdb
 Pose Range  Chain    PDB Range  |   #Residues         #Atoms

0001 -- 0076    A 0001  -- 0076  |   0076 residues;    01251 atoms
0077 -- 0152    B 0001  -- 0076  |   0076 residues;    01251 atoms
                           TOTAL |   0152 residues;    02502 atoms

protocols.grafting.util: {0} Deleting 50 residues from 1 to 50
删除后的PDB_info:
PDB file name: ./data/4R80.clean.pdb
 Pose Range  Chain    PDB Range  |   #Residues         #Atoms

0001 -- 0026    A 0051  -- 0076  |   0026 residues;    00412 atoms
0027 -- 0102    B 0001  -- 0076  |   0076 residues;    01251 atoms
                           TOTAL |   0102 residues;    01663 atoms

从pdb_info中可见，A链的1-50号氨基酸消失了。

2.6 Pose中单独氨基酸的删减操作¶

除了对链的合并之外，我们还可以对链中的氨基酸进行添加、删除的操作！具体的过程是用户需要创建一个独立的氨基酸(residue object)，并将这个氨基酸加载到现有的构像中。加载的方式可以是前置或后置，根据使用的函数不同而定。

In [16]:

# 获取初始信息
from pyrosetta.rosetta.core.conformation import ResidueFactory
from pyrosetta.rosetta.core.chemical import ChemicalManager

# print
pose = pose_from_pdb('./data/4R80.clean.pdb')
print(f'原始氨基酸总数:{pose.total_residue()}')
print(f'原始氨基酸序列:{pose.sequence()}\n')

core.import_pose.import_pose: {0} File './data/4R80.clean.pdb' automatically determined to be of type PDB
core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OXT on residue SER:CtermProteinFull 76
core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OXT on residue SER:CtermProteinFull 152
原始氨基酸总数:152
原始氨基酸序列:PSEEEEKRRAKQVAKEKILEQNPSSKVQVRRVQKQGNTIRVELEITENGKKTNITVEVEKQGNTFTVKRITETVGSPSEEEEKRRAKQVAKEKILEQNPSSKVQVRRVQKQGNTIRVELEITENGKKTNITVEVEKQGNTFTVKRITETVGS

In [17]:

# 通过ResidueFactory创建一个新的Residue(ALA)对象:
chm = ChemicalManager.get_instance()
rts = chm.residue_type_set("fa_standard")
new_rsd = ResidueFactory.create_residue(rts.name_map('ALA')) # 创建一个residue object

# 在第一个氨基酸前添加一个ALA
pose.prepend_polymer_residue_before_seqpos(new_rsd, 1, True) 

print(f'Pose的残基数量:{pose.total_residue()}')
print(f'氨基酸序列:{pose.sequence()}\n')

Pose的残基数量:153
氨基酸序列:APSEEEEKRRAKQVAKEKILEQNPSSKVQVRRVQKQGNTIRVELEITENGKKTNITVEVEKQGNTFTVKRITETVGSPSEEEEKRRAKQVAKEKILEQNPSSKVQVRRVQKQGNTIRVELEITENGKKTNITVEVEKQGNTFTVKRITETVGS

In [18]:

# 向后添加氨基酸
last_residue = pose.total_residue()
pose.append_polymer_residue_after_seqpos(new_rsd, last_residue, True)  # 在最后一个氨基酸后添加一个ALA

print(f'Pose的残基数量:{pose.total_residue()}')
print(f'氨基酸序列:{pose.sequence()}\n')

Pose的残基数量:154
氨基酸序列:APSEEEEKRRAKQVAKEKILEQNPSSKVQVRRVQKQGNTIRVELEITENGKKTNITVEVEKQGNTFTVKRITETVGSPSEEEEKRRAKQVAKEKILEQNPSSKVQVRRVQKQGNTIRVELEITENGKKTNITVEVEKQGNTFTVKRITETVGSA

In [19]:

# 删除氨基酸
pose.delete_polymer_residue(1)  # 删除第一个氨基酸

print(f'删除之后氨基酸总数:{pose.total_residue()}')
print(f'删除之后氨基酸序列:{pose.sequence()}\n')

删除之后氨基酸总数:153
删除之后氨基酸序列:PSEEEEKRRAKQVAKEKILEQNPSSKVQVRRVQKQGNTIRVELEITENGKKTNITVEVEKQGNTFTVKRITETVGSPSEEEEKRRAKQVAKEKILEQNPSSKVQVRRVQKQGNTIRVELEITENGKKTNITVEVEKQGNTFTVKRITETVGSA

In [20]:

# 还可以范围性的删除氨基酸
pose.delete_residue_range_slow(1,5) # 删除第一个至第五个氨基酸

print(f'删除之后氨基酸总数:{pose.total_residue()}')
print(f'删除之后氨基酸序列:{pose.sequence()}\n')

删除之后氨基酸总数:148
删除之后氨基酸序列:EKRRAKQVAKEKILEQNPSSKVQVRRVQKQGNTIRVELEITENGKKTNITVEVEKQGNTFTVKRITETVGSPSEEEEKRRAKQVAKEKILEQNPSSKVQVRRVQKQGNTIRVELEITENGKKTNITVEVEKQGNTFTVKRITETVGSA

对拓扑结构操作完后，千万记得PBDinfo更新!!

In [21]:

# 更新pdb_info; [别忘了!]
from pyrosetta.rosetta.core.pose import renumber_pdbinfo_based_on_conf_chains

renumber_pdbinfo_based_on_conf_chains(pose)  # 更新PDBinfo.

# 检查PDBinfo是否正确: Returns true if PDBInfo is obsolete and needs updating
print(f'PDBinfo是否需要被更新:{pose.pdb_info().obsolete()}')
print(pose.pdb_info())

PDBinfo是否需要被更新:False
PDB file name: ./data/4R80.clean.pdb
 Pose Range  Chain    PDB Range  |   #Residues         #Atoms

0001 -- 0071    A 0006  -- 0076  |   0071 residues;    01177 atoms
0072 -- 0148    B 0001  -- 0077  |   0077 residues;    01260 atoms
                           TOTAL |   0148 residues;    02437 atoms

2.7 Pose中连续region提取¶

在之前的章节里面我们提过，Pose中的每个氨基酸都是独立的构象，我们可以使用这个机制将Pose中一些连续的片段进行提取。

In [22]:

# 读取pose
pose = pose_from_pdb('./data/4R80.clean.pdb')
print(pose.pdb_info())

core.import_pose.import_pose: {0} File './data/4R80.clean.pdb' automatically determined to be of type PDB
core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OXT on residue SER:CtermProteinFull 76
core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OXT on residue SER:CtermProteinFull 152
PDB file name: ./data/4R80.clean.pdb
 Pose Range  Chain    PDB Range  |   #Residues         #Atoms

0001 -- 0076    A 0001  -- 0076  |   0076 residues;    01251 atoms
0077 -- 0152    B 0001  -- 0076  |   0076 residues;    01251 atoms
                           TOTAL |   0152 residues;    02502 atoms

In [23]:

# 新建一个空的Pose
sub_region_pose = Pose()

# 添加第一个氨基酸:
residue = pose.residue(1)
sub_region_pose.append_residue_by_jump(new_rsd=residue, jump_anchor_residue=1)
print(sub_region_pose.sequence())

In [24]:

# 添加第2-5个氨基酸:
for i in range(2, 6):
    residue = pose.residue(i)  # 索引原pose中的residue
    last_residue_pose_id = sub_region_pose.total_residue()  # 获取sub_region_pose中的最后一个氨基酸;
    sub_region_pose.append_polymer_residue_after_seqpos(new_rsd=residue, seqpos=last_residue_pose_id, build_ideal_geometry=False)  # 将氨基酸添加
print(sub_region_pose.sequence())
sub_region_pose.dump_pdb('./data/sub_region.pdb')

PSEEE

Out[24]:

True

In [25]:

# 这种非官方的操作方法，默认没有创建pdb_info!
print(sub_region_pose.pdb_info())

None

In [26]:

# 通过AddPDBInfoMover可以创建对应的pdb_info给到当前的Pose
from pyrosetta.rosetta.protocols.simple_moves import AddPDBInfoMover
pdb_mover = AddPDBInfoMover()
pdb_mover.apply(sub_region_pose)
print(sub_region_pose.pdb_info())

PDB file name: 
 Pose Range  Chain    PDB Range  |   #Residues         #Atoms

0001 -- 0005    A 0001  -- 0005  |   0005 residues;    00074 atoms
                           TOTAL |   0005 residues;    00074 atoms

2.8 Pose中氨基酸类型的调整(突变)¶

除了具体的化学键数据的调整，在PyRosetta中进行氨基酸的类型调整也是很方便的

In [27]:

# 调整氨基酸的类型
from pyrosetta.toolbox import mutate_residue
print(f'原始氨基酸类型:{pose.residue(1).name()}')

原始氨基酸类型:PRO:NtermProteinFull

In [28]:

print('突变氨基酸中...')
mutate_residue(pose, 1, 'C', 9.0)  # 1 代表氨基酸突变的pose编号，9.0代表对氨基酸附近9埃范围内的氨基酸进行侧链优化，适应新的突变。

突变氨基酸中...
core.scoring.ScoreFunctionFactory: {0} SCOREFUNCTION: ref2015
core.pack.task: {0} Packer task: initialize from command line()
core.pack.pack_rotamers: {0} built 161 rotamers at 8 positions.
core.pack.pack_rotamers: {0} Requesting all available threads for interaction graph computation.
core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating PDInteractionGraph
basic.thread_manager.RosettaThreadManager: {?} Creating a thread pool of 1 threads.
basic.thread_manager.RosettaThreadPool: {?} Launched 0 new threads.
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).

In [29]:

print(f'突变后氨基酸类型:{pose.residue(1).name()}')

突变后氨基酸类型:CYS:NtermProteinFull

三、Pose中的自定义信息储存¶

Pose中含有让用户自定义写入任何信息的功能，比如在程序设计过程中，中间生成的临时数值或字符都可以写入到PoseExtraScore中，这些信息会随着Pose一并输出到PDB或则Silent文件中，在后续的分析和处理的过程中非常方便。

In [30]:

# 给pose加入额外的信息: 比如filter计算的值就可以储存.
from pyrosetta.rosetta.core.pose import setPoseExtraScore, getPoseExtraScore

setPoseExtraScore(pose, "distance", 1.0)
setPoseExtraScore(pose, "angle", 120.5)

In [31]:

# 提取信息
print(getPoseExtraScore(pose, 'distance'))
print(getPoseExtraScore(pose, 'angle'))

1.0
120.5

练习¶

尝试写一个程序，将Pose(单链)中某一个连续的结构域部分提取出来。
尝试写一个程序，将Pose(单链)中某两个不同的连续结构域提取出来，并重新分为两条链。

In [ ]: