Notebook

TaskOperation API¶

@Author: 吴炜坤

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

本章节主要详尽地介绍TaskOperation的API，主要参考页面:

http://new.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/TaskOperations/TaskOperations-RosettaScripts#specialized-operations_packer-behavior-modification

注意:

一些TaskOperation由于时代久远，只能配合xmlobject一同使用。xmlobject的详情请参考第九章，此处仅列出使用语法；
一些TaskOperation年久失修，已经不能正常运行，此处也略去不做介绍；
一些TaskOperation最新发布，在代码中尚未实装，本文也列举出来，在未来可能会进行更新。

TaskOperation从构建逻辑上来分类共计有两种类型:¶

Residue Level TaskOperations: 根据Selector设定选择范围内位点的Rotamer自由度(手动挡);
Specialized Operations: 根据预设好逻辑，对位点进行全局Rotamer操作(自动挡);

一、Residue Level TaskOperations¶

Residue Level TaskOperations(RLT)一般需要配合Selector来指定操作的范围。用户可以直观地将RLT理解为一个自定义版本的Specialized Operations。特别注意的是:RLT是无法直接被TaskFactory所读取，其必须通过OperateOnResidueSubset函数来生成一个标准的TaskOperations。

Rosetta中目前支持的所有RTL的列表:

RestrictToRepackingRLT
PreventRepackingRLT
RestrictAbsentCanonicalAASExceptNativeRLT
RestrictAbsentCanonicalAASRLT
DisallowIfNonnativeRLT
IncludeCurrentRLT
ExtraRotamersGenericRLT

In [1]:

# 初始化PyRosetta并读取一段螺旋结构的PDB。
from pyrosetta import *
init()
pose = pose_from_pdb('./data/helix.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=-10988823 seed_offset=0 real_seed=-10988823 thread_index=0
basic.random.init_random_generator: {0} RandomGenerator:init: Normal mode, seed=-10988823 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 0.696495 seconds.
core.import_pose.import_pose: {0} File './data/helix.pdb' automatically determined to be of type PDB
core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OXT on residue GLY:CtermProteinFull 14

RestrictToRepackingRLT在上一章节中已经介绍，此处不再赘述。

In [2]:

# 预先定义好 氨基酸的作用范围。
from pyrosetta.rosetta.core.pack.task.operation import *
from pyrosetta.rosetta.core.pack.task.operation import OperateOnResidueSubset
from pyrosetta.rosetta.core.select.residue_selector import ResidueIndexSelector
from pyrosetta.rosetta.core.pack.task import TaskFactory
# 选择氨基酸范围
select_pos = ResidueIndexSelector('2,3,4,5,6,7,8,9,10,11,12,13')

1.1 PreventRepackingRLT¶

将选择区域的氨基酸Rotamer自由度完全关闭，其侧链构象维持不变。

In [3]:

# 使用OperateOnResidueSubset生成TaskOperations
packing_taskop = OperateOnResidueSubset(PreventRepackingRLT(), select_pos, False)

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(packing_taskop)

# 生成PackerTask
packer_task = pack_tf.create_task_and_apply_taskoperations(pose)
print(packer_task)

#Packer_Task

Threads to request: ALL AVAILABLE

resid	pack?	design?	allowed_aas
1	TRUE	TRUE	ALA:NtermProteinFull,CYS:NtermProteinFull,ASP:NtermProteinFull,GLU:NtermProteinFull,PHE:NtermProteinFull,GLY:NtermProteinFull,HIS:NtermProteinFull,HIS_D:NtermProteinFull,ILE:NtermProteinFull,LYS:NtermProteinFull,LEU:NtermProteinFull,MET:NtermProteinFull,ASN:NtermProteinFull,PRO:NtermProteinFull,GLN:NtermProteinFull,ARG:NtermProteinFull,SER:NtermProteinFull,THR:NtermProteinFull,VAL:NtermProteinFull,TRP:NtermProteinFull,TYR:NtermProteinFull
2	FALSE	FALSE	
3	FALSE	FALSE	
4	FALSE	FALSE	
5	FALSE	FALSE	
6	FALSE	FALSE	
7	FALSE	FALSE	
8	FALSE	FALSE	
9	FALSE	FALSE	
10	FALSE	FALSE	
11	FALSE	FALSE	
12	FALSE	FALSE	
13	FALSE	FALSE	
14	TRUE	TRUE	ALA:CtermProteinFull,CYS:CtermProteinFull,ASP:CtermProteinFull,GLU:CtermProteinFull,PHE:CtermProteinFull,GLY:CtermProteinFull,HIS:CtermProteinFull,HIS_D:CtermProteinFull,ILE:CtermProteinFull,LYS:CtermProteinFull,LEU:CtermProteinFull,MET:CtermProteinFull,ASN:CtermProteinFull,PRO:CtermProteinFull,GLN:CtermProteinFull,ARG:CtermProteinFull,SER:CtermProteinFull,THR:CtermProteinFull,VAL:CtermProteinFull,TRP:CtermProteinFull,TYR:CtermProteinFull

1.2 RestrictAbsentCanonicalAASExceptNativeRLT¶

将Rotamer自由度限定在给定的氨基酸类型列表，并允许保留当前位点氨基酸类型的Rotamer。

In [4]:

# 定义自由度
design_with_wt = RestrictAbsentCanonicalAASExceptNativeRLT()
design_with_wt.aas_to_keep('QKI')

# 使用OperateOnResidueSubset生成TaskOperations
packing_taskop = OperateOnResidueSubset(design_with_wt, select_pos, False)

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(packing_taskop)

# 生成PackerTask
packer_task = pack_tf.create_task_and_apply_taskoperations(pose)
print(packer_task)

#Packer_Task

Threads to request: ALL AVAILABLE

resid	pack?	design?	allowed_aas
1	TRUE	TRUE	ALA:NtermProteinFull,CYS:NtermProteinFull,ASP:NtermProteinFull,GLU:NtermProteinFull,PHE:NtermProteinFull,GLY:NtermProteinFull,HIS:NtermProteinFull,HIS_D:NtermProteinFull,ILE:NtermProteinFull,LYS:NtermProteinFull,LEU:NtermProteinFull,MET:NtermProteinFull,ASN:NtermProteinFull,PRO:NtermProteinFull,GLN:NtermProteinFull,ARG:NtermProteinFull,SER:NtermProteinFull,THR:NtermProteinFull,VAL:NtermProteinFull,TRP:NtermProteinFull,TYR:NtermProteinFull
2	TRUE	TRUE	GLU,ILE,LYS,GLN
3	TRUE	TRUE	ILE,LYS,LEU,GLN
4	TRUE	TRUE	ILE,LYS,GLN
5	TRUE	TRUE	ILE,LYS,GLN
6	TRUE	TRUE	ILE,LYS,GLN,TRP
7	TRUE	TRUE	ILE,LYS,GLN,VAL
8	TRUE	TRUE	GLU,ILE,LYS,GLN
9	TRUE	TRUE	ILE,LYS,GLN
10	TRUE	TRUE	ALA,ILE,LYS,GLN
11	TRUE	TRUE	GLU,ILE,LYS,GLN
12	TRUE	TRUE	ILE,LYS,GLN,ARG
13	TRUE	TRUE	ILE,LYS,ASN,GLN
14	TRUE	TRUE	ALA:CtermProteinFull,CYS:CtermProteinFull,ASP:CtermProteinFull,GLU:CtermProteinFull,PHE:CtermProteinFull,GLY:CtermProteinFull,HIS:CtermProteinFull,HIS_D:CtermProteinFull,ILE:CtermProteinFull,LYS:CtermProteinFull,LEU:CtermProteinFull,MET:CtermProteinFull,ASN:CtermProteinFull,PRO:CtermProteinFull,GLN:CtermProteinFull,ARG:CtermProteinFull,SER:CtermProteinFull,THR:CtermProteinFull,VAL:CtermProteinFull,TRP:CtermProteinFull,TYR:CtermProteinFull

1.3 RestrictAbsentCanonicalAASRLT¶

功能与RestrictAbsentCanonicalAASExceptNativeRLT类似，将Rotamer自由度限定在给定的氨基酸类型列表。唯一的差别在于RestrictAbsentCanonicalAASRLT会忘记当前的氨基酸类型。

In [5]:

# 定义自由度
design_to = RestrictAbsentCanonicalAASRLT()
design_to.aas_to_keep('QKI')

# 使用OperateOnResidueSubset生成TaskOperations
packing_taskop = OperateOnResidueSubset(design_to, select_pos, False)

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(packing_taskop)

# 生成PackerTask
packer_task = pack_tf.create_task_and_apply_taskoperations(pose)
print(packer_task)

#Packer_Task

Threads to request: ALL AVAILABLE

resid	pack?	design?	allowed_aas
1	TRUE	TRUE	ALA:NtermProteinFull,CYS:NtermProteinFull,ASP:NtermProteinFull,GLU:NtermProteinFull,PHE:NtermProteinFull,GLY:NtermProteinFull,HIS:NtermProteinFull,HIS_D:NtermProteinFull,ILE:NtermProteinFull,LYS:NtermProteinFull,LEU:NtermProteinFull,MET:NtermProteinFull,ASN:NtermProteinFull,PRO:NtermProteinFull,GLN:NtermProteinFull,ARG:NtermProteinFull,SER:NtermProteinFull,THR:NtermProteinFull,VAL:NtermProteinFull,TRP:NtermProteinFull,TYR:NtermProteinFull
2	TRUE	TRUE	ILE,LYS,GLN
3	TRUE	TRUE	ILE,LYS,GLN
4	TRUE	TRUE	ILE,LYS,GLN
5	TRUE	TRUE	ILE,LYS,GLN
6	TRUE	TRUE	ILE,LYS,GLN
7	TRUE	TRUE	ILE,LYS,GLN
8	TRUE	TRUE	ILE,LYS,GLN
9	TRUE	TRUE	ILE,LYS,GLN
10	TRUE	TRUE	ILE,LYS,GLN
11	TRUE	TRUE	ILE,LYS,GLN
12	TRUE	TRUE	ILE,LYS,GLN
13	TRUE	TRUE	ILE,LYS,GLN
14	TRUE	TRUE	ALA:CtermProteinFull,CYS:CtermProteinFull,ASP:CtermProteinFull,GLU:CtermProteinFull,PHE:CtermProteinFull,GLY:CtermProteinFull,HIS:CtermProteinFull,HIS_D:CtermProteinFull,ILE:CtermProteinFull,LYS:CtermProteinFull,LEU:CtermProteinFull,MET:CtermProteinFull,ASN:CtermProteinFull,PRO:CtermProteinFull,GLN:CtermProteinFull,ARG:CtermProteinFull,SER:CtermProteinFull,THR:CtermProteinFull,VAL:CtermProteinFull,TRP:CtermProteinFull,TYR:CtermProteinFull

1.4 DisallowIfNonnativeRLT¶

不允许突变为列表中指定氨基酸类型，但允许保留当前位点氨基酸类型的Rotamer。

In [6]:

# 定义自由度
not_design_to = DisallowIfNonnativeRLT()
not_design_to.disallow_aas('HLQKILRA')

# 使用OperateOnResidueSubset生成TaskOperations
packing_taskop = OperateOnResidueSubset(not_design_to, select_pos, False)

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(packing_taskop)

# 生成PackerTask
packer_task = pack_tf.create_task_and_apply_taskoperations(pose)
print(packer_task)

#Packer_Task

Threads to request: ALL AVAILABLE

resid	pack?	design?	allowed_aas
1	TRUE	TRUE	ALA:NtermProteinFull,CYS:NtermProteinFull,ASP:NtermProteinFull,GLU:NtermProteinFull,PHE:NtermProteinFull,GLY:NtermProteinFull,HIS:NtermProteinFull,HIS_D:NtermProteinFull,ILE:NtermProteinFull,LYS:NtermProteinFull,LEU:NtermProteinFull,MET:NtermProteinFull,ASN:NtermProteinFull,PRO:NtermProteinFull,GLN:NtermProteinFull,ARG:NtermProteinFull,SER:NtermProteinFull,THR:NtermProteinFull,VAL:NtermProteinFull,TRP:NtermProteinFull,TYR:NtermProteinFull
2	TRUE	TRUE	CYS,ASP,GLU,PHE,GLY,MET,ASN,PRO,SER,THR,VAL,TRP,TYR
3	TRUE	TRUE	CYS,ASP,GLU,PHE,GLY,LEU,MET,ASN,PRO,SER,THR,VAL,TRP,TYR
4	TRUE	TRUE	CYS,ASP,GLU,PHE,GLY,MET,ASN,PRO,GLN,SER,THR,VAL,TRP,TYR
5	TRUE	TRUE	CYS,ASP,GLU,PHE,GLY,LYS,MET,ASN,PRO,SER,THR,VAL,TRP,TYR
6	TRUE	TRUE	CYS,ASP,GLU,PHE,GLY,MET,ASN,PRO,SER,THR,VAL,TRP,TYR
7	TRUE	TRUE	CYS,ASP,GLU,PHE,GLY,MET,ASN,PRO,SER,THR,VAL,TRP,TYR
8	TRUE	TRUE	CYS,ASP,GLU,PHE,GLY,MET,ASN,PRO,SER,THR,VAL,TRP,TYR
9	TRUE	TRUE	CYS,ASP,GLU,PHE,GLY,MET,ASN,PRO,GLN,SER,THR,VAL,TRP,TYR
10	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,MET,ASN,PRO,SER,THR,VAL,TRP,TYR
11	TRUE	TRUE	CYS,ASP,GLU,PHE,GLY,MET,ASN,PRO,SER,THR,VAL,TRP,TYR
12	TRUE	TRUE	CYS,ASP,GLU,PHE,GLY,MET,ASN,PRO,ARG,SER,THR,VAL,TRP,TYR
13	TRUE	TRUE	CYS,ASP,GLU,PHE,GLY,MET,ASN,PRO,SER,THR,VAL,TRP,TYR
14	TRUE	TRUE	ALA:CtermProteinFull,CYS:CtermProteinFull,ASP:CtermProteinFull,GLU:CtermProteinFull,PHE:CtermProteinFull,GLY:CtermProteinFull,HIS:CtermProteinFull,HIS_D:CtermProteinFull,ILE:CtermProteinFull,LYS:CtermProteinFull,LEU:CtermProteinFull,MET:CtermProteinFull,ASN:CtermProteinFull,PRO:CtermProteinFull,GLN:CtermProteinFull,ARG:CtermProteinFull,SER:CtermProteinFull,THR:CtermProteinFull,VAL:CtermProteinFull,TRP:CtermProteinFull,TYR:CtermProteinFull

1.5 IncludeCurrentRLT¶

设定Packer在执行期间，考虑Pose输入时的Rotamer状态。

In [7]:

# 使用OperateOnResidueSubset生成TaskOperations
packing_taskop = OperateOnResidueSubset(IncludeCurrentRLT(), select_pos, False)

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(packing_taskop)

# 生成PackerTask
packer_task = pack_tf.create_task_and_apply_taskoperations(pose)

# 检查是否Pack中是否包含input的rotamer构象:
packer_task.include_current(2)

Out[7]:

True

In [8]:

# 检查是否Pack中是否包含input的rotamer构象:
packer_task.include_current(1)

Out[8]:

False

1.6 ExtraRotamersGenericRLT¶

Rosetta Pack采样Rotamer时是离散的，默认只会采纳每个格点的中心富集的构象，我们可以通过Extra Rotamer相关控制手段来增加Rotamer的采样，默认扩充采样时，采集Rotamer时会额外考虑平均 $\chi$ 的+/-1个标准差的构象。

ExtraRotamersGenericRLT有3个定义的参数:

ex?: “?”可选值为1-4，指定对侧链中第几个 $\chi$ 角进行扩大采样。
- ex1: 额外采样 $\chi_{1}$ 二面角
- ex1aro: 额外采样 $\chi_{1}$ 二面角(只考虑芳香族氨基酸(FHWY))
- ex1aro_exposed: 额外采样 $\chi_{1}$ 二面角(只考虑芳香族氨基酸(FHWY)), 仅限暴露在蛋白外部的氨基酸位点。
- ex2: 额外采样 $\chi_{2}$ 二面角
- ex2aro: 额外采样 $\chi_{2}$ 二面角(只考虑芳香族氨基酸(FHWY))
- ex2aro_exposed: 额外采样 $\chi_{2}$ 二面角(只考虑芳香族氨基酸(FHWY)), 仅限暴露在蛋白外部的氨基酸位点。
- ex3: 额外采样 $\chi_{3}$ 二面角
- ex4: 额外采样 $\chi_{4}$ 二面角
ex?_sample_level: 指定允许的 $\chi$ 角标准差范围。
- 0 ...... no extra chi angles
- 1 ...... sample at 1 standard deviation
- 2 ...... sample at 1/2 standard deviation
- 3 ...... sample at two full standard deviations
- 4 ...... sample at two 1/2 standard deviations
- 5 ...... sample at four 1/2 standard deviations
- 6 ...... sample at three 1/3 standard deviations
- 7 ...... sample at six 1/4 standard deviations
extrachi_cutoff: Rosetta默认不会对处于蛋白表面的氨基酸进行额外Rotamer采集，除非用户显式地设置(EX_CUTOFF >=1-3等)。默认每个氨基酸计算10埃范围内残基数量，当数量大于阈值时，认为是"包埋"的氨基酸，进行额外的Rotamer采样。因此通常EX_CUTOFF显式地设置为0，考虑所有的氨基酸位点都做Rotamer。

In [9]:

# 设定额外rotamer采样:
from pyrosetta.rosetta.core.select.residue_selector import ChainSelector
from pyrosetta.rosetta.core.pack.task.operation import RestrictToRepacking
from pyrosetta.rosetta.core.pack.task.operation import ExtraRotamers
from pyrosetta.rosetta.core.pack.task import ExtraRotSample

extract_chi = ExtraRotamersGenericRLT()
extract_chi.ex1(True)
extract_chi.ex2aro(True)
# extract_chi.ex1_sample_level(ExtraRotSample.EX_ONE_STDDEV) #【1~7 定义 chi标准误范围】
# extract_chi.ex2aro_sample_level(ExtraRotSample.EX_ONE_STDDEV) #【1~7 定义 chi标准误范围】
extract_chi.extrachi_cutoff(0) #定义一个残基必须有几个邻近采集方可增强chi采样。 0 = 默认不考虑邻近阈值。默认为18

# 使用OperateOnResidueSubset生成TaskOperations
select_pos = ChainSelector('1')
packing_taskop = OperateOnResidueSubset(extract_chi, select_pos, False)

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(RestrictToRepacking()) # 全局设置为只能repacking
pack_tf.push_back(packing_taskop)

# 生成PackerTask
packer_task = pack_tf.create_task_and_apply_taskoperations(pose)

# 查看每个残基的Rotamer采样级别:
print(packer_task.task_string(pose))

start
1 A  NATAA  EX ARO 1 EX ARO 2 EX_CUTOFF 0
2 A  NATAA  EX ARO 1 EX ARO 2 EX_CUTOFF 0
3 A  NATAA  EX ARO 1 EX ARO 2 EX_CUTOFF 0
4 A  NATAA  EX ARO 1 EX ARO 2 EX_CUTOFF 0
5 A  NATAA  EX ARO 1 EX ARO 2 EX_CUTOFF 0
6 A  NATAA  EX ARO 1 EX ARO 2 EX_CUTOFF 0
7 A  NATAA  EX ARO 1 EX ARO 2 EX_CUTOFF 0
8 A  NATAA  EX ARO 1 EX ARO 2 EX_CUTOFF 0
9 A  NATAA  EX ARO 1 EX ARO 2 EX_CUTOFF 0
10 A  NATAA  EX ARO 1 EX ARO 2 EX_CUTOFF 0
11 A  NATAA  EX ARO 1 EX ARO 2 EX_CUTOFF 0
12 A  NATAA  EX ARO 1 EX ARO 2 EX_CUTOFF 0
13 A  NATAA  EX ARO 1 EX ARO 2 EX_CUTOFF 0
14 A  NATAA  EX ARO 1 EX ARO 2 EX_CUTOFF 0

In [10]:

from pyrosetta.rosetta.protocols.minimization_packing import PackRotamersMover
pack_mover = PackRotamersMover()
pack_mover.task_factory(pack_tf)
pack_mover.apply(pose)

protocols.minimization_packing.PackRotamersMover: {0} [ WARNING ] undefined ScoreFunction -- creating a default one
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
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 0.190938 seconds to load from binary
core.pack.pack_rotamers: {0} built 717 rotamers at 14 positions.
core.pack.pack_rotamers: {0} Requesting all available threads for interaction graph computation.
core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph
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).

查看运行日志: “built 717 rotamers at 14 positions.” 此时在计算InteractionGraph的时候使用了717个rotamer。

思考¶

尝试改变“ex?”的参数，看看InteractionGraph的rotamer数量的变化情况？

二、Specialized Operations¶

2.1 Position/Identity Specification¶

这部分的TaskOperations分类主要根据残基的位置和类型信息进行自动化的定义。主要分为:

General Specification(基本都能使用Residue Level TaskOperations实现，因此此部分不做介绍)
General Design Specification(部分与Residue Level TaskOperations重合，因此仅挑选部分进行阐述)
Property-based specification
Interface/Neighborhood Specifications
Input-based design

这一部分包含了绝大数与实际工作相关的TaskOperations。

2.1.1 General Design Specification¶

1. RestrictToSpecifiedBaseResidueTypes¶

对于BaseResidueTypes的操作是在生成PackerTask之前，对PackerPalettes做调整。 PackerPalettes用于定义“默认”的氨基酸列表，默认允许20种天然氨基酸的Rotamer被采样。当氨基酸类型没有在预设列表中时，在后续过程中，这类氨基酸将不会出现。

In [11]:

from pyrosetta.rosetta.core.pack.task.operation import RestrictToSpecifiedBaseResidueTypes
from pyrosetta.rosetta.core.pack.task.operation import RestrictToRepacking
from pyrosetta.rosetta.utility import vector1_std_string
# allow basetype
mut_table = "TYR,VAL,TRP,CYS,"
mut_table_list = vector1_std_string()
for aa in mut_table.split(','):
    mut_table_list.append(aa)

# restrict to baestype list
restric_to_basetype = RestrictToSpecifiedBaseResidueTypes()
restric_to_basetype.set_base_types(mut_table_list)

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(restric_to_basetype)
pack_tf.push_back(RestrictToRepacking())

# 生成PackerTask
packer_task = pack_tf.create_task_and_apply_taskoperations(pose)
print(packer_task)

#Packer_Task

Threads to request: ALL AVAILABLE

resid	pack?	design?	allowed_aas
1	FALSE	FALSE	
2	FALSE	FALSE	
3	FALSE	FALSE	
4	FALSE	FALSE	
5	FALSE	FALSE	
6	TRUE	FALSE	TRP
7	TRUE	FALSE	VAL
8	FALSE	FALSE	
9	FALSE	FALSE	
10	FALSE	FALSE	
11	FALSE	FALSE	
12	FALSE	FALSE	
13	FALSE	FALSE	
14	FALSE	FALSE

可见，尽管将所有的Rotamer状态设置为repacking，当氨基酸类型在PackerPalettes预设列表中删除后，一些位点Rotamer自由度变“空”！

2. ProhibitSpecifiedBaseResidueTypes¶

同理于RestrictToSpecifiedBaseResidueTypes的逻辑，ProhibitSpecifiedBaseResidueTypes设定了哪些氨基酸类型应当被“禁止”。

In [12]:

from pyrosetta.rosetta.core.pack.task.operation import ProhibitSpecifiedBaseResidueTypes
from pyrosetta.rosetta.utility import vector1_std_string
# allow basetype
not_mut_table = "ALA,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR"
not_mut_table_list = vector1_std_string()
for aa in not_mut_table.split(','):
    not_mut_table_list.append(aa)

# restrict to baestype list
restric_to_basetype = ProhibitSpecifiedBaseResidueTypes()
restric_to_basetype.set_base_types(not_mut_table_list)

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(restric_to_basetype)

# 生成PackerTask
packer_task = pack_tf.create_task_and_apply_taskoperations(pose)
print(packer_task)

#Packer_Task

Threads to request: ALL AVAILABLE

resid	pack?	design?	allowed_aas
1	TRUE	TRUE	CYS:NtermProteinFull,VAL:NtermProteinFull,TRP:NtermProteinFull,TYR:NtermProteinFull
2	TRUE	TRUE	CYS,VAL,TRP,TYR
3	TRUE	TRUE	CYS,VAL,TRP,TYR
4	TRUE	TRUE	CYS,VAL,TRP,TYR
5	TRUE	TRUE	CYS,VAL,TRP,TYR
6	TRUE	TRUE	CYS,VAL,TRP,TYR
7	TRUE	TRUE	CYS,VAL,TRP,TYR
8	TRUE	TRUE	CYS,VAL,TRP,TYR
9	TRUE	TRUE	CYS,VAL,TRP,TYR
10	TRUE	TRUE	CYS,VAL,TRP,TYR
11	TRUE	TRUE	CYS,VAL,TRP,TYR
12	TRUE	TRUE	CYS,VAL,TRP,TYR
13	TRUE	TRUE	CYS,VAL,TRP,TYR
14	TRUE	TRUE	CYS:CtermProteinFull,VAL:CtermProteinFull,TRP:CtermProteinFull,TYR:CtermProteinFull

3. ReadResfile¶

之前我们讲了Resfile的编写规则，此处我们将resfile写成如下格式:

NATAA
EX 1 EX 2
START
1 A PIKAA A
2 A PIKAA AKR
3 A PIKAA APM
4 A PIKAA APT

这个Resfile定义的自由度为: NATAA至当前未指定的氨基酸都只能进行Repacking。此外，A链1号位点只能突变成ALA，A链2号位点只能突变成ALA，LYS和ARG如此类推。

In [13]:

from pyrosetta.rosetta.core.pack.task.operation import ReadResfile
# restrict to baestype list
resfile_type = ReadResfile('./data/mutation.resfile')

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(resfile_type)

# 生成PackerTask
packer_task = pack_tf.create_task_and_apply_taskoperations(pose)
print(packer_task)

#Packer_Task

Threads to request: ALL AVAILABLE

resid	pack?	design?	allowed_aas
1	TRUE	TRUE	ALA:NtermProteinFull
2	TRUE	TRUE	ALA,LYS,ARG
3	TRUE	TRUE	ALA,MET,PRO
4	TRUE	TRUE	ALA,PRO,THR
5	TRUE	FALSE	LYS
6	TRUE	FALSE	TRP
7	TRUE	FALSE	VAL
8	TRUE	FALSE	GLU
9	TRUE	FALSE	GLN
10	TRUE	FALSE	ALA
11	TRUE	FALSE	GLU
12	TRUE	FALSE	ARG
13	TRUE	FALSE	ASN
14	TRUE	FALSE	GLY:CtermProteinFull

4. LinkResidues¶

“铁锁连环”，当设定一个氨基酸与另外一些氨基酸必须同时突变为一样类型的Rotamer。但这部分的代码在pyrosetta中一直会造成内核错误。暂无法使用(2017-2021)

2.1.2 Property-based specification¶

1. RestrictToResidueProperties¶

根据给定的氨基酸性质来对PackerPalettes预设列表中的氨基酸类型进行指定和修改。

氨基酸的性质可选列表都记录在pyrosetta.rosetta.core.chemical.ResidueProperty中。一般常用可选:

METAL: 金属离子
POLAR: 极性氨基酸
HYDROPHOBIC: 疏水氨基酸
CHARGED: 带电氨基酸
NEGATIVE_CHARGE: 带负电氨基酸
POSITIVE_CHARGE: 带正电氨基酸
AROMATIC: 芳香族氨基酸

In [14]:

from pyrosetta.rosetta.core.pack.task.operation import RestrictToResidueProperties
from pyrosetta.rosetta.core.chemical import ResidueProperty
from pyrosetta.rosetta.utility import vector1_core_chemical_ResidueProperty

# allow basetype
properties = vector1_core_chemical_ResidueProperty()
properties.append(ResidueProperty.NEGATIVE_CHARGE)  # 只允许带负电氨基酸。

restrict_to_properties = RestrictToResidueProperties()
restrict_to_properties.set_properties(properties)
# 可以指定选择的范围:
# restrict_to_properties.set_selector()

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(restrict_to_properties)

# 生成PackerTask
packer_task = pack_tf.create_task_and_apply_taskoperations(pose)
print(packer_task)

#Packer_Task

Threads to request: ALL AVAILABLE

resid	pack?	design?	allowed_aas
1	TRUE	TRUE	ASP:NtermProteinFull,GLU:NtermProteinFull
2	TRUE	TRUE	ASP,GLU
3	TRUE	TRUE	ASP,GLU
4	TRUE	TRUE	ASP,GLU
5	TRUE	TRUE	ASP,GLU
6	TRUE	TRUE	ASP,GLU
7	TRUE	TRUE	ASP,GLU
8	TRUE	TRUE	ASP,GLU
9	TRUE	TRUE	ASP,GLU
10	TRUE	TRUE	ASP,GLU
11	TRUE	TRUE	ASP,GLU
12	TRUE	TRUE	ASP,GLU
13	TRUE	TRUE	ASP,GLU
14	TRUE	TRUE	ASP:CtermProteinFull,GLU:CtermProteinFull

2. ProhibitResidueProperties¶

同理于RestrictToResidueProperties的逻辑，ProhibitResidueProperties设定了满足哪些性质的氨基酸类型应当被“删除”。

In [15]:

from pyrosetta.rosetta.core.pack.task.operation import ProhibitResidueProperties
from pyrosetta.rosetta.core.chemical import ResidueProperty
from pyrosetta.rosetta.utility import vector1_core_chemical_ResidueProperty

# allow basetype
not_properties = vector1_core_chemical_ResidueProperty()
not_properties.append(ResidueProperty.POLAR)  # 添加氨基酸的属性为极性氨基酸。

restrict_to_properties = ProhibitResidueProperties()
restrict_to_properties.set_properties(not_properties)
# 可以指定选择的范围:
# restrict_to_properties.set_selector()

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(restrict_to_properties)

# 生成PackerTask
packer_task = pack_tf.create_task_and_apply_taskoperations(pose)
print(packer_task)

#Packer_Task

Threads to request: ALL AVAILABLE

resid	pack?	design?	allowed_aas
1	TRUE	TRUE	ALA:NtermProteinFull,CYS:NtermProteinFull,PHE:NtermProteinFull,GLY:NtermProteinFull,ILE:NtermProteinFull,LEU:NtermProteinFull,MET:NtermProteinFull,PRO:NtermProteinFull,VAL:NtermProteinFull,TRP:NtermProteinFull,TYR:NtermProteinFull
2	TRUE	TRUE	ALA,CYS,PHE,GLY,ILE,LEU,MET,PRO,VAL,TRP,TYR
3	TRUE	TRUE	ALA,CYS,PHE,GLY,ILE,LEU,MET,PRO,VAL,TRP,TYR
4	TRUE	TRUE	ALA,CYS,PHE,GLY,ILE,LEU,MET,PRO,VAL,TRP,TYR
5	TRUE	TRUE	ALA,CYS,PHE,GLY,ILE,LEU,MET,PRO,VAL,TRP,TYR
6	TRUE	TRUE	ALA,CYS,PHE,GLY,ILE,LEU,MET,PRO,VAL,TRP,TYR
7	TRUE	TRUE	ALA,CYS,PHE,GLY,ILE,LEU,MET,PRO,VAL,TRP,TYR
8	TRUE	TRUE	ALA,CYS,PHE,GLY,ILE,LEU,MET,PRO,VAL,TRP,TYR
9	TRUE	TRUE	ALA,CYS,PHE,GLY,ILE,LEU,MET,PRO,VAL,TRP,TYR
10	TRUE	TRUE	ALA,CYS,PHE,GLY,ILE,LEU,MET,PRO,VAL,TRP,TYR
11	TRUE	TRUE	ALA,CYS,PHE,GLY,ILE,LEU,MET,PRO,VAL,TRP,TYR
12	TRUE	TRUE	ALA,CYS,PHE,GLY,ILE,LEU,MET,PRO,VAL,TRP,TYR
13	TRUE	TRUE	ALA,CYS,PHE,GLY,ILE,LEU,MET,PRO,VAL,TRP,TYR
14	TRUE	TRUE	ALA:CtermProteinFull,CYS:CtermProteinFull,PHE:CtermProteinFull,GLY:CtermProteinFull,ILE:CtermProteinFull,LEU:CtermProteinFull,MET:CtermProteinFull,PRO:CtermProteinFull,VAL:CtermProteinFull,TRP:CtermProteinFull,TYR:CtermProteinFull

此时允许被设计的氨基酸类型被设定为非极性氨基酸。

3. ConservativeDesignOperation¶

根据氨基酸替换频率的思想来设计蛋白质，ConservativeDesignOperation根据给定的氨基酸替换矩阵来决定每个位置上氨基酸的类型，如Blosum62等。当得分大于0时。所有允许出现的氨基酸类型即此位点的自由度范围。

In [16]:

from pyrosetta.rosetta.protocols.task_operations import ConservativeDesignOperation
Conserve_design = ConservativeDesignOperation()
Conserve_design.set_data_source('blosum62')  # chothia_76, Blosum62(30-100) 选择使用哪种比对矩阵。

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(Conserve_design)

# 生成PackerTask
packer_task = pack_tf.create_task_and_apply_taskoperations(pose)
print(packer_task)

protocols.task_operations.ConservativeDesignOperation: {0} Loading conservative mutational data
#Packer_Task

Threads to request: ALL AVAILABLE

resid	pack?	design?	allowed_aas
1	TRUE	TRUE	ASP:NtermProteinFull,GLU:NtermProteinFull,ASN:NtermProteinFull,GLN:NtermProteinFull,SER:NtermProteinFull
2	TRUE	TRUE	ASP,GLU,HIS,HIS_D,LYS,ASN,GLN,ARG,SER
3	TRUE	TRUE	PHE,ILE,LEU,MET,VAL
4	TRUE	TRUE	ASP,GLU,HIS,HIS_D,LYS,MET,ASN,GLN,ARG,SER
5	TRUE	TRUE	GLU,LYS,ASN,GLN,ARG,SER
6	TRUE	TRUE	PHE,TRP,TYR
7	TRUE	TRUE	ALA,ILE,LEU,MET,THR,VAL
8	TRUE	TRUE	ASP,GLU,HIS,HIS_D,LYS,ASN,GLN,ARG,SER
9	TRUE	TRUE	ASP,GLU,HIS,HIS_D,LYS,MET,ASN,GLN,ARG,SER
10	TRUE	TRUE	ALA,CYS,GLY,SER,THR,VAL
11	TRUE	TRUE	ASP,GLU,HIS,HIS_D,LYS,ASN,GLN,ARG,SER
12	TRUE	TRUE	GLU,HIS,HIS_D,LYS,ASN,GLN,ARG
13	TRUE	TRUE	ASP,GLU,GLY,HIS,HIS_D,LYS,ASN,GLN,ARG,SER,THR
14	TRUE	TRUE	ALA:CtermProteinFull,GLY:CtermProteinFull,ASN:CtermProteinFull,SER:CtermProteinFull

4. ConsensusLoopDesign¶

ConsensuLoopDesign首先定义的二级结构寻找Loop区域, 基于Pose的二面角定义Loop的组成类型（ABEGO字符串）。如一段4个氨基酸长度的loop区二面角类型为GGBB，通过搜索数据库，将相同类型的Loop的序列获取，并统计每个位点上的氨基酸频率，通过富集计算，筛选出那些在该二面角空间出现频率较高的氨基酸来定义自由度。因此对于一些存在正则结构的loop设计十分有用！

In [17]:

# denovo_pose
denovo_pose = pose_from_pdb('./data/EHEE_rd4_0976.pdb')

# 获取pose的二级结构:
from pyrosetta.rosetta.protocols.membrane import get_secstruct
secstruct = ''.join(get_secstruct(denovo_pose))

# ConsensusLoopDesign
from pyrosetta.rosetta.protocols.denovo_design.task_operations import ConsensusLoopDesignOperation
consensu_loop_design = ConsensusLoopDesignOperation()
# 或如'EHHHL'设置序列的二级结构
consensu_loop_design.set_secstruct(secstruct)
# 考虑loop邻近+1/-1氨基酸, 使得该区域也采取保守性设计，比如有一些loop的周围更加倾向于天然存在PRO.（默认为False）
consensu_loop_design.set_include_adjacent_residues(False) 
# 如果富集度低于阈值，那么该位点将不被设计，0.5比0.0更加严格，要求更高的富集度。
consensu_loop_design.set_enrichment_threshold(0.3) 

core.import_pose.import_pose: {0} File './data/EHEE_rd4_0976.pdb' automatically determined to be of type PDB
protocols.DsspMover: {0} LEEEEELLHHHHHHHHHHHHHLLLLEEEEEELLEEEEEEL

In [18]:

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(consensu_loop_design)

# 生成PackerTask
packer_task = pack_tf.create_task_and_apply_taskoperations(denovo_pose)
print(packer_task)

core.select.residue_selector.SecondaryStructureSelector: {0} Using given pose secondary structure: LEEEEELLHHHHHHHHHHHHHLLLLEEEEEELLEEEEEEL
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} Restricting AAs in loop: Start: 7 Abego: BBEA Before: E After: H
basic.io.database: {0} Database file opened: protocol_data/denovo_design/aa_abego_frequencies.gz
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} Residue: 7; forbidden aas: DEFGHIKLNPQRVY
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} Residue: 8; forbidden aas: ACDEFHIKLMNPQRSTVY
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} Restricting AAs in loop: Start: 22 Abego: AAGBBB Before: H After: E
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} Residue: 22; forbidden aas: CDFGIPSTVW
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} Residue: 23; forbidden aas: ACDEFHILMPQRSTVWY
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} Residue: 24; forbidden aas: ACDEFGHNPQRSTW
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} Residue: 25; forbidden aas: ACDFGHILMNQSTVWY
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} Restricting AAs in loop: Start: 32 Abego: BGGB Before: E After: E
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} Residue: 32; forbidden aas: ACEFGHIKLMPQRSTVWY
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} Residue: 33; forbidden aas: ACDEFHIKLMNPQRSTVWY
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} #Packer_Task
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} Threads to request: ALL AVAILABLE
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} resid	pack?	design?	allowed_aas
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 1	TRUE	TRUE	ALA:NtermProteinFull,CYS:NtermProteinFull,ASP:NtermProteinFull,GLU:NtermProteinFull,PHE:NtermProteinFull,GLY:NtermProteinFull,HIS:NtermProteinFull,HIS_D:NtermProteinFull,ILE:NtermProteinFull,LYS:NtermProteinFull,LEU:NtermProteinFull,MET:NtermProteinFull,ASN:NtermProteinFull,PRO:NtermProteinFull,GLN:NtermProteinFull,ARG:NtermProteinFull,SER:NtermProteinFull,THR:NtermProteinFull,VAL:NtermProteinFull,TRP:NtermProteinFull,TYR:NtermProteinFull
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 2	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 3	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 4	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 5	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 6	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 7	TRUE	TRUE	ALA,CYS,MET,SER,THR,TRP
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 8	TRUE	TRUE	GLY,TRP
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 9	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 10	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 11	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 12	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 13	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 14	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 15	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 16	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 17	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 18	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 19	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 20	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 21	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 22	TRUE	TRUE	ALA,GLU,HIS,HIS_D,LYS,LEU,MET,ASN,GLN,ARG,TYR
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 23	TRUE	TRUE	GLY,LYS,ASN
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 24	TRUE	TRUE	ILE,LYS,LEU,MET,VAL,TYR
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 25	TRUE	TRUE	GLU,LYS,PRO,ARG
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 26	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 27	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 28	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 29	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 30	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 31	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 32	TRUE	TRUE	ASP,ASN
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 33	TRUE	FALSE	GLY
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 34	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 35	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 36	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 37	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 38	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 39	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
protocols.denovo_design.task_operations.ConsensusLoopDesignOperation: {0} 40	TRUE	TRUE	ALA:CtermProteinFull,CYS:CtermProteinFull,ASP:CtermProteinFull,GLU:CtermProteinFull,PHE:CtermProteinFull,GLY:CtermProteinFull,HIS:CtermProteinFull,HIS_D:CtermProteinFull,ILE:CtermProteinFull,LYS:CtermProteinFull,LEU:CtermProteinFull,MET:CtermProteinFull,ASN:CtermProteinFull,PRO:CtermProteinFull,GLN:CtermProteinFull,ARG:CtermProteinFull,SER:CtermProteinFull,THR:CtermProteinFull,VAL:CtermProteinFull,TRP:CtermProteinFull,TYR:CtermProteinFull
#Packer_Task

Threads to request: ALL AVAILABLE

resid	pack?	design?	allowed_aas
1	TRUE	TRUE	ALA:NtermProteinFull,CYS:NtermProteinFull,ASP:NtermProteinFull,GLU:NtermProteinFull,PHE:NtermProteinFull,GLY:NtermProteinFull,HIS:NtermProteinFull,HIS_D:NtermProteinFull,ILE:NtermProteinFull,LYS:NtermProteinFull,LEU:NtermProteinFull,MET:NtermProteinFull,ASN:NtermProteinFull,PRO:NtermProteinFull,GLN:NtermProteinFull,ARG:NtermProteinFull,SER:NtermProteinFull,THR:NtermProteinFull,VAL:NtermProteinFull,TRP:NtermProteinFull,TYR:NtermProteinFull
2	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
3	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
4	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
5	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
6	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
7	TRUE	TRUE	ALA,CYS,MET,SER,THR,TRP
8	TRUE	TRUE	GLY,TRP
9	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
10	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
11	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
12	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
13	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
14	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
15	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
16	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
17	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
18	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
19	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
20	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
21	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
22	TRUE	TRUE	ALA,GLU,HIS,HIS_D,LYS,LEU,MET,ASN,GLN,ARG,TYR
23	TRUE	TRUE	GLY,LYS,ASN
24	TRUE	TRUE	ILE,LYS,LEU,MET,VAL,TYR
25	TRUE	TRUE	GLU,LYS,PRO,ARG
26	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
27	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
28	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
29	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
30	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
31	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
32	TRUE	TRUE	ASP,ASN
33	TRUE	FALSE	GLY
34	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
35	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
36	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
37	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
38	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
39	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
40	TRUE	TRUE	ALA:CtermProteinFull,CYS:CtermProteinFull,ASP:CtermProteinFull,GLU:CtermProteinFull,PHE:CtermProteinFull,GLY:CtermProteinFull,HIS:CtermProteinFull,HIS_D:CtermProteinFull,ILE:CtermProteinFull,LYS:CtermProteinFull,LEU:CtermProteinFull,MET:CtermProteinFull,ASN:CtermProteinFull,PRO:CtermProteinFull,GLN:CtermProteinFull,ARG:CtermProteinFull,SER:CtermProteinFull,THR:CtermProteinFull,VAL:CtermProteinFull,TRP:CtermProteinFull,TYR:CtermProteinFull

可见，Loop区域7，8，22，23，24，32，33都被设置为常出现在当前Loop构型中的氨基酸类型。尝试调整enrichment_threshold的参数，看看自由度的变化？

5. DsspDesign¶

根据设定的二级结构的类型指定氨基酸的Rotamer范围，二级结构氨基酸突变的范围定义如下:

Helix: ADEFIKLNQRSTVWY
Strand: DEFHIKLNQRSTVWY
Loop: ACDEFGHIKLMNPQRSTVWY
HelixStart: ADEFHIKLNPQRSTVWY
HelixCapping: DNST
Nterm: ACDEFGHIKLMNPQRSTVWY
Cterm: ACDEFGHIKLMNPQRSTVWY

In [19]:

from pyrosetta.rosetta.protocols.task_operations import DsspDesignOperation
dssp_design = DsspDesignOperation()

# 如果需要调整二级结构氨基酸类型,可以加载更多设定的语句:
# dssp_design.set_restrictions_aa('Helix','ADEF') #二级结构、范围、（重新设定二级结构氨基酸突变范围）
# dssp_design.set_restrictions_append('Helix','ADEF') #二级结构、范围、(添加二级结构氨基酸突变范围)
# dssp_design.set_restrictions_exclude('Helix','ADEF') #二级结构、范围、(删除二级结构氨基酸突变范围)

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(dssp_design)

# 生成PackerTask
packer_task = pack_tf.create_task_and_apply_taskoperations(denovo_pose)
print(packer_task)

protocols.TaskOperations.DsspDesignOperation: {0} Initializing DSSP regions with default residues
protocols.TaskOperations.DsspDesignOperation: {0} Secondary structure: LEEEEELLHHHHHHHHHHHHHLLLLEEEEEELLEEEEEEL
#Packer_Task

Threads to request: ALL AVAILABLE

resid	pack?	design?	allowed_aas
1	TRUE	TRUE	ALA:NtermProteinFull,CYS:NtermProteinFull,ASP:NtermProteinFull,GLU:NtermProteinFull,PHE:NtermProteinFull,GLY:NtermProteinFull,HIS:NtermProteinFull,HIS_D:NtermProteinFull,ILE:NtermProteinFull,LYS:NtermProteinFull,LEU:NtermProteinFull,MET:NtermProteinFull,ASN:NtermProteinFull,PRO:NtermProteinFull,GLN:NtermProteinFull,ARG:NtermProteinFull,SER:NtermProteinFull,THR:NtermProteinFull,VAL:NtermProteinFull,TRP:NtermProteinFull,TYR:NtermProteinFull
2	TRUE	TRUE	ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
3	TRUE	TRUE	ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
4	TRUE	TRUE	ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
5	TRUE	TRUE	ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
6	TRUE	TRUE	ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
7	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
8	TRUE	TRUE	ASP,ASN,SER,THR
9	TRUE	TRUE	ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
10	TRUE	TRUE	ALA,ASP,GLU,PHE,ILE,LYS,LEU,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
11	TRUE	TRUE	ALA,ASP,GLU,PHE,ILE,LYS,LEU,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
12	TRUE	TRUE	ALA,ASP,GLU,PHE,ILE,LYS,LEU,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
13	TRUE	TRUE	ALA,ASP,GLU,PHE,ILE,LYS,LEU,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
14	TRUE	TRUE	ALA,ASP,GLU,PHE,ILE,LYS,LEU,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
15	TRUE	TRUE	ALA,ASP,GLU,PHE,ILE,LYS,LEU,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
16	TRUE	TRUE	ALA,ASP,GLU,PHE,ILE,LYS,LEU,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
17	TRUE	TRUE	ALA,ASP,GLU,PHE,ILE,LYS,LEU,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
18	TRUE	TRUE	ALA,ASP,GLU,PHE,ILE,LYS,LEU,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
19	TRUE	TRUE	ALA,ASP,GLU,PHE,ILE,LYS,LEU,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
20	TRUE	TRUE	ALA,ASP,GLU,PHE,ILE,LYS,LEU,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
21	TRUE	TRUE	ALA,ASP,GLU,PHE,ILE,LYS,LEU,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
22	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
23	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
24	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
25	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
26	TRUE	TRUE	ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
27	TRUE	TRUE	ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
28	TRUE	TRUE	ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
29	TRUE	TRUE	ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
30	TRUE	TRUE	ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
31	TRUE	TRUE	ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
32	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
33	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
34	TRUE	TRUE	ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
35	TRUE	TRUE	ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
36	TRUE	TRUE	ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
37	TRUE	TRUE	ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
38	TRUE	TRUE	ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
39	TRUE	TRUE	ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
40	TRUE	TRUE	ALA:CtermProteinFull,CYS:CtermProteinFull,ASP:CtermProteinFull,GLU:CtermProteinFull,PHE:CtermProteinFull,GLY:CtermProteinFull,HIS:CtermProteinFull,HIS_D:CtermProteinFull,ILE:CtermProteinFull,LYS:CtermProteinFull,LEU:CtermProteinFull,MET:CtermProteinFull,ASN:CtermProteinFull,PRO:CtermProteinFull,GLN:CtermProteinFull,ARG:CtermProteinFull,SER:CtermProteinFull,THR:CtermProteinFull,VAL:CtermProteinFull,TRP:CtermProteinFull,TYR:CtermProteinFull

6. DesignByCavityProximity（等待发布）¶

2021年新增的TaskOperations，其主要作用是识别蛋白内部的空腔，并根据这些空腔的近似大小来选择可用的氨基酸自由度。一些参数说明:

region_shell: 被选定的氨基酸周围附近X埃的氨基酸均被设定为可突变，默认为8埃
regions_to_design: 选择多少个可被设计的氨基酸中心？默认为1
repack_non_selected: 顾名思义，那些处于region_shell以外的氨基酸都只能进行repacking

In [20]:

# from pyrosetta.rosetta.protocols import rosetta_scripts
# xml = rosetta_scripts.XmlObjects.create_from_string('''
# <TASKOPERATIONS>
#     <DesignByCavityProximity name="des_cavity" region_shell="8.0" regions_to_design="1" repack_non_selected="0" />
# </TASKOPERATIONS>
# ''')
# des_cavity = xml.get_task_operation('des_cavity')

# # 将TaskOperations加载至TaskFactory中
# pack_tf = TaskFactory()
# pack_tf.push_back(des_cavity)

# # 生成PackerTask
# packer_task = pack_tf.create_task_and_apply_taskoperations(denovo_pose)
# print(packer_task)

7. DesignByResidueCentrality（等待发布）¶

2021年新增的TaskOperations，其根据蛋白质内部的氨基酸相互作用网络来决定哪些氨基酸位点可以被设计。具体的做法是: 先计算整个Pose的intra-protein interaction network，然后根据氨基酸的Centrality来决定位点被选择的概率。Centrality越高说明有越多的其他氨基酸在他的周围。因此推测，每次的PackerTask的自由度组成都是不同的，算法会偏向于选择那些对结构或功能有重要作用的氨基酸进行设计。而那些对稳定性贡献较小的区域被设计的概率就会降低。

In [21]:

# from pyrosetta.rosetta.protocols import rosetta_scripts
# xml = rosetta_scripts.XmlObjects.create_from_string('''
# <TASKOPERATIONS>
#     <DesignByResidueCentrality name="des_by_centrality" region_shell="8.0" regions_to_design="1" repack_non_selected="0" />
# </TASKOPERATIONS>
# ''')
# des_by_centrality = xml.get_task_operation('des_by_centrality')

# # 将TaskOperations加载至TaskFactory中
# pack_tf = TaskFactory()
# pack_tf.push_back(des_by_centrality)

# # 生成PackerTask
# packer_task = pack_tf.create_task_and_apply_taskoperations(denovo_pose)
# print(packer_task)

8. DesignRandomRegion（等待发布）¶

2021年新增的TaskOperations，简单地随机选择一些Pose中的氨基酸来进行设计。设计的逻辑依然是region_shell的方法。

In [22]:

# from pyrosetta.rosetta.protocols import rosetta_scripts
# xml = rosetta_scripts.XmlObjects.create_from_string('''
# <TASKOPERATIONS>
#     <DesignRandomRegion name="des_random" region_shell="8.0" regions_to_design="1" repack_non_selected="0" />
# </TASKOPERATIONS>
# ''')
# des_random = xml.get_task_operation('des_random')

# # 将TaskOperations加载至TaskFactory中
# pack_tf = TaskFactory()
# pack_tf.push_back(des_random)

# # 生成PackerTask
# packer_task = pack_tf.create_task_and_apply_taskoperations(denovo_pose)
# print(packer_task)

9. NoRepackDisulfides¶

将Pose的二硫键位点设置为no_repack。

In [23]:

from pyrosetta.rosetta.core.pack.task.operation import NoRepackDisulfides
norepack_ss = NoRepackDisulfides()

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(norepack_ss)

# 生成PackerTask
packer_task = pack_tf.create_task_and_apply_taskoperations(denovo_pose)
print(packer_task)

#Packer_Task

Threads to request: ALL AVAILABLE

resid	pack?	design?	allowed_aas
1	TRUE	TRUE	ALA:NtermProteinFull,CYS:NtermProteinFull,ASP:NtermProteinFull,GLU:NtermProteinFull,PHE:NtermProteinFull,GLY:NtermProteinFull,HIS:NtermProteinFull,HIS_D:NtermProteinFull,ILE:NtermProteinFull,LYS:NtermProteinFull,LEU:NtermProteinFull,MET:NtermProteinFull,ASN:NtermProteinFull,PRO:NtermProteinFull,GLN:NtermProteinFull,ARG:NtermProteinFull,SER:NtermProteinFull,THR:NtermProteinFull,VAL:NtermProteinFull,TRP:NtermProteinFull,TYR:NtermProteinFull
2	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
3	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
4	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
5	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
6	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
7	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
8	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
9	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
10	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
11	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
12	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
13	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
14	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
15	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
16	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
17	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
18	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
19	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
20	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
21	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
22	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
23	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
24	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
25	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
26	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
27	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
28	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
29	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
30	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
31	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
32	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
33	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
34	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
35	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
36	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
37	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
38	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
39	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
40	TRUE	TRUE	ALA:CtermProteinFull,CYS:CtermProteinFull,ASP:CtermProteinFull,GLU:CtermProteinFull,PHE:CtermProteinFull,GLY:CtermProteinFull,HIS:CtermProteinFull,HIS_D:CtermProteinFull,ILE:CtermProteinFull,LYS:CtermProteinFull,LEU:CtermProteinFull,MET:CtermProteinFull,ASN:CtermProteinFull,PRO:CtermProteinFull,GLN:CtermProteinFull,ARG:CtermProteinFull,SER:CtermProteinFull,THR:CtermProteinFull,VAL:CtermProteinFull,TRP:CtermProteinFull,TYR:CtermProteinFull

由于体系中没有二硫键，因此TaskOperations没有起到相应的作用。

10. LayerDesign¶

LayerDesign即将Pose分为core, surface, boundary三个区域，并根据所在的layer决定氨基酸Rotamer的自由度。目前已经有点过时了，最新的方式是使用Layer ResidueSelector进行以及RTL的方案进行替代(自由度极高)，以下介绍如何正确设置LayerDesign的范例:

In [24]:

from pyrosetta import init, pose_from_pdb
from pyrosetta.rosetta.core.select.residue_selector import LayerSelector
from pyrosetta.rosetta.core.select.residue_selector import SecondaryStructureSelector
from pyrosetta.rosetta.core.select.residue_selector import AndResidueSelector, NotResidueSelector
from pyrosetta.rosetta.core.select.residue_selector import PrimarySequenceNeighborhoodSelector, ChainSelector
from pyrosetta.rosetta.core.pack.task.operation import DesignRestrictions
from pyrosetta.rosetta.core.pack.task.operation import RestrictToRepacking
from pyrosetta.rosetta.core.pack.task.operation import RestrictAbsentCanonicalAASRLT

def layer_selection(pick_core, pick_boundary, pick_surface):
    # layer选择器
    layer = LayerSelector()
    layer.set_use_sc_neighbors(True)
    layer.set_layers(pick_core, pick_boundary, pick_surface)
    layer.set_ball_radius(2.0)
    layer.set_cutoffs(3.5, 1.5)  # >= 4 neighbor defined as core residuie. for miniprotein.

    return layer

def ss_selection(ss, min_E, min_H, is_overlap, is_include_ter_loop):
    # 设置二级结构选择
    ss_selector = SecondaryStructureSelector(ss)
    ss_selector.set_minE(min_E)
    ss_selector.set_minH(min_H)
    ss_selector.set_overlap(is_overlap)
    ss_selector.set_use_dssp(True)
    ss_selector.set_include_terminal_loops(is_include_ter_loop)
    return ss_selector

def restrict_to_design(residue_list):
    design_to = RestrictAbsentCanonicalAASRLT()
    design_to.aas_to_keep(residue_list)
    return design_to


# define selector
core_layer = layer_selection(1, 0, 0)
boundary_layer = layer_selection(0, 1, 0)
surface_layer = layer_selection(0, 0, 1)
sheet_selector = ss_selection('E', 2, 3, False, False)
entire_loop_selector = ss_selection('L', 2, 3, False, True)
entire_helix_selector = ss_selection('H', 2, 3, False, False)

# cap
helix_cap_selector = AndResidueSelector(entire_loop_selector, PrimarySequenceNeighborhoodSelector(1, 0, entire_helix_selector))
helix_start_selector = AndResidueSelector(entire_helix_selector, PrimarySequenceNeighborhoodSelector(0, 1, helix_cap_selector))
helix_selector = AndResidueSelector(entire_helix_selector, NotResidueSelector(helix_start_selector))
loop_selector = AndResidueSelector(entire_loop_selector, NotResidueSelector(helix_cap_selector))

# TASKOPERATIONS
layer_design_restrict = DesignRestrictions()
layer_design_restrict.add_selector_rlto_pair(AndResidueSelector(surface_layer, helix_start_selector), restrict_to_design('DEHKPQR'))
layer_design_restrict.add_selector_rlto_pair(AndResidueSelector(surface_layer, helix_selector), restrict_to_design('EHKQR'))
layer_design_restrict.add_selector_rlto_pair(AndResidueSelector(surface_layer, sheet_selector), restrict_to_design('EHKNQRST'))
layer_design_restrict.add_selector_rlto_pair(AndResidueSelector(surface_layer, loop_selector), restrict_to_design('DEGHKNPQRST'))
layer_design_restrict.add_selector_rlto_pair(AndResidueSelector(boundary_layer, helix_start_selector), restrict_to_design('ADEHIKLMNPQRSTVWY'))
layer_design_restrict.add_selector_rlto_pair(AndResidueSelector(boundary_layer, helix_selector), restrict_to_design('ADEHIKLMNQRSTVWY'))
layer_design_restrict.add_selector_rlto_pair(AndResidueSelector(boundary_layer, sheet_selector), restrict_to_design('DEFHIKLMNQRSTVWY'))
layer_design_restrict.add_selector_rlto_pair(AndResidueSelector(boundary_layer, loop_selector), restrict_to_design('ADEFGHIKLMNPQRSTVWY'))
layer_design_restrict.add_selector_rlto_pair(AndResidueSelector(core_layer, helix_start_selector), restrict_to_design('AFILMPVWY'))
layer_design_restrict.add_selector_rlto_pair(AndResidueSelector(core_layer, helix_selector), restrict_to_design('AFILMVWY'))
layer_design_restrict.add_selector_rlto_pair(AndResidueSelector(core_layer, sheet_selector), restrict_to_design('FILMVWY'))
layer_design_restrict.add_selector_rlto_pair(AndResidueSelector(core_layer, loop_selector), restrict_to_design('AFGILMPVWY'))
layer_design_restrict.add_selector_rlto_pair(helix_cap_selector, restrict_to_design('DNST'))

core.select.residue_selector.LayerSelector: {0} Setting LayerSelector to use sidechain neighbors to determine burial.
core.select.residue_selector.LayerSelector: {0} Set cutoffs for core and surface to 5.2 and 2, respectively, in LayerSelector.
core.select.residue_selector.LayerSelector: {0} Setting LayerSelector to use sidechain neighbors to determine burial.
core.select.residue_selector.LayerSelector: {0} Setting core=true boundary=false surface=false in LayerSelector.
core.select.residue_selector.LayerSelector: {0} Setting radius for rolling ball algorithm to 2 in LayerSelector.  (Note that this will have no effect if the sidechain neighbors method is used.)
core.select.residue_selector.LayerSelector: {0} Set cutoffs for core and surface to 3.5 and 1.5, respectively, in LayerSelector.
core.select.residue_selector.LayerSelector: {0} Setting LayerSelector to use sidechain neighbors to determine burial.
core.select.residue_selector.LayerSelector: {0} Set cutoffs for core and surface to 5.2 and 2, respectively, in LayerSelector.
core.select.residue_selector.LayerSelector: {0} Setting LayerSelector to use sidechain neighbors to determine burial.
core.select.residue_selector.LayerSelector: {0} Setting core=false boundary=true surface=false in LayerSelector.
core.select.residue_selector.LayerSelector: {0} Setting radius for rolling ball algorithm to 2 in LayerSelector.  (Note that this will have no effect if the sidechain neighbors method is used.)
core.select.residue_selector.LayerSelector: {0} Set cutoffs for core and surface to 3.5 and 1.5, respectively, in LayerSelector.
core.select.residue_selector.LayerSelector: {0} Setting LayerSelector to use sidechain neighbors to determine burial.
core.select.residue_selector.LayerSelector: {0} Set cutoffs for core and surface to 5.2 and 2, respectively, in LayerSelector.
core.select.residue_selector.LayerSelector: {0} Setting LayerSelector to use sidechain neighbors to determine burial.
core.select.residue_selector.LayerSelector: {0} Setting core=false boundary=false surface=true in LayerSelector.
core.select.residue_selector.LayerSelector: {0} Setting radius for rolling ball algorithm to 2 in LayerSelector.  (Note that this will have no effect if the sidechain neighbors method is used.)
core.select.residue_selector.LayerSelector: {0} Set cutoffs for core and surface to 3.5 and 1.5, respectively, in LayerSelector.

In [25]:

from pyrosetta.rosetta.core.pack.task import TaskFactory
# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(layer_design_restrict)

# 生成PackerTask
packer_task = pack_tf.create_task_and_apply_taskoperations(pose)
print(packer_task)

core.select.residue_selector.SecondaryStructureSelector: {0} Using dssp for secondary structure: LHHHHHHHHHHHLL
core.select.residue_selector.SecondaryStructureSelector: {0} Using dssp for secondary structure: LHHHHHHHHHHHLL
core.select.residue_selector.SecondaryStructureSelector: {0} Using dssp for secondary structure: LHHHHHHHHHHHLL
core.select.residue_selector.PrimarySequenceNeighborhoodSelector: {0} ]
core.select.residue_selector.PrimarySequenceNeighborhoodSelector: {0} ]
core.select.residue_selector.SecondaryStructureSelector: {0} Using dssp for secondary structure: LHHHHHHHHHHHLL
core.select.residue_selector.SecondaryStructureSelector: {0} Using dssp for secondary structure: LHHHHHHHHHHHLL
core.select.residue_selector.SecondaryStructureSelector: {0} Using dssp for secondary structure: LHHHHHHHHHHHLL
core.select.residue_selector.SecondaryStructureSelector: {0} Using dssp for secondary structure: LHHHHHHHHHHHLL
core.select.residue_selector.PrimarySequenceNeighborhoodSelector: {0} ]
core.select.residue_selector.PrimarySequenceNeighborhoodSelector: {0} ]
core.select.residue_selector.SecondaryStructureSelector: {0} Using dssp for secondary structure: LHHHHHHHHHHHLL
core.select.residue_selector.SecondaryStructureSelector: {0} Using dssp for secondary structure: LHHHHHHHHHHHLL
core.select.residue_selector.SecondaryStructureSelector: {0} Using dssp for secondary structure: LHHHHHHHHHHHLL
core.select.residue_selector.SecondaryStructureSelector: {0} Using dssp for secondary structure: LHHHHHHHHHHHLL
core.select.residue_selector.PrimarySequenceNeighborhoodSelector: {0} ]
core.select.residue_selector.SecondaryStructureSelector: {0} Using dssp for secondary structure: LHHHHHHHHHHHLL
core.select.residue_selector.SecondaryStructureSelector: {0} Using dssp for secondary structure: LHHHHHHHHHHHLL
core.select.residue_selector.SecondaryStructureSelector: {0} Using dssp for secondary structure: LHHHHHHHHHHHLL
core.select.residue_selector.PrimarySequenceNeighborhoodSelector: {0} ]
core.select.residue_selector.PrimarySequenceNeighborhoodSelector: {0} ]
core.select.residue_selector.SecondaryStructureSelector: {0} Using dssp for secondary structure: LHHHHHHHHHHHLL
core.select.residue_selector.SecondaryStructureSelector: {0} Using dssp for secondary structure: LHHHHHHHHHHHLL
core.select.residue_selector.SecondaryStructureSelector: {0} Using dssp for secondary structure: LHHHHHHHHHHHLL
core.select.residue_selector.SecondaryStructureSelector: {0} Using dssp for secondary structure: LHHHHHHHHHHHLL
core.select.residue_selector.PrimarySequenceNeighborhoodSelector: {0} ]
core.select.residue_selector.PrimarySequenceNeighborhoodSelector: {0} ]
core.select.residue_selector.SecondaryStructureSelector: {0} Using dssp for secondary structure: LHHHHHHHHHHHLL
core.select.residue_selector.SecondaryStructureSelector: {0} Using dssp for secondary structure: LHHHHHHHHHHHLL
core.select.residue_selector.SecondaryStructureSelector: {0} Using dssp for secondary structure: LHHHHHHHHHHHLL
core.select.residue_selector.SecondaryStructureSelector: {0} Using dssp for secondary structure: LHHHHHHHHHHHLL
core.select.residue_selector.PrimarySequenceNeighborhoodSelector: {0} ]
core.select.residue_selector.SecondaryStructureSelector: {0} Using dssp for secondary structure: LHHHHHHHHHHHLL
core.select.residue_selector.SecondaryStructureSelector: {0} Using dssp for secondary structure: LHHHHHHHHHHHLL
core.select.residue_selector.SecondaryStructureSelector: {0} Using dssp for secondary structure: LHHHHHHHHHHHLL
core.select.residue_selector.PrimarySequenceNeighborhoodSelector: {0} ]
core.select.residue_selector.PrimarySequenceNeighborhoodSelector: {0} ]
core.select.residue_selector.SecondaryStructureSelector: {0} Using dssp for secondary structure: LHHHHHHHHHHHLL
core.select.residue_selector.SecondaryStructureSelector: {0} Using dssp for secondary structure: LHHHHHHHHHHHLL
core.select.residue_selector.SecondaryStructureSelector: {0} Using dssp for secondary structure: LHHHHHHHHHHHLL
core.select.residue_selector.SecondaryStructureSelector: {0} Using dssp for secondary structure: LHHHHHHHHHHHLL
core.select.residue_selector.PrimarySequenceNeighborhoodSelector: {0} ]
core.select.residue_selector.PrimarySequenceNeighborhoodSelector: {0} ]
core.select.residue_selector.SecondaryStructureSelector: {0} Using dssp for secondary structure: LHHHHHHHHHHHLL
core.select.residue_selector.SecondaryStructureSelector: {0} Using dssp for secondary structure: LHHHHHHHHHHHLL
core.select.residue_selector.SecondaryStructureSelector: {0} Using dssp for secondary structure: LHHHHHHHHHHHLL
core.select.residue_selector.SecondaryStructureSelector: {0} Using dssp for secondary structure: LHHHHHHHHHHHLL
core.select.residue_selector.PrimarySequenceNeighborhoodSelector: {0} ]
core.select.residue_selector.SecondaryStructureSelector: {0} Using dssp for secondary structure: LHHHHHHHHHHHLL
core.select.residue_selector.SecondaryStructureSelector: {0} Using dssp for secondary structure: LHHHHHHHHHHHLL
core.select.residue_selector.PrimarySequenceNeighborhoodSelector: {0} ]
#Packer_Task

Threads to request: ALL AVAILABLE

resid	pack?	design?	allowed_aas
1	TRUE	TRUE	ASP:NtermProteinFull,ASN:NtermProteinFull,SER:NtermProteinFull,THR:NtermProteinFull
2	TRUE	TRUE	ASP,GLU,HIS,HIS_D,LYS,PRO,GLN,ARG
3	TRUE	TRUE	GLU,HIS,HIS_D,LYS,GLN,ARG
4	TRUE	TRUE	GLU,HIS,HIS_D,LYS,GLN,ARG
5	TRUE	TRUE	GLU,HIS,HIS_D,LYS,GLN,ARG
6	TRUE	TRUE	GLU,HIS,HIS_D,LYS,GLN,ARG
7	TRUE	TRUE	GLU,HIS,HIS_D,LYS,GLN,ARG
8	TRUE	TRUE	GLU,HIS,HIS_D,LYS,GLN,ARG
9	TRUE	TRUE	GLU,HIS,HIS_D,LYS,GLN,ARG
10	TRUE	TRUE	GLU,HIS,HIS_D,LYS,GLN,ARG
11	TRUE	TRUE	GLU,HIS,HIS_D,LYS,GLN,ARG
12	TRUE	TRUE	GLU,HIS,HIS_D,LYS,GLN,ARG
13	TRUE	TRUE	ASP,GLU,GLY,HIS,HIS_D,LYS,ASN,PRO,GLN,ARG,SER,THR
14	TRUE	TRUE	ASP:CtermProteinFull,GLU:CtermProteinFull,GLY:CtermProteinFull,HIS:CtermProteinFull,HIS_D:CtermProteinFull,LYS:CtermProteinFull,ASN:CtermProteinFull,PRO:CtermProteinFull,GLN:CtermProteinFull,ARG:CtermProteinFull,SER:CtermProteinFull,THR:CtermProteinFull

11. SelectResiduesWithinChain¶

根据内部链编号，选择链中的氨基酸Rotamer自由度，如果modify unselected residues参数设置为true，则所有其他residues都设置为norepack。

In [26]:

# 定义氨基酸范围:
from pyrosetta.rosetta.protocols.task_operations import SelectResiduesWithinChainOperation
repacking_define = SelectResiduesWithinChainOperation()
repacking_define.chain(1)  # 1,2,3 按照pose的顺序
for i in [1,2,3,7,8,9]:
    repacking_define.add_res(i) # which residues within the chain

# 定义Pack状态:
repacking_define.allow_design(False) 
repacking_define.allow_repacking(True)
repacking_define.modify_unselected_residues(True)  # 是否对未选择区域设置为no_repack?（快速操作）

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(repacking_define)

# 生成PackerTask
packer_task = pack_tf.create_task_and_apply_taskoperations(pose)
print(packer_task)

protocols.TaskOperations.SelectResiduesWithinChainOperation: {0} Residues set to repacking (all others are prevented from repacking): 1,2,3,7,8,9,
#Packer_Task

Threads to request: ALL AVAILABLE

resid	pack?	design?	allowed_aas
1	TRUE	FALSE	ASP:NtermProteinFull
2	TRUE	FALSE	GLU
3	TRUE	FALSE	LEU
4	FALSE	FALSE	
5	FALSE	FALSE	
6	FALSE	FALSE	
7	TRUE	FALSE	VAL
8	TRUE	FALSE	GLU
9	TRUE	FALSE	GLN
10	FALSE	FALSE	
11	FALSE	FALSE	
12	FALSE	FALSE	
13	FALSE	FALSE	
14	FALSE	FALSE

12. SelectBySASAOperation¶

根据SASA值来选择蛋白质的Layer区域(core, surface, boundary)，并根据所在的layer决定氨基酸Rotamer的自由度。参数的解释:

mode: sc = 侧链SASA综合, mc = 主链+CB的SASA总和。
state: "monomer"(将每条链进行分离独立的pose进行计算), "bound"(不做额外处理), "unbound"(根据jump的设定,将几个链平移1000A后在进行评估SASA)
probe_radius: 默认2.2, 比1.4大，但是也能满足需求。
core_asa: 默认0, sasa小于该值，认为是core.
surface_asa: 默认30，sasa大于该值，认为是surface.
jumps: 默认1, 定义从哪条链开始视为jump点.如果mode设置为"unbound". 如果jump设置为2，那么chain1,2视为一体.
is_design_core: 该区域能否设计？
is_design_boundary: 该区域能否设计？
is_design_surface: 该区域能否设计？
sym_dof_names: 控制同源多聚体对称化操作, 输入对称性的定义变量名。

In [27]:

# 定义参数:
from pyrosetta.rosetta.protocols.task_operations import SelectBySASAOperation
mode="mc"
state="bound"
probe_radius=2.0
core_asa=20
surface_asa=40
jump = '1'
sym_dof_names = '' # 对称化自由度的代号                                  
core = True     
boundary = False
surface = False
select_sasa = SelectBySASAOperation(mode, state, probe_radius, core_asa, surface_asa, jump, sym_dof_names, core, boundary, surface)

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(select_sasa)

# 生成PackerTask
packer_task = pack_tf.create_task_and_apply_taskoperations(denovo_pose)
print(packer_task)

#Packer_Task

Threads to request: ALL AVAILABLE

resid	pack?	design?	allowed_aas
1	FALSE	FALSE	
2	FALSE	FALSE	
3	FALSE	FALSE	
4	FALSE	FALSE	
5	FALSE	FALSE	
6	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
7	FALSE	FALSE	
8	FALSE	FALSE	
9	FALSE	FALSE	
10	FALSE	FALSE	
11	FALSE	FALSE	
12	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
13	FALSE	FALSE	
14	FALSE	FALSE	
15	FALSE	FALSE	
16	FALSE	FALSE	
17	FALSE	FALSE	
18	FALSE	FALSE	
19	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
20	FALSE	FALSE	
21	FALSE	FALSE	
22	FALSE	FALSE	
23	FALSE	FALSE	
24	FALSE	FALSE	
25	FALSE	FALSE	
26	FALSE	FALSE	
27	FALSE	FALSE	
28	FALSE	FALSE	
29	FALSE	FALSE	
30	FALSE	FALSE	
31	FALSE	FALSE	
32	FALSE	FALSE	
33	FALSE	FALSE	
34	FALSE	FALSE	
35	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
36	FALSE	FALSE	
37	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
38	FALSE	FALSE	
39	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
40	FALSE	FALSE

此处，蛋白质的core部分是被允许进行设计的。

13. RestrictToTermini¶

在指定的Pose链中，只允许N端第一个残基或C端最后一个残基进行repack。

In [28]:

from pyrosetta.rosetta.protocols.task_operations import RestrictToTerminiOperation
nc_repack = RestrictToTerminiOperation(chain=1, restrict_n_terminus=True, restrict_c_terminus=True)

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(nc_repack)

# 生成PackerTask
packer_task = pack_tf.create_task_and_apply_taskoperations(pose)
print(packer_task)

#Packer_Task

Threads to request: ALL AVAILABLE

resid	pack?	design?	allowed_aas
1	TRUE	FALSE	ASP:NtermProteinFull
2	FALSE	FALSE	
3	FALSE	FALSE	
4	FALSE	FALSE	
5	FALSE	FALSE	
6	FALSE	FALSE	
7	FALSE	FALSE	
8	FALSE	FALSE	
9	FALSE	FALSE	
10	FALSE	FALSE	
11	FALSE	FALSE	
12	FALSE	FALSE	
13	FALSE	FALSE	
14	TRUE	FALSE	GLY:CtermProteinFull

2.1.3 Interface/Neighborhood Specifications¶

1. DesignAround¶

最早的region_shell机制的TaskOperations，根据指定的氨基酸位点来确定Design shell和repack shell半径。处于相应shell中的氨基酸Rotamer状态设置为Design或Repacking。其余剩下部分均设置为no_repack。

In [29]:

from pyrosetta.rosetta.protocols.task_operations import DesignAroundOperation
# 设定指定热点残基
around = DesignAroundOperation ()
for i in [7]:
    around.include_residue(i)

around.design_shell(7.0) # design层半径（不包括指定的残基）
around.repack_shell(10.0) # repack层半径, 大于等于epack_shell（不包括指定的残基）
around.resnums_allow_design(1) # 只允许指定的resnum list中氨基酸进行设计；
around.allow_design(1) # 允许Desgin层进行设计;

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(around)

# 生成PackerTask
packer_task = pack_tf.create_task_and_apply_taskoperations(pose)
print(packer_task)

#Packer_Task

Threads to request: ALL AVAILABLE

resid	pack?	design?	allowed_aas
1	TRUE	FALSE	ASP:NtermProteinFull
2	FALSE	FALSE	
3	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
4	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
5	TRUE	FALSE	LYS
6	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
7	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
8	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
9	TRUE	FALSE	GLN
10	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
11	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
12	TRUE	FALSE	ARG
13	FALSE	FALSE	
14	FALSE	FALSE

2. DetectProteinLigandInterface¶

该Operation只关注底物-蛋白PPI界面上的残基设置，根据cut1，cut2参数确定design shell，根据cut3和cut4确定repack shell。特别注意，init的时候需要把-ignore_unrecognized_res进行设置，否则底物会被忽略导致识别失败。

In [30]:

from pyrosetta.rosetta.protocols import rosetta_scripts
# ligand pose;
init('-ignore_unrecognized_res false')
ligand_complex_pose = pose_from_pdb('./data/1ckn.pdb')

# pick selection;
xml = rosetta_scripts.XmlObjects.create_from_string('''
<TASKOPERATIONS>
    <DetectProteinLigandInterface name="ligand_interface" cut1="6.0" cut2="8.0" cut3="10.0" cut4="12.0"
    design="true"/>
</TASKOPERATIONS>
''')
ligand_design = xml.get_task_operation('ligand_interface')

# 将TaskOperations加载至TaskFactory中
tf = TaskFactory()
tf.push_back(ligand_design)

# 生成PackerTask
packer_task = tf.create_task_and_apply_taskoperations(ligand_complex_pose)
print(packer_task)

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 -ignore_unrecognized_res false -database /opt/miniconda3/lib/python3.7/site-packages/pyrosetta/database
basic.random.init_random_generator: {0} 'RNG device' seed mode, using '/dev/urandom', seed=-706432799 seed_offset=0 real_seed=-706432799 thread_index=0
basic.random.init_random_generator: {0} RandomGenerator:init: Normal mode, seed=-706432799 RG_type=mt19937
core.import_pose.import_pose: {0} File './data/1ckn.pdb' automatically determined to be of type PDB
core.io.pose_from_sfr.chirality_resolution: {0} Flipping atom xyz for OP1 and OP2 for residue GTP
core.io.pose_from_sfr.chirality_resolution: {0} Flipping atom xyz for  H21 and  H22 for residue GTP
core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OXT on residue PHE:CtermProteinFull 317
protocols.rosetta_scripts.RosettaScriptsParser: {0} Generating XML Schema for rosetta_scripts...
protocols.rosetta_scripts.RosettaScriptsParser: {0} ...done
protocols.rosetta_scripts.RosettaScriptsParser: {0} Initializing schema validator...
protocols.rosetta_scripts.RosettaScriptsParser: {0} ...done
protocols.rosetta_scripts.RosettaScriptsParser: {0} Validating input script...
protocols.rosetta_scripts.RosettaScriptsParser: {0} ...done
protocols.rosetta_scripts.RosettaScriptsParser: {0} Parsed script:
<ROSETTASCRIPTS>
	<TASKOPERATIONS>
		<DetectProteinLigandInterface cut1="6.0" cut2="8.0" cut3="10.0" cut4="12.0" design="true" name="ligand_interface"/>
	</TASKOPERATIONS>
	<PROTOCOLS/>
</ROSETTASCRIPTS>
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/PairEPotential/pdb_pair_stats_fine
basic.io.database: {0} Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt
basic.io.database: {0} Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt
basic.io.database: {0} Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt
basic.io.database: {0} Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt
basic.io.database: {0} Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt
basic.io.database: {0} Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt
core.scoring.ramachandran: {0} shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.
basic.io.database: {0} Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb
basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/avg_L_rama.dat
core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/avg_L_rama.dat.
basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/sym_all_rama.dat
core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/sym_all_rama.dat.
basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/sym_G_rama.dat
core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/sym_G_rama.dat.
basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/sym_P_rama.dat
core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/sym_P_rama.dat.
basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/avg_L_rama_str.dat
core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/avg_L_rama_str.dat.
basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/sym_all_rama_str.dat
core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/sym_all_rama_str.dat.
basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/sym_G_rama_str.dat
core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/sym_G_rama_str.dat.
basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/sym_P_rama_str.dat
core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/sym_P_rama_str.dat.
protocols.jd2.parser.TaskOperationLoader: {0} Defined TaskOperation named "ligand_interface" of type DetectProteinLigandInterface
protocols.rosetta_scripts.ParsedProtocol: {0} ParsedProtocol mover with the following settings
protocols.enzdes.EnzdesTaskOperations: {0} Choosing the following residues as targets for detecting interface: 318+
protocols.enzdes.EnzdesTaskOperations: {0} Design Interface: detected 21 design-shell residues and 46 repack-shell residues, shell sizes cut1-4 used were 6 8 10 12
protocols.enzdes.EnzdesTaskOperations: {0} Design-shell Residues(pose-numbering): 48+49+50+51+70+72+73+75+76+77+96+119+121+136+137+178+203+206+208+222+224+
protocols.enzdes.EnzdesTaskOperations: {0} Repack-shell Residues(pose-numbering): 46+52+53+68+69+71+74+78+79+95+120+122+123+134+135+151+177+179+180+196+200+201+202+204+205+207+215+216+217+218+219+223+225+226+231+232+233+234+271+292+295+296+299+300+303+318+
protocols.enzdes.EnzdesTaskOperations: {0} Final Design Shell Residues: 48, 49, 50, 51, 70, 72, 73, 75, 76, 77, 96, 119, 121, 136, 137, 178, 203, 206, 208, 222, 224,
protocols.enzdes.EnzdesTaskOperations: {0} Final Repack Shell Residues: 46, 48, 49, 50, 51, 52, 53, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 95, 96, 119, 120, 121, 122, 123, 134, 135, 136, 137, 151, 177, 178, 179, 180, 196, 200, 201, 202, 203, 204, 205, 206, 207, 208, 215, 216, 217, 218, 219, 222, 223, 224, 225, 226, 231, 232, 233, 234, 271, 292, 295, 296, 299, 300, 303, 318,
#Packer_Task

Threads to request: ALL AVAILABLE

resid	pack?	design?	allowed_aas
1	FALSE	FALSE	
2	FALSE	FALSE	
3	FALSE	FALSE	
4	FALSE	FALSE	
5	FALSE	FALSE	
6	FALSE	FALSE	
7	FALSE	FALSE	
8	FALSE	FALSE	
9	FALSE	FALSE	
10	FALSE	FALSE	
11	FALSE	FALSE	
12	FALSE	FALSE	
13	FALSE	FALSE	
14	FALSE	FALSE	
15	FALSE	FALSE	
16	FALSE	FALSE	
17	FALSE	FALSE	
18	FALSE	FALSE	
19	FALSE	FALSE	
20	FALSE	FALSE	
21	FALSE	FALSE	
22	FALSE	FALSE	
23	FALSE	FALSE	
24	FALSE	FALSE	
25	FALSE	FALSE	
26	FALSE	FALSE	
27	FALSE	FALSE	
28	FALSE	FALSE	
29	FALSE	FALSE	
30	FALSE	FALSE	
31	FALSE	FALSE	
32	FALSE	FALSE	
33	FALSE	FALSE	
34	FALSE	FALSE	
35	FALSE	FALSE	
36	FALSE	FALSE	
37	FALSE	FALSE	
38	FALSE	FALSE	
39	FALSE	FALSE	
40	FALSE	FALSE	
41	FALSE	FALSE	
42	FALSE	FALSE	
43	FALSE	FALSE	
44	FALSE	FALSE	
45	FALSE	FALSE	
46	TRUE	FALSE	LEU
47	FALSE	FALSE	
48	TRUE	TRUE	ALA,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
49	TRUE	TRUE	ALA,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
50	TRUE	TRUE	ALA,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
51	TRUE	TRUE	ALA,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
52	TRUE	FALSE	VAL
53	TRUE	FALSE	SER
54	FALSE	FALSE	
55	FALSE	FALSE	
56	FALSE	FALSE	
57	FALSE	FALSE	
58	FALSE	FALSE	
59	FALSE	FALSE	
60	FALSE	FALSE	
61	FALSE	FALSE	
62	FALSE	FALSE	
63	FALSE	FALSE	
64	FALSE	FALSE	
65	FALSE	FALSE	
66	FALSE	FALSE	
67	FALSE	FALSE	
68	TRUE	FALSE	VAL
69	TRUE	FALSE	VAL
70	TRUE	TRUE	ALA,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
71	TRUE	FALSE	GLU
72	TRUE	TRUE	ALA,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
73	TRUE	TRUE	ALA,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
74	TRUE	FALSE	ASP
75	TRUE	TRUE	ALA,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
76	TRUE	TRUE	ALA,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
77	TRUE	TRUE	ALA,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
78	TRUE	FALSE	PHE
79	TRUE	FALSE	MET
80	FALSE	FALSE	
81	FALSE	FALSE	
82	FALSE	FALSE	
83	FALSE	FALSE	
84	FALSE	FALSE	
85	FALSE	FALSE	
86	FALSE	FALSE	
87	FALSE	FALSE	
88	FALSE	FALSE	
89	FALSE	FALSE	
90	FALSE	FALSE	
91	FALSE	FALSE	
92	FALSE	FALSE	
93	FALSE	FALSE	
94	FALSE	FALSE	
95	TRUE	FALSE	ASP
96	TRUE	TRUE	ALA,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
97	FALSE	FALSE	
98	FALSE	FALSE	
99	FALSE	FALSE	
100	FALSE	FALSE	
101	FALSE	FALSE	
102	FALSE	FALSE	
103	FALSE	FALSE	
104	FALSE	FALSE	
105	FALSE	FALSE	
106	FALSE	FALSE	
107	FALSE	FALSE	
108	FALSE	FALSE	
109	FALSE	FALSE	
110	FALSE	FALSE	
111	FALSE	FALSE	
112	FALSE	FALSE	
113	FALSE	FALSE	
114	FALSE	FALSE	
115	FALSE	FALSE	
116	FALSE	FALSE	
117	FALSE	FALSE	
118	FALSE	FALSE	
119	TRUE	TRUE	ALA,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
120	TRUE	FALSE	GLY
121	TRUE	TRUE	ALA,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
122	TRUE	FALSE	LEU
123	TRUE	FALSE	CYS
124	FALSE	FALSE	
125	FALSE	FALSE	
126	FALSE	FALSE	
127	FALSE	FALSE	
128	FALSE	FALSE	
129	FALSE	FALSE	
130	FALSE	FALSE	
131	FALSE	FALSE	
132	FALSE	FALSE	
133	FALSE	FALSE	
134	TRUE	FALSE	VAL
135	TRUE	FALSE	LEU
136	TRUE	TRUE	ALA,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
137	TRUE	TRUE	ALA,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
138	FALSE	FALSE	
139	FALSE	FALSE	
140	FALSE	FALSE	
141	FALSE	FALSE	
142	FALSE	FALSE	
143	FALSE	FALSE	
144	FALSE	FALSE	
145	FALSE	FALSE	
146	FALSE	FALSE	
147	FALSE	FALSE	
148	FALSE	FALSE	
149	FALSE	FALSE	
150	FALSE	FALSE	
151	TRUE	FALSE	LEU
152	FALSE	FALSE	
153	FALSE	FALSE	
154	FALSE	FALSE	
155	FALSE	FALSE	
156	FALSE	FALSE	
157	FALSE	FALSE	
158	FALSE	FALSE	
159	FALSE	FALSE	
160	FALSE	FALSE	
161	FALSE	FALSE	
162	FALSE	FALSE	
163	FALSE	FALSE	
164	FALSE	FALSE	
165	FALSE	FALSE	
166	FALSE	FALSE	
167	FALSE	FALSE	
168	FALSE	FALSE	
169	FALSE	FALSE	
170	FALSE	FALSE	
171	FALSE	FALSE	
172	FALSE	FALSE	
173	FALSE	FALSE	
174	FALSE	FALSE	
175	FALSE	FALSE	
176	FALSE	FALSE	
177	TRUE	FALSE	TYR
178	TRUE	TRUE	ALA,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
179	TRUE	FALSE	GLU
180	TRUE	FALSE	TRP
181	FALSE	FALSE	
182	FALSE	FALSE	
183	FALSE	FALSE	
184	FALSE	FALSE	
185	FALSE	FALSE	
186	FALSE	FALSE	
187	FALSE	FALSE	
188	FALSE	FALSE	
189	FALSE	FALSE	
190	FALSE	FALSE	
191	FALSE	FALSE	
192	FALSE	FALSE	
193	FALSE	FALSE	
194	FALSE	FALSE	
195	FALSE	FALSE	
196	TRUE	FALSE	ALA
197	FALSE	FALSE	
198	FALSE	FALSE	
199	FALSE	FALSE	
200	TRUE	FALSE	TYR
201	TRUE	FALSE	HIS,HIS_D
202	TRUE	FALSE	THR
203	TRUE	TRUE	ALA,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
204	TRUE	FALSE	GLY
205	TRUE	FALSE	LEU
206	TRUE	TRUE	ALA,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
207	TRUE	FALSE	ILE
208	TRUE	TRUE	ALA,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
209	FALSE	FALSE	
210	FALSE	FALSE	
211	FALSE	FALSE	
212	FALSE	FALSE	
213	FALSE	FALSE	
214	FALSE	FALSE	
215	TRUE	FALSE	ILE
216	TRUE	FALSE	TYR
217	TRUE	FALSE	GLY
218	TRUE	FALSE	ARG
219	TRUE	FALSE	ASN
220	FALSE	FALSE	
221	FALSE	FALSE	
222	TRUE	TRUE	ALA,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
223	TRUE	FALSE	PHE
224	TRUE	TRUE	ALA,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
225	TRUE	FALSE	LEU
226	TRUE	FALSE	LYS
227	FALSE	FALSE	
228	FALSE	FALSE	
229	FALSE	FALSE	
230	FALSE	FALSE	
231	TRUE	FALSE	HIS,HIS_D
232	TRUE	FALSE	THR
233	TRUE	FALSE	ILE
234	TRUE	FALSE	ASP
235	FALSE	FALSE	
236	FALSE	FALSE	
237	FALSE	FALSE	
238	FALSE	FALSE	
239	FALSE	FALSE	
240	FALSE	FALSE	
241	FALSE	FALSE	
242	FALSE	FALSE	
243	FALSE	FALSE	
244	FALSE	FALSE	
245	FALSE	FALSE	
246	FALSE	FALSE	
247	FALSE	FALSE	
248	FALSE	FALSE	
249	FALSE	FALSE	
250	FALSE	FALSE	
251	FALSE	FALSE	
252	FALSE	FALSE	
253	FALSE	FALSE	
254	FALSE	FALSE	
255	FALSE	FALSE	
256	FALSE	FALSE	
257	FALSE	FALSE	
258	FALSE	FALSE	
259	FALSE	FALSE	
260	FALSE	FALSE	
261	FALSE	FALSE	
262	FALSE	FALSE	
263	FALSE	FALSE	
264	FALSE	FALSE	
265	FALSE	FALSE	
266	FALSE	FALSE	
267	FALSE	FALSE	
268	FALSE	FALSE	
269	FALSE	FALSE	
270	FALSE	FALSE	
271	TRUE	FALSE	GLU
272	FALSE	FALSE	
273	FALSE	FALSE	
274	FALSE	FALSE	
275	FALSE	FALSE	
276	FALSE	FALSE	
277	FALSE	FALSE	
278	FALSE	FALSE	
279	FALSE	FALSE	
280	FALSE	FALSE	
281	FALSE	FALSE	
282	FALSE	FALSE	
283	FALSE	FALSE	
284	FALSE	FALSE	
285	FALSE	FALSE	
286	FALSE	FALSE	
287	FALSE	FALSE	
288	FALSE	FALSE	
289	FALSE	FALSE	
290	FALSE	FALSE	
291	FALSE	FALSE	
292	TRUE	FALSE	ASN
293	FALSE	FALSE	
294	FALSE	FALSE	
295	TRUE	FALSE	LEU
296	TRUE	FALSE	THR
297	FALSE	FALSE	
298	FALSE	FALSE	
299	TRUE	FALSE	LYS
300	TRUE	FALSE	THR
301	FALSE	FALSE	
302	FALSE	FALSE	
303	TRUE	FALSE	ASN
304	FALSE	FALSE	
305	FALSE	FALSE	
306	FALSE	FALSE	
307	FALSE	FALSE	
308	FALSE	FALSE	
309	FALSE	FALSE	
310	FALSE	FALSE	
311	FALSE	FALSE	
312	FALSE	FALSE	
313	FALSE	FALSE	
314	FALSE	FALSE	
315	FALSE	FALSE	
316	FALSE	FALSE	
317	FALSE	FALSE	
318	TRUE	FALSE	RGU:UpperRNA:5PrimePackTriPhos

3. ProteinInterfaceDesign¶

该Operation只关注蛋白-蛋白PPI界面上的残基设置(默认8A)，非界面处的残基将会被设置为no_repack。并且默认会排除氨基酸设计为C, G, P三种不利的氨基酸。

In [31]:

from pyrosetta.rosetta.protocols.task_operations import ProteinInterfaceDesignOperation
# 加载一个dimmer的coil coil结构:
interface_pose = pose_from_pdb('./data/6yek.pdb')
print(interface_pose.pdb_info())  # 查看链信息

core.import_pose.import_pose: {0} File './data/6yek.pdb' automatically determined to be of type PDB
core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OXT on residue ALA:CtermProteinFull 24
core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OXT on residue ALA:CtermProteinFull 48
PDB file name: ./data/6yek.pdb
 Pose Range  Chain    PDB Range  |   #Residues         #Atoms

0001 -- 0024    A 0300  -- 0323  |   0024 residues;    00396 atoms
0025 -- 0048    B 0300  -- 0323  |   0024 residues;    00396 atoms
                           TOTAL |   0048 residues;    00792 atoms

In [32]:

# 此案例以chain1可以被设计，chain2只能repacking作为逻辑。
interface_design = ProteinInterfaceDesignOperation()
interface_design.jump(1) # jump点设置.之前的认定为chain1，之后的为chain2。2条链以上需要设置！
interface_design.interface_distance_cutoff(8.0)
interface_design.repack_chain1(True)  # 是否允许chain1 repack
interface_design.repack_chain2(True)  # 是否允许chain2 repack
interface_design.design_chain1(True)  # 是否允许chain1 design
interface_design.design_chain2(False)  # 是否允许chain design
interface_design.allow_all_aas(False) # allow all amino acids to be designed at all positions, do not exclude C, G, P

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(interface_design)

# 生成PackerTask
packer_task = pack_tf.create_task_and_apply_taskoperations(interface_pose)
print(packer_task)

#Packer_Task

Threads to request: ALL AVAILABLE

resid	pack?	design?	allowed_aas
1	FALSE	FALSE	
2	TRUE	TRUE	ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
3	TRUE	TRUE	ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
4	FALSE	FALSE	
5	TRUE	TRUE	ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
6	TRUE	TRUE	ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
7	TRUE	TRUE	ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
8	FALSE	FALSE	
9	TRUE	TRUE	ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
10	TRUE	TRUE	ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
11	FALSE	FALSE	
12	TRUE	TRUE	ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
13	TRUE	TRUE	ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
14	FALSE	FALSE	
15	FALSE	FALSE	
16	TRUE	TRUE	ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
17	TRUE	TRUE	ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
18	FALSE	FALSE	
19	TRUE	TRUE	ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
20	TRUE	TRUE	ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
21	FALSE	FALSE	
22	FALSE	FALSE	
23	TRUE	TRUE	ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR
24	TRUE	TRUE	ALA:CtermProteinFull,ASP:CtermProteinFull,GLU:CtermProteinFull,PHE:CtermProteinFull,HIS:CtermProteinFull,HIS_D:CtermProteinFull,ILE:CtermProteinFull,LYS:CtermProteinFull,LEU:CtermProteinFull,MET:CtermProteinFull,ASN:CtermProteinFull,GLN:CtermProteinFull,ARG:CtermProteinFull,SER:CtermProteinFull,THR:CtermProteinFull,VAL:CtermProteinFull,TRP:CtermProteinFull,TYR:CtermProteinFull
25	FALSE	FALSE	
26	TRUE	FALSE	LEU
27	TRUE	FALSE	LYS
28	FALSE	FALSE	
29	TRUE	FALSE	GLN
30	TRUE	FALSE	ALA
31	FALSE	FALSE	
32	FALSE	FALSE	
33	TRUE	FALSE	TYR
34	TRUE	FALSE	LYS
35	FALSE	FALSE	
36	TRUE	FALSE	ASP
37	TRUE	FALSE	PHE
38	FALSE	FALSE	
39	FALSE	FALSE	
40	TRUE	FALSE	GLU
41	TRUE	FALSE	ARG
42	FALSE	FALSE	
43	TRUE	FALSE	ALA
44	TRUE	FALSE	ARG
45	FALSE	FALSE	
46	FALSE	FALSE	
47	TRUE	FALSE	LEU
48	TRUE	FALSE	ALA:CtermProteinFull

4. RestrictToInterface¶

根据jump点和截断半径的设置，将蛋白-蛋白界面进行design，非界面区全部设置为no_repack。如果需要控制其中的自由度，还需要引入其他的TaskOperations，没有ProteinInterfaceDesign自定义程度高。

In [33]:

from pyrosetta.rosetta.protocols.simple_task_operations import RestrictToInterface
Design_interface = RestrictToInterface(rb_jump_in=1, distance_in=8)

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(Design_interface)

# 生成PackerTask
packer_task = pack_tf.create_task_and_apply_taskoperations(interface_pose)
print(packer_task)

#Packer_Task

Threads to request: ALL AVAILABLE

resid	pack?	design?	allowed_aas
1	FALSE	FALSE	
2	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
3	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
4	FALSE	FALSE	
5	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
6	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
7	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
8	FALSE	FALSE	
9	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
10	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
11	FALSE	FALSE	
12	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
13	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
14	FALSE	FALSE	
15	FALSE	FALSE	
16	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
17	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
18	FALSE	FALSE	
19	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
20	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
21	FALSE	FALSE	
22	FALSE	FALSE	
23	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
24	TRUE	TRUE	ALA:CtermProteinFull,CYS:CtermProteinFull,ASP:CtermProteinFull,GLU:CtermProteinFull,PHE:CtermProteinFull,GLY:CtermProteinFull,HIS:CtermProteinFull,HIS_D:CtermProteinFull,ILE:CtermProteinFull,LYS:CtermProteinFull,LEU:CtermProteinFull,MET:CtermProteinFull,ASN:CtermProteinFull,PRO:CtermProteinFull,GLN:CtermProteinFull,ARG:CtermProteinFull,SER:CtermProteinFull,THR:CtermProteinFull,VAL:CtermProteinFull,TRP:CtermProteinFull,TYR:CtermProteinFull
25	FALSE	FALSE	
26	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
27	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
28	FALSE	FALSE	
29	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
30	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
31	FALSE	FALSE	
32	FALSE	FALSE	
33	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
34	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
35	FALSE	FALSE	
36	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
37	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
38	FALSE	FALSE	
39	FALSE	FALSE	
40	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
41	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
42	FALSE	FALSE	
43	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
44	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
45	FALSE	FALSE	
46	FALSE	FALSE	
47	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
48	TRUE	TRUE	ALA:CtermProteinFull,CYS:CtermProteinFull,ASP:CtermProteinFull,GLU:CtermProteinFull,PHE:CtermProteinFull,GLY:CtermProteinFull,HIS:CtermProteinFull,HIS_D:CtermProteinFull,ILE:CtermProteinFull,LYS:CtermProteinFull,LEU:CtermProteinFull,MET:CtermProteinFull,ASN:CtermProteinFull,PRO:CtermProteinFull,GLN:CtermProteinFull,ARG:CtermProteinFull,SER:CtermProteinFull,THR:CtermProteinFull,VAL:CtermProteinFull,TRP:CtermProteinFull,TYR:CtermProteinFull

5. RestrictToInterfaceVectorOperation¶

使用向量法计算界面。首先根据CB_dist_cutoff的距离判断出一个大致的shell区域，然后根据遍历每个残基侧链原子与其他氨基酸的原子距离，确认是否都小于nearby_atom_cutoff，如果满足条件，那么这些都是interface的残基。如果剩余的残基没有通过第一个标准，将使用第二个标准进行判断，计算残基的CA-CB原子向量以及CB原子与Interface上其他原子CB的向量(CB-CB)，这两个向量的夹角如何小于vector_angle_cutoff。那么这些残基也是Interface上的残基，并且这些两个向量的距离不得大于vector_dist_cutoff。

CB_dist_cutoff: CB-CB距离(range:8.0~15.0)
nearby_atom_cutoff: CA-CB距离(range:4.0~8.0)
vector_angle_cutoff: CA-CB、CB-CB向量的点乘. 向量的角度截断(range:60~90)
vector_dist_cutoff: CA-CB、CB-CB向量距离的限制 (range:7.0~12.0)

In [34]:

from pyrosetta.rosetta.protocols.task_operations import RestrictToInterfaceVectorOperation
# 定义参数:
lower_chain_id = 1
upper_chain_id = 2
CB_dist_cutoff = 8.0
nearby_atom_cutoff = 5.0
vector_angle_cutoff = 75
vector_dist_cutoff = 9.0
include_all_water = False
restrict_to_interface = RestrictToInterfaceVectorOperation(lower_chain_id, upper_chain_id, CB_dist_cutoff, nearby_atom_cutoff,
                                                           vector_angle_cutoff, vector_dist_cutoff, include_all_water)

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(restrict_to_interface)

# 生成PackerTask
packer_task = pack_tf.create_task_and_apply_taskoperations(interface_pose)
print(packer_task)

#Packer_Task

Threads to request: ALL AVAILABLE

resid	pack?	design?	allowed_aas
1	FALSE	FALSE	
2	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
3	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
4	FALSE	FALSE	
5	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
6	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
7	FALSE	FALSE	
8	FALSE	FALSE	
9	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
10	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
11	FALSE	FALSE	
12	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
13	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
14	FALSE	FALSE	
15	FALSE	FALSE	
16	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
17	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
18	FALSE	FALSE	
19	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
20	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
21	FALSE	FALSE	
22	FALSE	FALSE	
23	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
24	TRUE	TRUE	ALA:CtermProteinFull,CYS:CtermProteinFull,ASP:CtermProteinFull,GLU:CtermProteinFull,PHE:CtermProteinFull,GLY:CtermProteinFull,HIS:CtermProteinFull,HIS_D:CtermProteinFull,ILE:CtermProteinFull,LYS:CtermProteinFull,LEU:CtermProteinFull,MET:CtermProteinFull,ASN:CtermProteinFull,PRO:CtermProteinFull,GLN:CtermProteinFull,ARG:CtermProteinFull,SER:CtermProteinFull,THR:CtermProteinFull,VAL:CtermProteinFull,TRP:CtermProteinFull,TYR:CtermProteinFull
25	FALSE	FALSE	
26	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
27	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
28	FALSE	FALSE	
29	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
30	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
31	FALSE	FALSE	
32	FALSE	FALSE	
33	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
34	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
35	FALSE	FALSE	
36	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
37	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
38	FALSE	FALSE	
39	FALSE	FALSE	
40	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
41	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
42	FALSE	FALSE	
43	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
44	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
45	FALSE	FALSE	
46	FALSE	FALSE	
47	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
48	TRUE	TRUE	ALA:CtermProteinFull,CYS:CtermProteinFull,ASP:CtermProteinFull,GLU:CtermProteinFull,PHE:CtermProteinFull,GLY:CtermProteinFull,HIS:CtermProteinFull,HIS_D:CtermProteinFull,ILE:CtermProteinFull,LYS:CtermProteinFull,LEU:CtermProteinFull,MET:CtermProteinFull,ASN:CtermProteinFull,PRO:CtermProteinFull,GLN:CtermProteinFull,ARG:CtermProteinFull,SER:CtermProteinFull,THR:CtermProteinFull,VAL:CtermProteinFull,TRP:CtermProteinFull,TYR:CtermProteinFull

2.1.4 Input-based design¶

输入依赖的TaskOperations大多和序列比对有关。

1. AlignedThread¶

使用经过比对的序列作为输入，与同源家族中的序列进行比对，gap区域、保守的区域设置为no_repack，并将比对上的区域的序列替换为同源序列的氨基酸。

In [35]:

# 目前pose的序列
pose.sequence()

Out[35]:

'DELQKWVEQAERNG'

制作一个假的aligned.fatsa:

> pose
DELQKWVEQAERNG
> fake_homology
DELQKLKKQAEQNG

In [36]:

from pyrosetta.rosetta.protocols.task_operations import AlignedThreadOperation
Aligned = AlignedThreadOperation()
Aligned.alignment_file('./data/align.fasta') # 仅支持fasta文件
Aligned.query_name('fake_homology')  # 比对文件中的query序列的代号，指同源序列的名字
Aligned.template_name('pose')  # 比对文件中的template序列的代号，应该要和输入的pose一致
Aligned.start_res(1)  # 确定从哪个氨基酸开始比对

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(Aligned)

# 生成PackerTask
packer_task = pack_tf.create_task_and_apply_taskoperations(pose)
print(packer_task)

protocols.TaskOperations.AlignedThreadOperation: {0} template seq:
DELQKWVEQAERNG
query seq:
DELQKLKKQAEQNGDELQKMKKQAEQNGDELQKMKKQAEQNG
protocols.TaskOperations.AlignedThreadOperation: {0} sequence for threading: 
DELQKLKKQAEQNG
#Packer_Task

Threads to request: ALL AVAILABLE

resid	pack?	design?	allowed_aas
1	TRUE	FALSE	ASP:NtermProteinFull
2	TRUE	FALSE	GLU
3	TRUE	FALSE	LEU
4	TRUE	FALSE	GLN
5	TRUE	FALSE	LYS
6	TRUE	TRUE	LEU
7	TRUE	TRUE	LYS
8	TRUE	TRUE	LYS
9	TRUE	FALSE	GLN
10	TRUE	FALSE	ALA
11	TRUE	FALSE	GLU
12	TRUE	TRUE	GLN
13	TRUE	FALSE	ASN
14	TRUE	FALSE	GLY:CtermProteinFull

2. RestrictNativeResidues¶

将现有的pose与ref_pose(对照)进行比对(并且两个pose的长度必须一致！)，根据序列一致性，将ref和native pose中保守的氨基酸位点，设置为repack或Design.

In [37]:

# 读取ref_pose
ref_pose = pose_from_pdb('./data/helix_ref.pdb')

core.import_pose.import_pose: {0} File './data/helix_ref.pdb' automatically determined to be of type PDB
core.io.pose_from_sfr.PoseFromSFRBuilder: {0} [ WARNING ] discarding 2 atoms at position 3 in file ./data/helix_ref.pdb. Best match rsd_type:  MET
core.io.pose_from_sfr.PoseFromSFRBuilder: {0} [ WARNING ] discarding 1 atoms at position 6 in file ./data/helix_ref.pdb. Best match rsd_type:  ASN
core.io.pose_from_sfr.PoseFromSFRBuilder: {0} [ WARNING ] discarding 4 atoms at position 9 in file ./data/helix_ref.pdb. Best match rsd_type:  HIS
core.io.pose_from_sfr.PoseFromSFRBuilder: {0} [ WARNING ] discarding 1 atoms at position 13 in file ./data/helix_ref.pdb. Best match rsd_type:  LEU
core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OXT on residue GLY:CtermProteinFull 14
core.io.pose_from_sfr.PoseFromSFRBuilder: {0} [ WARNING ] can't find pose atom for file-residue 3 atom 3HB  (trying to store temperature in PDBInfo)
core.io.pose_from_sfr.PoseFromSFRBuilder: {0} [ WARNING ] can't find pose atom for file-residue 3 atom 3HG  (trying to store temperature in PDBInfo)
core.io.pose_from_sfr.PoseFromSFRBuilder: {0} [ WARNING ] can't find pose atom for file-residue 6 atom 3HB  (trying to store temperature in PDBInfo)
core.io.pose_from_sfr.PoseFromSFRBuilder: {0} [ WARNING ] can't find pose atom for file-residue 9 atom 1HE  (trying to store temperature in PDBInfo)
core.io.pose_from_sfr.PoseFromSFRBuilder: {0} [ WARNING ] can't find pose atom for file-residue 9 atom 2HD  (trying to store temperature in PDBInfo)
core.io.pose_from_sfr.PoseFromSFRBuilder: {0} [ WARNING ] can't find pose atom for file-residue 9 atom 2HE  (trying to store temperature in PDBInfo)
core.io.pose_from_sfr.PoseFromSFRBuilder: {0} [ WARNING ] can't find pose atom for file-residue 9 atom 3HB  (trying to store temperature in PDBInfo)
core.io.pose_from_sfr.PoseFromSFRBuilder: {0} [ WARNING ] can't find pose atom for file-residue 13 atom 3HB  (trying to store temperature in PDBInfo)

In [38]:

# 发现3，5，8，12位点序列有差异。
print(ref_pose.sequence())
print(pose.sequence())

DEMQKNVEHAERLG
DELQKWVEQAERNG

In [39]:

from pyrosetta.rosetta.protocols.task_operations import RestrictNativeResiduesOperation
no_pack_to_native = RestrictNativeResiduesOperation()
no_pack_to_native.reference_pose(ref_pose)
no_pack_to_native.prevent_repacking(1) # 1 = 仅设计非保守区段，其余设为no_repack. 0 = 设计非保守区段，其余设置为repack.

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(no_pack_to_native)

# 生成PackerTask
packer_task = pack_tf.create_task_and_apply_taskoperations(pose)
print(packer_task)

protocols.task_operations.RestrictNativeResiduesOperation: {0} 4 non-native, designable residues found in pose
#Packer_Task

Threads to request: ALL AVAILABLE

resid	pack?	design?	allowed_aas
1	FALSE	FALSE	
2	FALSE	FALSE	
3	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
4	FALSE	FALSE	
5	FALSE	FALSE	
6	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
7	FALSE	FALSE	
8	FALSE	FALSE	
9	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
10	FALSE	FALSE	
11	FALSE	FALSE	
12	FALSE	FALSE	
13	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
14	FALSE	FALSE

In [40]:

from pyrosetta.rosetta.protocols.task_operations import RestrictNativeResiduesOperation
no_pack_to_native = RestrictNativeResiduesOperation()
no_pack_to_native.reference_pose(ref_pose)
no_pack_to_native.prevent_repacking(0) # 1 = 仅设计非保守区段，其余设为no_repack. 0 = 设计非保守区段，其余设置为repack.

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(no_pack_to_native)

# 生成PackerTask
packer_task = pack_tf.create_task_and_apply_taskoperations(pose)
print(packer_task)

protocols.task_operations.RestrictNativeResiduesOperation: {0} 4 non-native, designable residues found in pose
#Packer_Task

Threads to request: ALL AVAILABLE

resid	pack?	design?	allowed_aas
1	TRUE	FALSE	ASP:NtermProteinFull
2	TRUE	FALSE	GLU
3	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
4	TRUE	FALSE	GLN
5	TRUE	FALSE	LYS
6	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
7	TRUE	FALSE	VAL
8	TRUE	FALSE	GLU
9	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
10	TRUE	FALSE	ALA
11	TRUE	FALSE	GLU
12	TRUE	FALSE	ARG
13	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
14	TRUE	FALSE	GLY:CtermProteinFull

3. RestrictIdentitiesAtAlignedPositions¶

与输入的PDB结构序列进行比对，只有比对得上的位点得到保留，其他的位置可以进行Design，不要求PDB结构之间长度完全相同，但需要指定design aligment的区域不能大于pose的本身长度。

In [41]:

pose1 = pose_from_pdb('./data/three_helix_pose.pdb')
pose2 = pose_from_pdb('./data/homo1.pdb')  # ref pose;

core.import_pose.import_pose: {0} File './data/three_helix_pose.pdb' automatically determined to be of type PDB
core.import_pose.import_pose: {0} File './data/homo1.pdb' automatically determined to be of type PDB

(图片来源: 晶泰科技团队)

In [42]:

from pyrosetta.rosetta.protocols.task_operations import RestrictIdentitiesAtAlignedPositionsOperation
aligned_position_design = RestrictIdentitiesAtAlignedPositionsOperation()
aligned_position_design.source_pose('./data/homo1.pdb')  # pose1=ref_pose
aligned_position_design.chain(1)  # 设定pose_ref中第几条链被用于比对
aligned_position_design.design_only_target_residues(False) # 允许reapckshell中氨基酸进行repack. 默认False
aligned_position_design.prevent_repacking(False) # 是否不允许repack?

# 当ref_pose和pose中不等长时，需要指定在哪个范围内进行alignment。
vector1 = pyrosetta.rosetta.utility.vector1_unsigned_long()
for i in range(1, pose1.total_residue()):
    vector1.append(i)
aligned_position_design.res_ids(vector1)

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(aligned_position_design)

# 生成PackerTask
packer_task = pack_tf.create_task_and_apply_taskoperations(pose1)
print(packer_task)

core.import_pose.import_pose: {0} File './data/homo1.pdb' automatically determined to be of type PDB
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} Residue nearest is: 1
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} Residue nearest is: ASP1
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} Residue nearest is: 2
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} Residue nearest is: GLU2
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} Residue nearest is: 3
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} Residue nearest is: LEU3
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} Residue nearest is: 3
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} Residue nearest is: GLN4
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} Residue nearest is: 5
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} Residue nearest is: LYS5
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} Residue nearest is: 6
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} Residue nearest is: TRP6
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} Residue nearest is: 23
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} Residue nearest is: VAL7
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} Residue nearest is: 7
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} Residue nearest is: GLU8
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} Residue nearest is: 10
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} Residue nearest is: GLN9
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} [ WARNING ] could not find a residue near to 10
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} Residue nearest is: 20
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} Residue nearest is: GLU11
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} [ WARNING ] could not find a residue near to 12
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} Residue nearest is: 16
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} Residue nearest is: ASN13
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} Residue nearest is: 16
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} Residue nearest is: GLY14
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} [ WARNING ] could not find a residue near to 15
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} [ WARNING ] could not find a residue near to 16
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} [ WARNING ] could not find a residue near to 17
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} [ WARNING ] could not find a residue near to 18
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} [ WARNING ] could not find a residue near to 19
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} [ WARNING ] could not find a residue near to 20
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} [ WARNING ] could not find a residue near to 21
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} [ WARNING ] could not find a residue near to 22
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} [ WARNING ] could not find a residue near to 23
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} [ WARNING ] could not find a residue near to 24
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} [ WARNING ] could not find a residue near to 25
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} [ WARNING ] could not find a residue near to 26
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} [ WARNING ] could not find a residue near to 27
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} [ WARNING ] could not find a residue near to 28
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} [ WARNING ] could not find a residue near to 29
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} [ WARNING ] could not find a residue near to 30
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} [ WARNING ] could not find a residue near to 31
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} [ WARNING ] could not find a residue near to 32
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} [ WARNING ] could not find a residue near to 33
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} [ WARNING ] could not find a residue near to 34
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} Residue nearest is: 28
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} Residue nearest is: ARG35
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} Residue nearest is: 25
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} Residue nearest is: PHE36
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} [ WARNING ] could not find a residue near to 37
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} [ WARNING ] could not find a residue near to 38
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} [ WARNING ] could not find a residue near to 39
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} [ WARNING ] could not find a residue near to 40
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} [ WARNING ] could not find a residue near to 41
protocols.TaskOperations.RestrictIdentitiesAtAlignedPositionsOperation: {0} [ WARNING ] could not find a residue near to 42
#Packer_Task

Threads to request: ALL AVAILABLE

resid	pack?	design?	allowed_aas
1	TRUE	TRUE	ASP:NtermProteinFull
2	TRUE	FALSE	GLU
3	FALSE	FALSE	
4	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
5	TRUE	TRUE	LYS
6	TRUE	TRUE	TRP
7	TRUE	TRUE	GLU
8	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
9	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
10	TRUE	TRUE	GLN
11	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
12	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
13	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
14	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
15	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
16	FALSE	FALSE	
17	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
18	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
19	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
20	TRUE	TRUE	GLU
21	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
22	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
23	TRUE	TRUE	VAL
24	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
25	TRUE	TRUE	PHE
26	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
27	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
28	TRUE	TRUE	ARG
29	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
30	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
31	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
32	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
33	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
34	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
35	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
36	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
37	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
38	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
39	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
40	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
41	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
42	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
43	TRUE	TRUE	ALA:CtermProteinFull,CYS:CtermProteinFull,ASP:CtermProteinFull,GLU:CtermProteinFull,PHE:CtermProteinFull,GLY:CtermProteinFull,HIS:CtermProteinFull,HIS_D:CtermProteinFull,ILE:CtermProteinFull,LYS:CtermProteinFull,LEU:CtermProteinFull,MET:CtermProteinFull,ASN:CtermProteinFull,PRO:CtermProteinFull,GLN:CtermProteinFull,ARG:CtermProteinFull,SER:CtermProteinFull,THR:CtermProteinFull,VAL:CtermProteinFull,TRP:CtermProteinFull,TYR:CtermProteinFull

4. SeqprofConsensus¶

根据PSSM文件来定义序列设计的自由度。PSSM文件可以使用PSIBLAST工具和MSA比对文件来生成。此处依然使用伪造的MSA做示例:

msa.fasta内容如下:

>pose
DELQKWVEQAERNG
>fake_homology1
DELQKLKKQAEQNG
>fake_homology2
DELQKMKKQAEQNG
>fake_homology3
DELQKMKKQAEQNV
>fake_homology4
DELQKMMDQAEQNV
>fake_homology5
DELKDMMDQAEQNV

生成PSSM的命令:(结果文件可在data文件夹下找到)

psiblast -subject sequence.fasta -in_msa msa.fasta -out_ascii_pssm output.pssm

SeqprofConsensus自由度控制相关的关键参数:

filename: PSSM的输入文件名
min_aa_probability: PSSM score的阈值，只有大于阈值的氨基酸才会被考虑。值越大，需要氨基酸在PSSM中出现的频率越高。
probability_larger_than_current: 突变氨基酸的频率是否需要比当前Pose中的氨基酸频率高？
keep_native: 是否保留野生型氨基酸的自由度？

In [43]:

# load pssm
from pyrosetta.rosetta.protocols import rosetta_scripts
xml = rosetta_scripts.XmlObjects.create_from_string('''
<TASKOPERATIONS>
    <SeqprofConsensus name="pssm_design" 
    filename="./data/output.pssm" 
    min_aa_probability="0.0" 
    probability_larger_than_current="1" 
    convert_scores_to_probabilities="false"  
    keep_native="true"/>
</TASKOPERATIONS>
''')
pssm_design = xml.get_task_operation('pssm_design')

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(pssm_design)

# 生成PackerTask
packer_task = pack_tf.create_task_and_apply_taskoperations(pose)
print(packer_task)

protocols.rosetta_scripts.RosettaScriptsParser: {0} Generating XML Schema for rosetta_scripts...
protocols.rosetta_scripts.RosettaScriptsParser: {0} ...done
protocols.rosetta_scripts.RosettaScriptsParser: {0} Initializing schema validator...
protocols.rosetta_scripts.RosettaScriptsParser: {0} ...done
protocols.rosetta_scripts.RosettaScriptsParser: {0} Validating input script...
protocols.rosetta_scripts.RosettaScriptsParser: {0} ...done
protocols.rosetta_scripts.RosettaScriptsParser: {0} Parsed script:
<ROSETTASCRIPTS>
	<TASKOPERATIONS>
		<SeqprofConsensus convert_scores_to_probabilities="false" filename="./data/output.pssm" keep_native="true" min_aa_probability="0.0" name="pssm_design" probability_larger_than_current="1"/>
	</TASKOPERATIONS>
	<PROTOCOLS/>
</ROSETTASCRIPTS>
core.scoring.ScoreFunctionFactory: {0} SCOREFUNCTION: ref2015
protocols.task_operations.SeqprofConsensusOperation: {0} Loading seqprof from a file named: ./data/output.pssm
protocols.jd2.parser.TaskOperationLoader: {0} Defined TaskOperation named "pssm_design" of type SeqprofConsensus
protocols.rosetta_scripts.ParsedProtocol: {0} ParsedProtocol mover with the following settings
protocols.task_operations.SeqprofConsensusOperation: {0} Pose is NOT--SYMMETRIC!!!
protocols.task_operations.SeqprofConsensusOperation: {0} the size of sequence profile is: 14
protocols.task_operations.SeqprofConsensusOperation: {0} Adding native identities to allowed identities
protocols.task_operations.SeqprofConsensusOperation: {0} Allowing the following identities:
#Packer_Task

Threads to request: ALL AVAILABLE

resid	pack?	design?	allowed_aas
1	TRUE	FALSE	ASP:NtermProteinFull
2	TRUE	FALSE	GLU
3	TRUE	FALSE	LEU
4	TRUE	FALSE	GLN
5	TRUE	FALSE	LYS
6	TRUE	TRUE	PHE,ILE,LEU,MET,VAL,TRP
7	TRUE	TRUE	GLU,ILE,LYS,LEU,MET,GLN,ARG,VAL
8	TRUE	TRUE	ASP,GLU,LYS,ASN,GLN,ARG
9	TRUE	FALSE	GLN
10	TRUE	FALSE	ALA
11	TRUE	FALSE	GLU
12	TRUE	TRUE	GLU,LYS,GLN,ARG
13	TRUE	FALSE	ASN
14	TRUE	FALSE	GLY:CtermProteinFull

5. ThreadSequenceOperation¶

用于将一个序列“穿针”到一个Pose的所有位点上。

In [44]:

from pyrosetta.rosetta.protocols.task_operations import ThreadSequenceOperation
thread = ThreadSequenceOperation()
thread.target_sequence(pose2.sequence())

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(thread)

# 生成PackerTask
packer_task = pack_tf.create_task_and_apply_taskoperations(pose1)
print(packer_task)

#Packer_Task

Threads to request: ALL AVAILABLE

resid	pack?	design?	allowed_aas
1	TRUE	TRUE	ASP:NtermProteinFull
2	TRUE	FALSE	GLU
3	TRUE	FALSE	LEU
4	TRUE	TRUE	GLN
5	TRUE	TRUE	LYS
6	TRUE	TRUE	TRP
7	TRUE	TRUE	VAL
8	TRUE	TRUE	GLU
9	TRUE	TRUE	GLN
10	TRUE	TRUE	ALA
11	TRUE	TRUE	GLU
12	TRUE	TRUE	ARG
13	TRUE	TRUE	ASN
14	TRUE	TRUE	GLY
15	TRUE	TRUE	VAL
16	TRUE	TRUE	SER
17	TRUE	TRUE	LEU
18	TRUE	FALSE	GLU
19	TRUE	FALSE	GLU
20	TRUE	TRUE	ILE
21	TRUE	TRUE	GLU
22	TRUE	FALSE	LYS
23	TRUE	TRUE	TRP
24	TRUE	TRUE	ILE
25	TRUE	FALSE	LYS
26	TRUE	FALSE	LYS
27	TRUE	TRUE	ALA
28	TRUE	TRUE	GLY
29	TRUE	TRUE	ASP
30	TRUE	TRUE	GLU
31	TRUE	FALSE	GLU
32	TRUE	TRUE	LEU
33	TRUE	TRUE	LEU
34	TRUE	FALSE	LYS
35	TRUE	TRUE	ARG
36	TRUE	TRUE	PHE
37	TRUE	TRUE	GLN
38	TRUE	TRUE	LYS
39	TRUE	TRUE	LYS
40	TRUE	TRUE	VAL
41	TRUE	FALSE	LYS
42	TRUE	TRUE	GLU
43	TRUE	FALSE	ARG:CtermProteinFull

2.2 Rotamer Specification¶

2.2.1 InteractingRotamerExplosion¶

增强某一位点的Rotamer采样，如希望在设计所有氨基酸位点时，增强采样那些与第8号残基相互作用能量(two-body)大于-0.5个REU单位的Rotamer

In [45]:

from pyrosetta.rosetta.protocols import rosetta_scripts
xml = rosetta_scripts.XmlObjects.create_from_string('''
<TASKOPERATIONS>
    <InteractingRotamerExplosion name="rotexpl"
    ex_level="2" score_cutoff="0.5" target_seqpos="10A" debug="0" />
</TASKOPERATIONS>
''')
rotexpl = xml.get_task_operation('rotexpl')

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(rotexpl)

protocols.rosetta_scripts.RosettaScriptsParser: {0} Generating XML Schema for rosetta_scripts...
protocols.rosetta_scripts.RosettaScriptsParser: {0} ...done
protocols.rosetta_scripts.RosettaScriptsParser: {0} Initializing schema validator...
protocols.rosetta_scripts.RosettaScriptsParser: {0} ...done
protocols.rosetta_scripts.RosettaScriptsParser: {0} Validating input script...
protocols.rosetta_scripts.RosettaScriptsParser: {0} ...done
protocols.rosetta_scripts.RosettaScriptsParser: {0} Parsed script:
<ROSETTASCRIPTS>
	<TASKOPERATIONS>
		<InteractingRotamerExplosion debug="0" ex_level="2" name="rotexpl" score_cutoff="0.5" target_seqpos="10A"/>
	</TASKOPERATIONS>
	<PROTOCOLS/>
</ROSETTASCRIPTS>
core.scoring.ScoreFunctionFactory: {0} SCOREFUNCTION: ref2015
protocols.jd2.parser.TaskOperationLoader: {0} Defined TaskOperation named "rotexpl" of type InteractingRotamerExplosion
protocols.rosetta_scripts.ParsedProtocol: {0} ParsedProtocol mover with the following settings

2.2.2 ImportUnboundRotamers¶

可以用于增强采样输入的Ref PDB结构上的Rotamer。

In [46]:

from pyrosetta.rosetta.protocols.task_operations import ImportUnboundRotamersOperation
favor_native_rotamer_ex = ImportUnboundRotamersOperation()
init('-packing::unboundrot ./data/three_helix_pose.pdb')

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(favor_native_rotamer_ex)

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 -packing::unboundrot ./data/three_helix_pose.pdb -database /opt/miniconda3/lib/python3.7/site-packages/pyrosetta/database
basic.random.init_random_generator: {0} 'RNG device' seed mode, using '/dev/urandom', seed=-732456573 seed_offset=0 real_seed=-732456573 thread_index=0
basic.random.init_random_generator: {0} RandomGenerator:init: Normal mode, seed=-732456573 RG_type=mt19937

2.2.3 LimitAromaChi2¶

防止在Packer运行中使用PHE、TYR和HIS的那些 $\chi_{2}$ 角远离90度的Rotamer，因为这些Rotamer是罕见的。因此直接排除

include_trp: Trp的能量更加平滑，可以在更广的 $\chi_{2}$ 角空间出现，因此不推荐约束它。

In [47]:

from pyrosetta.rosetta.protocols import rosetta_scripts
xml = rosetta_scripts.XmlObjects.create_from_string('''
<TASKOPERATIONS>
    <LimitAromaChi2 name="limit_chi2" chi2max="110.0"
            chi2min="70.0" include_trp="false" />
</TASKOPERATIONS>
''')
limit_chi2 = xml.get_task_operation('limit_chi2')

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(limit_chi2)

protocols.rosetta_scripts.RosettaScriptsParser: {0} Generating XML Schema for rosetta_scripts...
protocols.rosetta_scripts.RosettaScriptsParser: {0} ...done
protocols.rosetta_scripts.RosettaScriptsParser: {0} Initializing schema validator...
protocols.rosetta_scripts.RosettaScriptsParser: {0} ...done
protocols.rosetta_scripts.RosettaScriptsParser: {0} Validating input script...
protocols.rosetta_scripts.RosettaScriptsParser: {0} ...done
protocols.rosetta_scripts.RosettaScriptsParser: {0} Parsed script:
<ROSETTASCRIPTS>
	<TASKOPERATIONS>
		<LimitAromaChi2 chi2max="110.0" chi2min="70.0" include_trp="false" name="limit_chi2"/>
	</TASKOPERATIONS>
	<PROTOCOLS/>
</ROSETTASCRIPTS>
core.scoring.ScoreFunctionFactory: {0} SCOREFUNCTION: ref2015
protocols.jd2.parser.TaskOperationLoader: {0} Defined TaskOperation named "limit_chi2" of type LimitAromaChi2
protocols.rosetta_scripts.ParsedProtocol: {0} ParsedProtocol mover with the following settings

2.2.4 SampleRotamersFromPDB¶

用于约束当前Rotamer采样范围与ref PDB结构中的Rotamer高度相似（如rotamer差异在+/-5度）。

In [48]:

from pyrosetta.rosetta.protocols import rosetta_scripts
from pyrosetta.rosetta.protocols.minimization_packing import PackRotamersMover

# load native rotamers;
init('-packing::unboundrot ./data/three_helix_pose.pdb')

xml = rosetta_scripts.XmlObjects.create_from_string('''
<TASKOPERATIONS>
    <SampleRotamersFromPDB name="restric_native_ex" add_rotamer="1" debug="0" ccd="0"/>
</TASKOPERATIONS>
''')
restric_native_ex = xml.get_task_operation('restric_native_ex')

pose1 = pose_from_pdb('./data/three_helix_pose.pdb')

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(restric_native_ex)
pack_tf.push_back(RestrictToRepacking())

# 生成PackerTask
packer_task = pack_tf.create_task_and_apply_taskoperations(pose1)
print(packer_task)

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 -packing::unboundrot ./data/three_helix_pose.pdb -database /opt/miniconda3/lib/python3.7/site-packages/pyrosetta/database
basic.random.init_random_generator: {0} 'RNG device' seed mode, using '/dev/urandom', seed=-631442782 seed_offset=0 real_seed=-631442782 thread_index=0
basic.random.init_random_generator: {0} RandomGenerator:init: Normal mode, seed=-631442782 RG_type=mt19937
protocols.rosetta_scripts.RosettaScriptsParser: {0} Generating XML Schema for rosetta_scripts...
protocols.rosetta_scripts.RosettaScriptsParser: {0} ...done
protocols.rosetta_scripts.RosettaScriptsParser: {0} Initializing schema validator...
protocols.rosetta_scripts.RosettaScriptsParser: {0} ...done
protocols.rosetta_scripts.RosettaScriptsParser: {0} Validating input script...
protocols.rosetta_scripts.RosettaScriptsParser: {0} ...done
protocols.rosetta_scripts.RosettaScriptsParser: {0} Parsed script:
<ROSETTASCRIPTS>
	<TASKOPERATIONS>
		<SampleRotamersFromPDB add_rotamer="1" ccd="0" debug="0" name="restric_native_ex"/>
	</TASKOPERATIONS>
	<PROTOCOLS/>
</ROSETTASCRIPTS>
core.scoring.ScoreFunctionFactory: {0} SCOREFUNCTION: ref2015
protocols.evaluation.ChiWellRmsdEvaluatorCreator: {0} Evaluation Creator active ...
protocols.jd2.parser.TaskOperationLoader: {0} Defined TaskOperation named "restric_native_ex" of type SampleRotamersFromPDB
protocols.rosetta_scripts.ParsedProtocol: {0} ParsedProtocol mover with the following settings
core.import_pose.import_pose: {0} File './data/three_helix_pose.pdb' automatically determined to be of type PDB
core.pack.rotamer_set.SampleRotamersFromPDB_RotamerSetOperation: {0} Adding rotamers from ./data/three_helix_pose.pdb
core.import_pose.import_pose: {0} File './data/three_helix_pose.pdb' automatically determined to be of type PDB
#Packer_Task

Threads to request: ALL AVAILABLE

resid	pack?	design?	allowed_aas
1	TRUE	FALSE	SER:NtermProteinFull
2	TRUE	FALSE	GLU
3	TRUE	FALSE	LEU
4	TRUE	FALSE	GLU
5	TRUE	FALSE	GLU
6	TRUE	FALSE	THR
7	TRUE	FALSE	LEU
8	TRUE	FALSE	ARG
9	TRUE	FALSE	ARG
10	TRUE	FALSE	LEU
11	TRUE	FALSE	ALA
12	TRUE	FALSE	GLN
13	TRUE	FALSE	THR
14	TRUE	FALSE	PRO
15	TRUE	FALSE	GLY
16	TRUE	FALSE	ALA
17	TRUE	FALSE	SER
18	TRUE	FALSE	GLU
19	TRUE	FALSE	GLU
20	TRUE	FALSE	LEU
21	TRUE	FALSE	LYS
22	TRUE	FALSE	LYS
23	TRUE	FALSE	LEU
24	TRUE	FALSE	VAL
25	TRUE	FALSE	LYS
26	TRUE	FALSE	LYS
27	TRUE	FALSE	ILE
28	TRUE	FALSE	ASN
29	TRUE	FALSE	ASN
30	TRUE	FALSE	PRO
31	TRUE	FALSE	GLU
32	TRUE	FALSE	ALA
33	TRUE	FALSE	GLU
34	TRUE	FALSE	LYS
35	TRUE	FALSE	TRP
36	TRUE	FALSE	LEU
37	TRUE	FALSE	ARG
38	TRUE	FALSE	GLU
39	TRUE	FALSE	TYR
40	TRUE	FALSE	GLN
41	TRUE	FALSE	LYS
42	TRUE	FALSE	LYS
43	TRUE	FALSE	ARG:CtermProteinFull

2.2.5 PruneBuriedUnsats¶

消除那些在会导致在结构中引入不饱和极性原子(无法配对产生氢键)的Rotamer。参数:

allow_even_trades - Allow residues that satisfy an unsat and create a new unsatisfiable one.
atomic_depth_probe_radius - Probe radius for atomic depth calculation to determine burial.
atomic_depth_resolution - Voxel resolution with which to calculate atomic depth.
atomic_depth_cutoff - Atomic depth at which atoms are considered buried.
Minimum energy (out of the typical rosetta -2.0) for a hbond to be considered to satisfy a polar.

In [49]:

from pyrosetta.rosetta.protocols.task_operations import PruneBuriedUnsatsOperation
prune_unsat = PruneBuriedUnsatsOperation()
prune_unsat.atomic_depth_cutoff(4.5)
prune_unsat.atomic_depth_probe_radius(2.3)
prune_unsat.atomic_depth_resolution(0.5)
prune_unsat.minimum_hbond_energy(-0.2)

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(prune_unsat)

2.3 Packer Behavior Modification¶

该部分的TaskOperations主要作用于Packer，可以设置一些改变Packer的采样或运行方式。

2.3.1 ModifyAnnealer¶

改变Packer模拟退火中的设置，包括:

high_temp: 起始温度
low_temp: 终止温度
disallow_quench: “淬火”即每次都接受低能量的构象，如果希望有更大的Rotamer多样性可以将此关闭。默认启用“淬火”

In [50]:

from pyrosetta.rosetta.protocols import rosetta_scripts
xml = rosetta_scripts.XmlObjects.create_from_string('''
<TASKOPERATIONS>
    <ModifyAnnealer name="modify_annealer" high_temp="100" low_temp="0.3" disallow_quench="0"/>
</TASKOPERATIONS>
''')

modify_annealer = xml.get_task_operation('modify_annealer')

# # 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(modify_annealer)

protocols.rosetta_scripts.RosettaScriptsParser: {0} Generating XML Schema for rosetta_scripts...
protocols.rosetta_scripts.RosettaScriptsParser: {0} ...done
protocols.rosetta_scripts.RosettaScriptsParser: {0} Initializing schema validator...
protocols.rosetta_scripts.RosettaScriptsParser: {0} ...done
protocols.rosetta_scripts.RosettaScriptsParser: {0} Validating input script...
protocols.rosetta_scripts.RosettaScriptsParser: {0} ...done
protocols.rosetta_scripts.RosettaScriptsParser: {0} Parsed script:
<ROSETTASCRIPTS>
	<TASKOPERATIONS>
		<ModifyAnnealer disallow_quench="0" high_temp="100" low_temp="0.3" name="modify_annealer"/>
	</TASKOPERATIONS>
	<PROTOCOLS/>
</ROSETTASCRIPTS>
core.scoring.ScoreFunctionFactory: {0} SCOREFUNCTION: ref2015
protocols.jd2.parser.TaskOperationLoader: {0} Defined TaskOperation named "modify_annealer" of type ModifyAnnealer
protocols.rosetta_scripts.ParsedProtocol: {0} ParsedProtocol mover with the following settings

2.3.2 RestrictInteractionGraphThreadsOperation¶

此TaskOperations可以控制Packer使用的线程数量。默认conda安装的pyrosetta都是单线程编译的，如果需要支持多线程进行Packer的，需要从Rosetta的源代码处从头编译multi-threaded版本的PyRosetta并安装（比较麻烦），当兼容多线程时，合理使用可以加速开发和测试时的速度。

In [51]:

from pyrosetta.rosetta.core.pack.task.operation import RestrictInteractionGraphThreadsOperation
init('-multithreading:total_threads 16 -multithreading:interaction_graph_threads 16')

# litmit thread setting;
litmit_thread = RestrictInteractionGraphThreadsOperation()
litmit_thread.set_thread_limit(8)

# # 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(litmit_thread)
pack_tf.push_back(RestrictToRepacking())

# run packer
from pyrosetta.rosetta.protocols.minimization_packing import PackRotamersMover
from pyrosetta import create_score_function
pack_mover = PackRotamersMover()
ref2015 = create_score_function('ref2015')
single_helix_pose = pose_from_pdb('./data/helix.pdb')

# 不需要导入PackTask，只需要输入TaskFactory即可。
pack_mover.task_factory(pack_tf)
pack_mover.score_function(ref2015)

# 执行repacking
pack_mover.apply(single_helix_pose)

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 -multithreading:total_threads 16 -multithreading:interaction_graph_threads 16 -database /opt/miniconda3/lib/python3.7/site-packages/pyrosetta/database
basic.random.init_random_generator: {0} 'RNG device' seed mode, using '/dev/urandom', seed=-2083723108 seed_offset=0 real_seed=-2083723108 thread_index=0
basic.random.init_random_generator: {0} RandomGenerator:init: Normal mode, seed=-2083723108 RG_type=mt19937
core.pack.task.operation.RestrictInteractionGraphThreadsOperation: {0} Configuring RestrictInteractionGraphThreadsOperation to allow 8 threads for interaction graph computation.
core.import_pose.import_pose: {0} File './data/helix.pdb' automatically determined to be of type PDB
core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OXT on residue GLY:CtermProteinFull 14
core.pack.pack_rotamers: {0} built 182 rotamers at 14 positions.
core.pack.pack_rotamers: {0} Requesting 8 threads for interaction graph computation.
core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph
basic.thread_manager.RosettaThreadPool: {0} [ WARNING ] Warning: 8 threads were requested, but only 1 exist in the RosettaThreadPool.
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (8 had been requested).

2.3.3 SetIGTypeOperation¶

此处TaskOperations可影响InteractionGraph的计算方法，默认有4种方式:

lin_mem_ig: 使用线性增长的内存机制，近期被计算的Rotamer pairs之间的能量会被重复使用，但是同一种Rotamer pairs之间的能量可能会被重复计算，因为超出一定数量时，相关的记忆就被丢失了。
lazy_ig: 推迟计算Rotamer pairs之间的能量，直到真正用到时，这样可以大幅减少预计算的量。
double_lazy_ig: 同时使用lin_mem_ig和double_lazy_ig。
precompute_ig: 完整计算所有的Rotamer pairs之间的能量。（O(N^2) interaction graph）

In [52]:

from pyrosetta.rosetta.protocols import rosetta_scripts
xml = rosetta_scripts.XmlObjects.create_from_string('''
<TASKOPERATIONS>
    <SetIGType name="set_ig" lin_mem_ig="1" lazy_ig="0" double_lazy_ig="0" precompute_ig="0"/>
</TASKOPERATIONS>
''')

set_ig = xml.get_task_operation('set_ig')

# # 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(set_ig)

protocols.rosetta_scripts.RosettaScriptsParser: {0} Generating XML Schema for rosetta_scripts...
protocols.rosetta_scripts.RosettaScriptsParser: {0} ...done
protocols.rosetta_scripts.RosettaScriptsParser: {0} Initializing schema validator...
protocols.rosetta_scripts.RosettaScriptsParser: {0} ...done
protocols.rosetta_scripts.RosettaScriptsParser: {0} Validating input script...
protocols.rosetta_scripts.RosettaScriptsParser: {0} ...done
protocols.rosetta_scripts.RosettaScriptsParser: {0} Parsed script:
<ROSETTASCRIPTS>
	<TASKOPERATIONS>
		<SetIGType double_lazy_ig="0" lazy_ig="0" lin_mem_ig="1" name="set_ig" precompute_ig="0"/>
	</TASKOPERATIONS>
	<PROTOCOLS/>
</ROSETTASCRIPTS>
core.scoring.ScoreFunctionFactory: {0} SCOREFUNCTION: ref2015
protocols.jd2.parser.TaskOperationLoader: {0} Defined TaskOperation named "set_ig" of type SetIGType
protocols.rosetta_scripts.ParsedProtocol: {0} ParsedProtocol mover with the following settings

2.4 Antibody and CDR Specific Operations¶

这一部分的TaskOperations是为抗体结构设计定制的，在抗体设计时引用会带来极大的便利性。核心两个部分: 控制CDR如何Design、控制region的Design和repack状态。

2.4.1 DisableAntibodyRegionOperation¶

抗体Pose的Region定义分为CDR区、Framework区、抗原区(如果Pose中是抗体抗原复合物的话)。DisableAntibodyRegionOperation可直接把特定区域的Rotamer自由度闭关或减少。

参数:

region可选:AntibodyRegionEnum.antigen_region/AntibodyRegionEnum.cdr_region/AntibodyRegionEnum.framework_region
disable_packing_and_design: True=norepack, False=allow_pack

In [53]:

from pyrosetta.rosetta.protocols.antibody import AntibodyInfo
from pyrosetta.rosetta.protocols.antibody.task_operations import DisableAntibodyRegionOperation
from pyrosetta.rosetta.protocols.antibody import AntibodyRegionEnum

# 读入抗体结构
init('-ex1 -ex2 -input_ab_scheme Chothia_Scheme -use_input_sc')
antibody_pose = pose_from_pdb('./data/7OBF_B.pdb') # nanobody

# 设置region自由度;
ab_info = AntibodyInfo(antibody_pose)
disable_region = DisableAntibodyRegionOperation(ab_info, AntibodyRegionEnum.framework_region,
                                                disable_packing_and_design=False)

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(disable_region)

# 生成PackerTask
packer_task = pack_tf.create_task_and_apply_taskoperations(antibody_pose)
print(packer_task)

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 -ex2 -input_ab_scheme Chothia_Scheme -use_input_sc -database /opt/miniconda3/lib/python3.7/site-packages/pyrosetta/database
basic.random.init_random_generator: {0} 'RNG device' seed mode, using '/dev/urandom', seed=-475246036 seed_offset=0 real_seed=-475246036 thread_index=0
basic.random.init_random_generator: {0} RandomGenerator:init: Normal mode, seed=-475246036 RG_type=mt19937
core.import_pose.import_pose: {0} File './data/7OBF_B.pdb' automatically determined to be of type PDB
core.conformation.Conformation: {0} Found disulfide between residues 21 95
core.conformation.Conformation: {0} current variant for 21 CYS
core.conformation.Conformation: {0} current variant for 95 CYS
core.conformation.Conformation: {0} current variant for 21 CYD
core.conformation.Conformation: {0} current variant for 95 CYD
basic.io.database: {0} Database file opened: sampling/antibodies/cluster_center_dihedrals.txt
protocols.antibody.AntibodyNumberingParser: {0} Antibody numbering scheme definitions read successfully
protocols.antibody.AntibodyNumberingParser: {0} Antibody CDR definition read successfully
antibody.AntibodyInfo: {0} Successfully finished the CDR definition
antibody.AntibodyInfo: {0}  Could not setup Vl Vh Packing angle for camelid antibody
antibody.AntibodyInfo: {0} AC Detecting Camelid CDR H3 Stem Type
antibody.AntibodyInfo: {0} AC Finished Detecting Camelid CDR H3 Stem Type: NEUTRAL
antibody.AntibodyInfo: {0} Setting up CDR Cluster for H1
protocols.antibody.cluster.CDRClusterMatcher: {0} Length: 13 Omega: TTTTTTTTTTTTT
antibody.AntibodyInfo: {0} Setting up CDR Cluster for H2
protocols.antibody.cluster.CDRClusterMatcher: {0} Length: 10 Omega: TTTTTTTTTT
antibody.AntibodyInfo: {0} Setting up CDR Cluster for H3
protocols.antibody.cluster.CDRClusterMatcher: {0} Length: 13 Omega: TTTTTTTTTTTTT
#Packer_Task

Threads to request: ALL AVAILABLE

resid	pack?	design?	allowed_aas
1	TRUE	FALSE	VAL:NtermProteinFull
2	TRUE	FALSE	GLN
3	TRUE	FALSE	LEU
4	TRUE	FALSE	LEU
5	TRUE	FALSE	GLU
6	TRUE	FALSE	SER
7	TRUE	FALSE	GLY
8	TRUE	FALSE	GLY
9	TRUE	FALSE	GLY
10	TRUE	FALSE	LEU
11	TRUE	FALSE	VAL
12	TRUE	FALSE	GLN
13	TRUE	FALSE	PRO
14	TRUE	FALSE	GLY
15	TRUE	FALSE	GLY
16	TRUE	FALSE	SER
17	TRUE	FALSE	LEU
18	TRUE	FALSE	ARG
19	TRUE	FALSE	LEU
20	TRUE	FALSE	SER
21	TRUE	FALSE	CYS:disulfide
22	TRUE	FALSE	ALA
23	TRUE	FALSE	ALA
24	TRUE	FALSE	SER
25	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
26	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
27	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
28	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
29	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
30	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
31	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
32	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
33	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
34	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
35	TRUE	FALSE	TRP
36	TRUE	FALSE	VAL
37	TRUE	FALSE	ARG
38	TRUE	FALSE	GLN
39	TRUE	FALSE	ALA
40	TRUE	FALSE	PRO
41	TRUE	FALSE	GLY
42	TRUE	FALSE	LYS
43	TRUE	FALSE	GLY
44	TRUE	FALSE	LEU
45	TRUE	FALSE	GLU
46	TRUE	FALSE	TRP
47	TRUE	FALSE	VAL
48	TRUE	FALSE	SER
49	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
50	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
51	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
52	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
53	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
54	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
55	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
56	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
57	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
58	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
59	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
60	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
61	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
62	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
63	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
64	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
65	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
66	TRUE	FALSE	ARG
67	TRUE	FALSE	PHE
68	TRUE	FALSE	THR
69	TRUE	FALSE	ILE
70	TRUE	FALSE	SER
71	TRUE	FALSE	ARG
72	TRUE	FALSE	ASP
73	TRUE	FALSE	ASN
74	TRUE	FALSE	SER
75	TRUE	FALSE	LYS
76	TRUE	FALSE	ASN
77	TRUE	FALSE	THR
78	TRUE	FALSE	LEU
79	TRUE	FALSE	TYR
80	TRUE	FALSE	LEU
81	TRUE	FALSE	GLN
82	TRUE	FALSE	MET
83	TRUE	FALSE	ASN
84	TRUE	FALSE	SER
85	TRUE	FALSE	LEU
86	TRUE	FALSE	ARG
87	TRUE	FALSE	ALA
88	TRUE	FALSE	GLU
89	TRUE	FALSE	ASP
90	TRUE	FALSE	THR
91	TRUE	FALSE	ALA
92	TRUE	FALSE	VAL
93	TRUE	FALSE	TYR
94	TRUE	FALSE	TYR
95	TRUE	FALSE	CYS:disulfide
96	TRUE	FALSE	ALA
97	TRUE	FALSE	SER
98	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
99	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
100	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
101	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
102	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
103	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
104	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
105	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
106	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
107	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
108	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
109	TRUE	FALSE	TRP
110	TRUE	FALSE	GLY
111	TRUE	FALSE	GLN
112	TRUE	FALSE	GLY
113	TRUE	FALSE	THR
114	TRUE	FALSE	LEU
115	TRUE	FALSE	VAL
116	TRUE	FALSE	THR
117	TRUE	FALSE	VAL
118	TRUE	FALSE	SER:CtermProteinFull

思考¶

尝试不同的region，看看他们在抗体上的结构分布都是在哪些区域？

2.4.2 DisableCDRsOperation¶

DisableCDRsOperation相比于单纯的DisableAntibodyRegionOperation，可以更加精细地去定义6个CDR区的单独状态！

In [54]:

from pyrosetta.rosetta.protocols.antibody.task_operations import DisableCDRsOperation

# 定义CDR区范围，目前1代表自定义CDR-H1。其他区不做定义。
cdr_allow = [1,1,0,0,0,0,0,0] # H1 H2 H3 H4 L1 L2 L3 L4
cdr_allow_vector1 = pyrosetta.rosetta.utility.vector1_bool()
for i in cdr_allow:
    cdr_allow_vector1.append(i)

# 将CDR-H1和CDR-H2的所有Rotamer自由度关闭:
disable_cdr = DisableCDRsOperation(ab_info, cdr_allow_vector1, disable_packing_and_design=True)

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(disable_cdr)

# 生成PackerTask
packer_task = pack_tf.create_task_and_apply_taskoperations(antibody_pose)
print(packer_task)

#Packer_Task

Threads to request: ALL AVAILABLE

resid	pack?	design?	allowed_aas
1	TRUE	TRUE	ALA:NtermProteinFull,CYS:NtermProteinFull,ASP:NtermProteinFull,GLU:NtermProteinFull,PHE:NtermProteinFull,GLY:NtermProteinFull,HIS:NtermProteinFull,HIS_D:NtermProteinFull,ILE:NtermProteinFull,LYS:NtermProteinFull,LEU:NtermProteinFull,MET:NtermProteinFull,ASN:NtermProteinFull,PRO:NtermProteinFull,GLN:NtermProteinFull,ARG:NtermProteinFull,SER:NtermProteinFull,THR:NtermProteinFull,VAL:NtermProteinFull,TRP:NtermProteinFull,TYR:NtermProteinFull
2	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
3	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
4	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
5	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
6	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
7	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
8	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
9	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
10	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
11	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
12	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
13	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
14	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
15	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
16	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
17	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
18	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
19	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
20	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
21	TRUE	FALSE	CYS:disulfide
22	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
23	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
24	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
25	FALSE	FALSE	
26	FALSE	FALSE	
27	FALSE	FALSE	
28	FALSE	FALSE	
29	FALSE	FALSE	
30	FALSE	FALSE	
31	FALSE	FALSE	
32	FALSE	FALSE	
33	FALSE	FALSE	
34	FALSE	FALSE	
35	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
36	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
37	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
38	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
39	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
40	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
41	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
42	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
43	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
44	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
45	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
46	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
47	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
48	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
49	FALSE	FALSE	
50	FALSE	FALSE	
51	FALSE	FALSE	
52	FALSE	FALSE	
53	FALSE	FALSE	
54	FALSE	FALSE	
55	FALSE	FALSE	
56	FALSE	FALSE	
57	FALSE	FALSE	
58	FALSE	FALSE	
59	FALSE	FALSE	
60	FALSE	FALSE	
61	FALSE	FALSE	
62	FALSE	FALSE	
63	FALSE	FALSE	
64	FALSE	FALSE	
65	FALSE	FALSE	
66	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
67	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
68	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
69	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
70	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
71	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
72	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
73	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
74	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
75	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
76	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
77	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
78	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
79	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
80	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
81	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
82	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
83	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
84	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
85	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
86	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
87	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
88	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
89	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
90	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
91	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
92	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
93	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
94	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
95	TRUE	FALSE	CYS:disulfide
96	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
97	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
98	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
99	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
100	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
101	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
102	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
103	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
104	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
105	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
106	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
107	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
108	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
109	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
110	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
111	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
112	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
113	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
114	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
115	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
116	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
117	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
118	TRUE	TRUE	ALA:CtermProteinFull,CYS:CtermProteinFull,ASP:CtermProteinFull,GLU:CtermProteinFull,PHE:CtermProteinFull,GLY:CtermProteinFull,HIS:CtermProteinFull,HIS_D:CtermProteinFull,ILE:CtermProteinFull,LYS:CtermProteinFull,LEU:CtermProteinFull,MET:CtermProteinFull,ASN:CtermProteinFull,PRO:CtermProteinFull,GLN:CtermProteinFull,ARG:CtermProteinFull,SER:CtermProteinFull,THR:CtermProteinFull,VAL:CtermProteinFull,TRP:CtermProteinFull,TYR:CtermProteinFull

2.4.3 AddCDRProfilesOperation¶

抗体的CDR-H1、H2、L1、L2、L3都是由正则结构的，因此可以被聚类成若干个簇。这些簇内部的序列有保守性也有多样性(Profiles)。 Profiles中记录了每种氨基酸在每种CDR簇中的频率分布，通过AddCDRProfilesOperation可以从Profiles中根据频率分布依次地、随机地挑选一个氨基酸类型添加到可被设计的列表中，因此每次Packer执行时，PackerTask都是不同的。set_picking_rounds设置在每个位点中挑选几次氨基酸，设置值越大，此位点Rotamer的自由度可能会增加。

注意: 当一些CDR结构多样性太少时，就会从保守性出发进行生成Rotamer的自由度。

因此此处有两种基本的生成策略:

PRIMARY STRATEGIES: 初始设计方案。【肯定的是,采样丰度更高了，但是有些位点反变得不可以控制】
- seq_design_profiles: 基于cluster的氨基酸频率采样（如在H1-13-1中采样）. #默认
- seq_design_profile_sets: 基于所有的cluster的氨基酸频率采样（如H1-13-1，H1-10-1…穷举）（实验阶段）
- seq_design_profile_sets_combined: profiles+profile_sets。组合（实验阶段）
- seq_design_conservative: 当找到不到cluster或则cluster中成员较少是，使用blosum62矩阵统计氨基酸频率。
- seq_design_basic: 可以被设置成20种氨基酸。
FALLBACK STRATEGIES: 如果找不到CDR图谱或则聚类中CDR序列过少，那么将自动调用备用策略。
- seq_design_conservative: 基于blosum62矩阵选择突变设计范围 #默认
- seq_design_basic: 允许20种氨基酸设计
- seq_design_none: 禁止设计

Cons_design_data_source: 使用的打分矩阵 'chothia_1976', 'BLOSUM30', 'blosum30', 'BLOSUM35', 'blosum35', 'BLOSUM40', 'blosum40', 'BLOSUM45', 'blosum45', 'BLOSUM50', 'blosum50', 'BLOSUM55', 'blosum55', 'BLOSUM60', 'blosum60', 'BLOSUM62', 'blosum62', 'BLOSUM65', 'blosum65', 'BLOSUM70', 'blosum70', 'BLOSUM75', 'blosum75', 'BLOSUM80', 'blosum80', 'BLOSUM85', 'blosum85', 'BLOSUM90', 'blosum90', 'BLOSUM100', 'blosum100'

特别注意: 轻链类型，cmd -light_chain 使用set模式时需要指定轻链的类型！[lambda, kappa]

In [55]:

from pyrosetta.rosetta.protocols.antibody import *
from pyrosetta.rosetta.protocols.antibody.task_operations import *
from pyrosetta.rosetta.protocols.antibody.design import *

add_cdr_profile = AddCDRProfilesOperation()
add_cdr_profile.set_include_native_type(True) # allowed wild type AA
add_cdr_profile.set_picking_rounds(2)  # 控制sequence sampling丰度

#选择某一个CDR计算.
add_cdr_profile.set_cdr_only(h1) # 选择cdr1

#控制采样方法
add_cdr_profile.set_primary_strategy(seq_design_profiles) # 如果设置为含set模式时，初始化需加入-light_chain选项
add_cdr_profile.set_fallback_strategy(seq_design_conservative)

#增加变异度(选1)
add_cdr_profile.set_no_probability(False) #在profile中，忽略氨基酸出现的频率，采集所有出现过的氨基酸类型.
add_cdr_profile.set_sample_zero_probs_at(False) #在profile中, 增加频率为0的氨基酸的频率，使得可能被采样。
add_cdr_profile.set_stats_cutoff(10) # profile截断，如果簇内少于10个成员，那么使用FALLBACK STRATEGIES
add_cdr_profile.set_use_outliers(False) #是否采样聚类中偏离较远的序列。
add_cdr_profile.set_cons_design_data_source('BLOSUM62') #改变保守设计使用的打分矩阵

protocols.task_operations.ConservativeDesignOperation: {0} Loading conservative mutational data

In [56]:

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(add_cdr_profile)

# 生成PackerTask
packer_task = pack_tf.create_task_and_apply_taskoperations(antibody_pose)
print(packer_task)

basic.io.database: {0} Database file opened: sampling/antibodies/cluster_center_dihedrals.txt
protocols.antibody.AntibodyNumberingParser: {0} Antibody numbering scheme definitions read successfully
protocols.antibody.AntibodyNumberingParser: {0} Antibody CDR definition read successfully
antibody.AntibodyInfo: {0} Successfully finished the CDR definition
antibody.AntibodyInfo: {0}  Could not setup Vl Vh Packing angle for camelid antibody
antibody.AntibodyInfo: {0} AC Detecting Camelid CDR H3 Stem Type
antibody.AntibodyInfo: {0} AC Finished Detecting Camelid CDR H3 Stem Type: NEUTRAL
antibody.AntibodyInfo: {0} Setting up CDR Cluster for H1
protocols.antibody.cluster.CDRClusterMatcher: {0} Length: 13 Omega: TTTTTTTTTTTTT
antibody.AntibodyInfo: {0} Setting up CDR Cluster for H2
protocols.antibody.cluster.CDRClusterMatcher: {0} Length: 10 Omega: TTTTTTTTTT
antibody.AntibodyInfo: {0} Setting up CDR Cluster for H3
protocols.antibody.cluster.CDRClusterMatcher: {0} Length: 13 Omega: TTTTTTTTTTTTT
basic.io.database: {0} [ WARNING ] Unable to locate database file /sampling/antibodies/antibody_database_rosetta_design.db
antibody.database.AntibodyDatabaseManager: {0} The antibody design database is not specified by the user.
antibody.database.AntibodyDatabaseManager: {0} Reading from: /opt/miniconda3/lib/python3.7/site-packages/pyrosetta/database//sampling/antibodies/antibody_database_rosetta_design_north_paper.db
antibody.database.AntibodyDatabaseManager: {0} Loaded H1-13-1 with 210 datapoints.
protocols.antibody.task_operations.AddCDRProfilesOperation: {0} applying prob task op
#Packer_Task

Threads to request: ALL AVAILABLE

resid	pack?	design?	allowed_aas
1	TRUE	TRUE	ALA:NtermProteinFull,CYS:NtermProteinFull,ASP:NtermProteinFull,GLU:NtermProteinFull,PHE:NtermProteinFull,GLY:NtermProteinFull,HIS:NtermProteinFull,HIS_D:NtermProteinFull,ILE:NtermProteinFull,LYS:NtermProteinFull,LEU:NtermProteinFull,MET:NtermProteinFull,ASN:NtermProteinFull,PRO:NtermProteinFull,GLN:NtermProteinFull,ARG:NtermProteinFull,SER:NtermProteinFull,THR:NtermProteinFull,VAL:NtermProteinFull,TRP:NtermProteinFull,TYR:NtermProteinFull
2	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
3	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
4	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
5	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
6	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
7	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
8	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
9	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
10	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
11	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
12	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
13	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
14	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
15	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
16	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
17	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
18	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
19	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
20	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
21	TRUE	FALSE	CYS:disulfide
22	TRUE	TRUE	ALA,SER
23	TRUE	TRUE	ALA,VAL
24	TRUE	FALSE	SER
25	TRUE	FALSE	GLY
26	TRUE	TRUE	PHE,TYR
27	TRUE	TRUE	ARG,SER,THR
28	TRUE	TRUE	PHE,ILE
29	TRUE	TRUE	ASN,SER,THR
30	TRUE	TRUE	ASP,THR
31	TRUE	TRUE	GLU,PHE,TYR
32	TRUE	TRUE	ASP,TRP,TYR
33	TRUE	FALSE	MET
34	TRUE	TRUE	GLU,GLY,SER
35	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
36	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
37	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
38	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
39	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
40	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
41	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
42	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
43	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
44	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
45	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
46	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
47	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
48	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
49	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
50	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
51	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
52	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
53	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
54	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
55	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
56	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
57	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
58	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
59	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
60	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
61	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
62	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
63	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
64	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
65	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
66	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
67	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
68	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
69	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
70	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
71	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
72	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
73	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
74	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
75	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
76	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
77	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
78	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
79	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
80	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
81	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
82	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
83	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
84	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
85	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
86	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
87	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
88	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
89	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
90	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
91	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
92	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
93	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
94	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
95	TRUE	FALSE	CYS:disulfide
96	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
97	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
98	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
99	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
100	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
101	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
102	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
103	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
104	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
105	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
106	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
107	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
108	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
109	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
110	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
111	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
112	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
113	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
114	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
115	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
116	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
117	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
118	TRUE	TRUE	ALA:CtermProteinFull,CYS:CtermProteinFull,ASP:CtermProteinFull,GLU:CtermProteinFull,PHE:CtermProteinFull,GLY:CtermProteinFull,HIS:CtermProteinFull,HIS_D:CtermProteinFull,ILE:CtermProteinFull,LYS:CtermProteinFull,LEU:CtermProteinFull,MET:CtermProteinFull,ASN:CtermProteinFull,PRO:CtermProteinFull,GLN:CtermProteinFull,ARG:CtermProteinFull,SER:CtermProteinFull,THR:CtermProteinFull,VAL:CtermProteinFull,TRP:CtermProteinFull,TYR:CtermProteinFull

思考¶

可见CDR-H1处的氨基酸自由度减少了。尝试重复运行上述代码，以及增大set_picking_rounds参数，你发现了什么现象？

2.4.4 AddCDRProfileSetsOperation¶

这个模块依然处于实验阶段。该TaskOperation每次生成PackTask时，它随机地选择一个CDR cluster（如H1-13-1 或 H1-13-2 或 H1-13-3）来统计氨基酸频率。因此不再受限于Pose中原有的CDR结构所在的那个簇。如果结构中本身的CDR没有对应的簇，那么将跳过该CDR的设计。

In [57]:

from pyrosetta.rosetta.protocols.antibody.task_operations import AddCDRProfileSetsOperation
add_cdr_profile_set = AddCDRProfileSetsOperation()
add_cdr_profile_set.set_include_native_type(True) # allowed wild type AA
add_cdr_profile_set.set_picking_rounds(1)  # 控制sequence sampling次数

# 设置多个CDR.
cdr_allow = [1,0,0,0,0,0,0,0] # H1 H2 H3 H4 L1 L2 L3 L4
vector1 = pyrosetta.rosetta.utility.vector1_bool()
for i in cdr_allow:
    vector1.append(i)
add_cdr_profile_set.set_cdrs(vector1)

#基于CDR长度的sampling设置:
#add_cdr_profile_set.set_limit_only_to_length(True) # 默认为 不限制链长.

# 设置策略2:
add_cdr_profile_set.set_cutoff(10) # profile截断，如果簇内少于10个成员，那么使用FALLBACK STRATEGIES
add_cdr_profile_set.set_use_outliers(False) #是否采样聚类中偏离较远的序列。

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(add_cdr_profile)

# 生成PackerTask
packer_task = pack_tf.create_task_and_apply_taskoperations(antibody_pose)
print(packer_task)

basic.io.database: {0} Database file opened: sampling/antibodies/cluster_center_dihedrals.txt
protocols.antibody.AntibodyNumberingParser: {0} Antibody numbering scheme definitions read successfully
protocols.antibody.AntibodyNumberingParser: {0} Antibody CDR definition read successfully
antibody.AntibodyInfo: {0} Successfully finished the CDR definition
antibody.AntibodyInfo: {0}  Could not setup Vl Vh Packing angle for camelid antibody
antibody.AntibodyInfo: {0} AC Detecting Camelid CDR H3 Stem Type
antibody.AntibodyInfo: {0} AC Finished Detecting Camelid CDR H3 Stem Type: NEUTRAL
antibody.AntibodyInfo: {0} Setting up CDR Cluster for H1
protocols.antibody.cluster.CDRClusterMatcher: {0} Length: 13 Omega: TTTTTTTTTTTTT
antibody.AntibodyInfo: {0} Setting up CDR Cluster for H2
protocols.antibody.cluster.CDRClusterMatcher: {0} Length: 10 Omega: TTTTTTTTTT
antibody.AntibodyInfo: {0} Setting up CDR Cluster for H3
protocols.antibody.cluster.CDRClusterMatcher: {0} Length: 13 Omega: TTTTTTTTTTTTT
basic.io.database: {0} [ WARNING ] Unable to locate database file /sampling/antibodies/antibody_database_rosetta_design.db
antibody.database.AntibodyDatabaseManager: {0} The antibody design database is not specified by the user.
antibody.database.AntibodyDatabaseManager: {0} Reading from: /opt/miniconda3/lib/python3.7/site-packages/pyrosetta/database//sampling/antibodies/antibody_database_rosetta_design_north_paper.db
antibody.database.AntibodyDatabaseManager: {0} Loaded H1-13-1 with 210 datapoints.
protocols.antibody.task_operations.AddCDRProfilesOperation: {0} applying prob task op
#Packer_Task

Threads to request: ALL AVAILABLE

resid	pack?	design?	allowed_aas
1	TRUE	TRUE	ALA:NtermProteinFull,CYS:NtermProteinFull,ASP:NtermProteinFull,GLU:NtermProteinFull,PHE:NtermProteinFull,GLY:NtermProteinFull,HIS:NtermProteinFull,HIS_D:NtermProteinFull,ILE:NtermProteinFull,LYS:NtermProteinFull,LEU:NtermProteinFull,MET:NtermProteinFull,ASN:NtermProteinFull,PRO:NtermProteinFull,GLN:NtermProteinFull,ARG:NtermProteinFull,SER:NtermProteinFull,THR:NtermProteinFull,VAL:NtermProteinFull,TRP:NtermProteinFull,TYR:NtermProteinFull
2	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
3	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
4	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
5	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
6	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
7	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
8	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
9	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
10	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
11	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
12	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
13	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
14	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
15	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
16	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
17	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
18	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
19	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
20	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
21	TRUE	FALSE	CYS:disulfide
22	TRUE	TRUE	ALA,LYS
23	TRUE	FALSE	ALA
24	TRUE	FALSE	SER
25	TRUE	FALSE	GLY
26	TRUE	TRUE	PHE,LEU
27	TRUE	TRUE	ILE,ASN,ARG
28	TRUE	TRUE	PHE,ILE
29	TRUE	TRUE	LYS,SER,THR
30	TRUE	TRUE	ASP,ARG
31	TRUE	TRUE	GLU,PHE,THR
32	TRUE	TRUE	ASP,TYR
33	TRUE	FALSE	MET
34	TRUE	TRUE	GLU,GLY,HIS,HIS_D
35	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
36	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
37	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
38	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
39	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
40	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
41	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
42	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
43	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
44	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
45	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
46	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
47	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
48	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
49	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
50	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
51	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
52	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
53	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
54	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
55	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
56	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
57	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
58	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
59	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
60	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
61	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
62	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
63	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
64	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
65	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
66	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
67	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
68	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
69	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
70	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
71	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
72	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
73	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
74	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
75	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
76	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
77	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
78	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
79	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
80	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
81	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
82	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
83	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
84	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
85	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
86	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
87	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
88	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
89	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
90	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
91	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
92	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
93	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
94	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
95	TRUE	FALSE	CYS:disulfide
96	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
97	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
98	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
99	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
100	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
101	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
102	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
103	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
104	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
105	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
106	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
107	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
108	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
109	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
110	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
111	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
112	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
113	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
114	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
115	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
116	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
117	TRUE	TRUE	ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
118	TRUE	TRUE	ALA:CtermProteinFull,CYS:CtermProteinFull,ASP:CtermProteinFull,GLU:CtermProteinFull,PHE:CtermProteinFull,GLY:CtermProteinFull,HIS:CtermProteinFull,HIS_D:CtermProteinFull,ILE:CtermProteinFull,LYS:CtermProteinFull,LEU:CtermProteinFull,MET:CtermProteinFull,ASN:CtermProteinFull,PRO:CtermProteinFull,GLN:CtermProteinFull,ARG:CtermProteinFull,SER:CtermProteinFull,THR:CtermProteinFull,VAL:CtermProteinFull,TRP:CtermProteinFull,TYR:CtermProteinFull

2.4.5 RestrictToCDRsAndNeighbors¶

将某些CDRs及它的邻近氨基酸的pack状态设置为repack, 其余残基一律设置为no_repack。

In [58]:

from pyrosetta.rosetta.protocols.antibody.task_operations import RestrictToCDRsAndNeighbors
from pyrosetta.rosetta.protocols.antibody import CDRNameEnum
from pyrosetta.rosetta.utility import vector1_bool

# 设置CDR的选择范围:
cdr_allow = [1, 1, 0, 0, 0, 0, 0, 0]  # H1 H2 H3 H4 L1 L2 L3 L4
vector1 = vector1_bool()
for i in cdr_allow:
    vector1.append(i)
print(vector1)

# # 约束CDR周围的氨基酸为Repack，非临近区域为no_repack;
restrict_cdr_nbr = RestrictToCDRsAndNeighbors()
restrict_cdr_nbr.set_cdrs(vector1)
restrict_cdr_nbr.set_allow_design_cdr(0)  # pack状态设置为Design/repack
restrict_cdr_nbr.set_allow_design_neighbor_framework(0)  # pack状态设置为Design/repack
restrict_cdr_nbr.set_allow_design_neighbor_antigen(0)  # pack状态设置为Design/repack
restrict_cdr_nbr.set_neighbor_distance(8.0)
restrict_cdr_nbr.set_stem_size(0)  # 在计算邻近氨基酸时,将CDR两端延长N个氨基酸来计算。(延长的氨基酸依然属于FR区)

# # 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
pack_tf.push_back(restrict_cdr_nbr)

# # 生成PackerTask(目前有bug.运行会报错)
# packer_task = pack_tf.create_task_and_apply_taskoperations(antibody_pose)
# print(packer_task)

vector1_bool[1, 1, 0, 0, 0, 0, 0, 0]