Notebook

TaskOperation & PackTask¶

@Author: 吴炜坤

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

上一节，我们详细介绍了Rotamer以及Rosetta Packer的基本工作原理。Packer有三种工作方式: “Repacking”、“Rotamer Trial”和“Design”。其中Rotamer就有可能存在3种基本状态:

Repacking: 该位点处Rotamer类型只能是同一种氨基酸;
Design: 该位点上Rotamer类型可以是多种氨酸;
Fixed: 该位点Rotamer不允许发生变化。

在本章节中，读者将学习到如何使用TaskOperations来控制Rotamer在Packer中的“行为规范”。

一、PackerTask与TaskFactory¶

如果把Packer想象成一位“蛋白构建大师”，他正在将一些建筑材料(Rotamer)安装在地基上(Backbone的 $C_{\alpha}$ 原子)。但是在施工之前，建筑大师必须知道他需要在每个地基点上能安装什么材料，并且经过他的深思熟虑(模拟退火)来构建出最完美的艺术品。此时，他需要我们的帮助，给他一张施工的蓝图。而这张蓝图就是PackerTask。

(图片来源: 晶泰科技团队)

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 2021.26+release.b308454c455dd04f6824cc8b23e54bbb9be2cdd7 2021-07-02T13:01:54] 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 r288 2021.26+release.b308454c455 b308454c455dd04f6824cc8b23e54bbb9be2cdd7 http://www.pyrosetta.org 2021-07-02T13:01:54
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=-778071707 seed_offset=0 real_seed=-778071707 thread_index=0
basic.random.init_random_generator: {0} RandomGenerator:init: Normal mode, seed=-778071707 RG_type=mt19937
core.chemical.GlobalResidueTypeSet: {0} Finished initializing fa_standard residue type set.  Created 984 residue types
core.chemical.GlobalResidueTypeSet: {0} Total time to initialize 0.684034 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

PackerTask需要从TaskFactory中进行自动生成。

In [2]:

# 从TaskFactory生成packer_task
from pyrosetta.rosetta.core.pack.task import TaskFactory
tf = TaskFactory()
packer_task = tf.create_packer_task(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: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

从上述结果可见，默认生成的Packer_Task包含三种数据:

残基位点编号信息
每个位点上，Rotamer的3种基本状态
每个位点上，被允许氨基酸Rotamer类型

并且默认的PackerTask是运行每个位点都包含20种氨基酸的Rotamer

二、什么是TaskOperations?¶

TaskOperations直译的意思即为"任务操作元件", TaskOperations被TaskFactory加载并创建PackerTask。

TaskOperations可以直观的理解为对指定位点氨基酸的Rotamer自由度进行消减的过程，类似做雕刻的过程，一开始默认的PackerTask允许所有20种氨基酸的Rotamer的出现，在加载不同的TaskOperations后，PackerTask的Rotamer自由度开始不断的缩减，直到满足用户设定的需求。其中一点是非常重要的。一旦将Rotamer的自由度缩减后，将无法在PackerTask中重新被激活。 如，第一个TaskOperations设定5号位点为“Fixed“的状态，第二个TaskOperations再重新设定5号位点为“Repacking“的状态。TaskFactory生成的PackerTask中5号位点依然为“Fixed(No_repack)“的状态。从底层逻辑来理解，TaskFactory将所有的TaskOperations中取Rotamer自由度越小的那个状态来生成PackerTask。

(图片来源: jadolfbr@gmail.com提供的ppt)

小结:

TaskOperations的三层自由度级别: Design/Repack/No_repack;
TaskOperations形象地类似于"冰雕设计", 它的作用是告诉TaskFactory在Pose中每个位点的Rotamer自由度大小;
一旦一个氨基酸或区域被设计定为低自由度状态时，那么这个位点将不能被重新设定为高自由度状态。

三、TaskOperations的分类¶

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);

3.1 Residue Level TaskOperations的使用示例¶

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。

此处举一个简单RestrictToRepackingRLT(顾明思议此RTL是将Rotamer约束到现有氨基酸类型上。)应用的例子：

In [3]:

from pyrosetta.rosetta.core.pack.task.operation import RestrictToRepackingRLT, OperateOnResidueSubset
from pyrosetta.rosetta.core.select.residue_selector import ResidueIndexSelector
# 选择氨基酸范围
select_pos3 = ResidueIndexSelector('1,3,5')

# 使用OperateOnResidueSubset生成TaskOperations
packing_taskop = OperateOnResidueSubset(RestrictToRepackingRLT(), select_pos3, 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	FALSE	ASP: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	FALSE	LEU
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	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: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

此时，通过PackerTask我们可以观测到，我们选择的1,3,5号氨基酸都只被允许为进行pack，氨基酸的类型也只剩下pose中原本的氨基酸类型。

除了RestrictToRepackingRLT以外，还有许多其他7种常用的RTL类型，此处做一个简单的列表解释用途:

RestrictToRepackingRLT: 将Rotamer自由度设置为repacking
PreventRepackingRLT: 将Rotamer自由度设置为no_repack
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
RestrictAbsentCanonicalAASRLT: 将Rotamer自由度限定在给定的氨基酸类型列表。
DisallowIfNonnativeRLT: 将Rotamer自由度限定在非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
IncludeCurrentRLT: 设定Packer在执行期间，考虑Pose输入时的Rotamer状态(并非全部忘记)。
ExtraRotamersGenericRLT: 设定在Rotamer采样中，是否考虑增加额外的数量，否则仅会考虑理想型的Rotamer。

上述的这些RTL和Selector就可以组合成任意的TaskOperations，更多RLT的API用法请参考TaskOperations API详解相关的章节。

思考¶

如果将OperateOnResidueSubset中的False转变为True，PackerTask会发生什么变化？

3.2 Specialized Operations的使用示例¶

Specialized Operations其实就是开发者预先设定好一些应用场景的TaskOperations，这类TaskOperations可以直接被TaskFactory所读取，一般的这种TaskOperations的应用范围都是全局性。

In [4]:

from pyrosetta.rosetta.core.pack.task.operation import RestrictToRepacking

# 将TaskOperations加载至TaskFactory中
pack_tf = TaskFactory()
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	TRUE	FALSE	ASP:NtermProteinFull
2	TRUE	FALSE	GLU
3	TRUE	FALSE	LEU
4	TRUE	FALSE	GLN
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

可见所有位点都被限制为repacking的状态，更多Specialized Operations的API用法请参考TaskOperations API详解相关的章节。

四、Pack Rotamer相关Mover¶

4.1 PackRotamersMover¶

上述内容已经清楚地阐释了PackerTask的作用，以及如何去利用TaskOperations和TaskFactory去生成特定用途的PackerTask。当有了这张清晰的“蓝图文件后”，就实际地在Pose结构上进行“施工”，而真正执行任务的Mover大多可以在pyrosetta.rosetta.protocols.minimization_packing的API下找到。此处我们以最简单的PackRotamersMover做实例示范。

In [5]:

from pyrosetta.rosetta.protocols.minimization_packing import PackRotamersMover
from pyrosetta import create_score_function
pack_mover = PackRotamersMover()
ref2015 = create_score_function('ref2015')
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(pose)
pose.dump_pdb('./data/repacked.pdb')

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
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
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 0.182942 seconds to load from binary
core.pack.pack_rotamers: {0} built 182 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).

Out[5]:

True

对比原始输入结构和repack之后的结构变化，发现只有侧链的rotamer发生了变化，和预期一致。

(图片来源: 晶泰科技团队)

4.2 FastRelax¶

上述的介绍的PackRotamersMover所做的就仅仅是处理侧链构象相关的模拟退火过程。但是在实际应用中Rosetta常常交替式运行Packer和Minimizer(MinMover)，这类组合型的Mover常有的有FastRelaxMover以及FastDesignMover。这些Mover可以同时优化侧链和骨架去寻找能量更低的构象。

一张图看懂FastRelax在做什么:

(图片来源: 晶泰科技团队)

In [6]:

# FastRelax
from pyrosetta.rosetta.protocols.relax import FastRelax
fastrelax = FastRelax()
fastrelax.set_scorefxn(ref2015)
fastrelax.set_default_movemap() #使用默认的Movemap()
fastrelax.apply(pose)
pose.dump_pdb('./data/fastrelaxed.pdb')

protocols.relax.RelaxScriptManager: {0} Reading relax scripts list from database.
core.scoring.ScoreFunctionFactory: {0} SCOREFUNCTION: ref2015
protocols.relax.RelaxScriptManager: {0} Looking for MonomerRelax2019.txt
protocols.relax.RelaxScriptManager: {0} ================== Reading script file: /opt/miniconda3/lib/python3.7/site-packages/pyrosetta/database/sampling/relax_scripts/MonomerRelax2019.txt ==================
protocols.relax.RelaxScriptManager: {0} repeat %%nrepeats%%
protocols.relax.RelaxScriptManager: {0} coord_cst_weight 1.0
protocols.relax.RelaxScriptManager: {0} scale:fa_rep 0.040
protocols.relax.RelaxScriptManager: {0} repack
protocols.relax.RelaxScriptManager: {0} scale:fa_rep 0.051
protocols.relax.RelaxScriptManager: {0} min 0.01
protocols.relax.RelaxScriptManager: {0} coord_cst_weight 0.5
protocols.relax.RelaxScriptManager: {0} scale:fa_rep 0.265
protocols.relax.RelaxScriptManager: {0} repack
protocols.relax.RelaxScriptManager: {0} scale:fa_rep 0.280
protocols.relax.RelaxScriptManager: {0} min 0.01
protocols.relax.RelaxScriptManager: {0} coord_cst_weight 0.0
protocols.relax.RelaxScriptManager: {0} scale:fa_rep 0.559
protocols.relax.RelaxScriptManager: {0} repack
protocols.relax.RelaxScriptManager: {0} scale:fa_rep 0.581
protocols.relax.RelaxScriptManager: {0} min 0.01
protocols.relax.RelaxScriptManager: {0} coord_cst_weight 0.0
protocols.relax.RelaxScriptManager: {0} scale:fa_rep 1
protocols.relax.RelaxScriptManager: {0} repack
protocols.relax.RelaxScriptManager: {0} min 0.00001
protocols.relax.RelaxScriptManager: {0} accept_to_best
protocols.relax.RelaxScriptManager: {0} endrepeat
protocols.relax.FastRelax: {0} CMD: repeat  -16.7505  0  0  0.55
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -16.7505  0  0  0.55
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -22.4175  0  0  0.022
core.pack.task: {0} Packer task: initialize from command line()
core.pack.pack_rotamers: {0} built 201 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
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -24.6338  0  0  0.022
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -24.4608  0  0  0.02805
protocols.relax.FastRelax: {0} CMD: min  -24.4789  0.000592829  0.000592829  0.02805
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -24.4789  0.000592829  0.000592829  0.02805
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -21.09  0.000592829  0.000592829  0.14575
core.pack.task: {0} Packer task: initialize from command line()
core.pack.pack_rotamers: {0} built 194 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
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -21.3231  0.000592829  0.000592829  0.14575
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -21.1753  0.000592829  0.000592829  0.154
protocols.relax.FastRelax: {0} CMD: min  -21.1948  0.000882851  0.000882851  0.154
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -21.1948  0.000882851  0.000882851  0.154
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -18.4693  0.000882851  0.000882851  0.30745
core.pack.task: {0} Packer task: initialize from command line()
core.pack.pack_rotamers: {0} built 194 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
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -19.3676  0.000882851  0.000882851  0.30745
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -19.2377  0.000882851  0.000882851  0.31955
protocols.relax.FastRelax: {0} CMD: min  -19.2466  0.00116297  0.00116297  0.31955
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -19.2466  0.00116297  0.00116297  0.31955
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -16.7738  0.00116297  0.00116297  0.55
core.pack.task: {0} Packer task: initialize from command line()
core.pack.pack_rotamers: {0} built 194 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
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -16.2946  0.00116297  0.00116297  0.55
protocols.relax.FastRelax: {0} CMD: min  -20.9544  0.271541  0.271541  0.55
protocols.relax.FastRelax: {0} MRP: 0  -20.9544  -20.9544  0.271541  0.271541
protocols.relax.FastRelax: {0} CMD: accept_to_best  -20.9544  0.271541  0.271541  0.55
protocols.relax.FastRelax: {0} CMD: endrepeat  -20.9544  0.271541  0.271541  0.55
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -20.9544  0.271541  0.271541  0.55
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -25.4018  0.271541  0.271541  0.022
core.pack.task: {0} Packer task: initialize from command line()
core.pack.pack_rotamers: {0} built 207 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
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -26.771  0.271541  0.271541  0.022
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -26.6961  0.271541  0.271541  0.02805
protocols.relax.FastRelax: {0} CMD: min  -26.7002  0.27138  0.27138  0.02805
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -26.7002  0.27138  0.27138  0.02805
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -25.2457  0.27138  0.27138  0.14575
core.pack.task: {0} Packer task: initialize from command line()
core.pack.pack_rotamers: {0} built 200 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
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -25.2457  0.27138  0.27138  0.14575
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -25.1438  0.27138  0.27138  0.154
protocols.relax.FastRelax: {0} CMD: min  -25.1559  0.270886  0.270886  0.154
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -25.1559  0.270886  0.270886  0.154
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -23.2676  0.270886  0.270886  0.30745
core.pack.task: {0} Packer task: initialize from command line()
core.pack.pack_rotamers: {0} built 196 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
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -23.2676  0.270886  0.270886  0.30745
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -23.1187  0.270886  0.270886  0.31955
protocols.relax.FastRelax: {0} CMD: min  -23.1555  0.269967  0.269967  0.31955
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -23.1555  0.269967  0.269967  0.31955
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -20.3431  0.269967  0.269967  0.55
core.pack.task: {0} Packer task: initialize from command line()
core.pack.pack_rotamers: {0} built 195 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
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -20.3651  0.269967  0.269967  0.55
protocols.relax.FastRelax: {0} CMD: min  -22.809  0.263703  0.263703  0.55
protocols.relax.FastRelax: {0} MRP: 1  -22.809  -22.809  0.263703  0.263703
protocols.relax.FastRelax: {0} CMD: accept_to_best  -22.809  0.263703  0.263703  0.55
protocols.relax.FastRelax: {0} CMD: endrepeat  -22.809  0.263703  0.263703  0.55
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -22.809  0.263703  0.263703  0.55
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -27.292  0.263703  0.263703  0.022
core.pack.task: {0} Packer task: initialize from command line()
core.pack.pack_rotamers: {0} built 210 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
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -27.4217  0.263703  0.263703  0.022
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -27.3649  0.263703  0.263703  0.02805
protocols.relax.FastRelax: {0} CMD: min  -27.3682  0.263861  0.263861  0.02805
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -27.3682  0.263861  0.263861  0.02805
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -26.2615  0.263861  0.263861  0.14575
core.pack.task: {0} Packer task: initialize from command line()
core.pack.pack_rotamers: {0} built 205 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
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -26.2615  0.263861  0.263861  0.14575
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -26.1839  0.263861  0.263861  0.154
protocols.relax.FastRelax: {0} CMD: min  -26.1858  0.263953  0.263953  0.154
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -26.1858  0.263953  0.263953  0.154
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -24.7424  0.263953  0.263953  0.30745
core.pack.task: {0} Packer task: initialize from command line()
core.pack.pack_rotamers: {0} built 201 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
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -24.7524  0.263953  0.263953  0.30745
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -24.6407  0.263953  0.263953  0.31955
protocols.relax.FastRelax: {0} CMD: min  -24.6416  0.263979  0.263979  0.31955
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -24.6416  0.263979  0.263979  0.31955
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -22.513  0.263979  0.263979  0.55
core.pack.task: {0} Packer task: initialize from command line()
core.pack.pack_rotamers: {0} built 200 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
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -22.513  0.263979  0.263979  0.55
protocols.relax.FastRelax: {0} CMD: min  -22.8052  0.264081  0.264081  0.55
protocols.relax.FastRelax: {0} MRP: 2  -22.8052  -22.809  0.263703  0.263703
protocols.relax.FastRelax: {0} CMD: accept_to_best  -22.8052  0.264081  0.264081  0.55
protocols.relax.FastRelax: {0} CMD: endrepeat  -22.8052  0.264081  0.264081  0.55
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -22.8052  0.264081  0.264081  0.55
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -27.2738  0.264081  0.264081  0.022
core.pack.task: {0} Packer task: initialize from command line()
core.pack.pack_rotamers: {0} built 210 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
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -27.3953  0.264081  0.264081  0.022
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -27.3397  0.264081  0.264081  0.02805
protocols.relax.FastRelax: {0} CMD: min  -27.343  0.264247  0.264247  0.02805
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -27.343  0.264247  0.264247  0.02805
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -26.2609  0.264247  0.264247  0.14575
core.pack.task: {0} Packer task: initialize from command line()
core.pack.pack_rotamers: {0} built 205 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
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -26.2608  0.264247  0.264247  0.14575
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -26.185  0.264247  0.264247  0.154
protocols.relax.FastRelax: {0} CMD: min  -26.1868  0.264353  0.264353  0.154
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -26.1868  0.264353  0.264353  0.154
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -24.7752  0.264353  0.264353  0.30745
core.pack.task: {0} Packer task: initialize from command line()
core.pack.pack_rotamers: {0} built 201 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
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -24.7752  0.264353  0.264353  0.30745
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -24.6639  0.264353  0.264353  0.31955
protocols.relax.FastRelax: {0} CMD: min  -24.6648  0.264378  0.264378  0.31955
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -24.6648  0.264378  0.264378  0.31955
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -22.5448  0.264378  0.264378  0.55
core.pack.task: {0} Packer task: initialize from command line()
core.pack.pack_rotamers: {0} built 200 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
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -22.571  0.264378  0.264378  0.55
protocols.relax.FastRelax: {0} CMD: min  -22.8064  0.262966  0.262966  0.55
protocols.relax.FastRelax: {0} MRP: 3  -22.8064  -22.809  0.263703  0.263703
protocols.relax.FastRelax: {0} CMD: accept_to_best  -22.8064  0.262966  0.262966  0.55
protocols.relax.FastRelax: {0} CMD: endrepeat  -22.8064  0.262966  0.262966  0.55
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -22.8064  0.262966  0.262966  0.55
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -27.2757  0.262966  0.262966  0.022
core.pack.task: {0} Packer task: initialize from command line()
core.pack.pack_rotamers: {0} built 210 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
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -27.4014  0.262966  0.262966  0.022
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -27.3455  0.262966  0.262966  0.02805
protocols.relax.FastRelax: {0} CMD: min  -27.3489  0.263132  0.263132  0.02805
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -27.3489  0.263132  0.263132  0.02805
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -26.2614  0.263132  0.263132  0.14575
core.pack.task: {0} Packer task: initialize from command line()
core.pack.pack_rotamers: {0} built 205 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
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -26.2614  0.263132  0.263132  0.14575
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -26.1851  0.263132  0.263132  0.154
protocols.relax.FastRelax: {0} CMD: min  -26.1869  0.263236  0.263236  0.154
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -26.1869  0.263236  0.263236  0.154
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -24.7684  0.263236  0.263236  0.30745
core.pack.task: {0} Packer task: initialize from command line()
core.pack.pack_rotamers: {0} built 201 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
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -24.7684  0.263236  0.263236  0.30745
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -24.6566  0.263236  0.263236  0.31955
protocols.relax.FastRelax: {0} CMD: min  -24.6576  0.263258  0.263258  0.31955
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -24.6576  0.263258  0.263258  0.31955
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -22.5273  0.263258  0.263258  0.55
core.pack.task: {0} Packer task: initialize from command line()
core.pack.pack_rotamers: {0} built 200 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
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -22.5578  0.263258  0.263258  0.55
protocols.relax.FastRelax: {0} CMD: min  -22.806  0.263123  0.263123  0.55
protocols.relax.FastRelax: {0} MRP: 4  -22.806  -22.809  0.263703  0.263703
protocols.relax.FastRelax: {0} CMD: accept_to_best  -22.806  0.263123  0.263123  0.55
protocols.relax.FastRelax: {0} CMD: endrepeat  -22.806  0.263123  0.263123  0.55
protocols::checkpoint: {0} Deleting checkpoints of FastRelax

Out[6]:

True

(图片来源: 晶泰科技团队)

尽管构象没有非常大的变化，但是可见骨架和侧链是同时被优化的。

4.3 FastDesign¶

FastDesign其实就是FastRelax的Design版本，允许序列被进行设计。此处我们定一个Task不允许1、3、5、7、9位点design，其余位点允许设计出20种氨基酸。

In [7]:

# 设置FastDesign的蓝图。
from pyrosetta.rosetta.protocols.denovo_design.movers import FastDesign

# 将TaskOperations加载至TaskFactory中
# 选择氨基酸范围
no_design_pos = ResidueIndexSelector('1,3,5,7,9')

# 使用OperateOnResidueSubset生成TaskOperations
design_taskop = OperateOnResidueSubset(RestrictToRepackingRLT(), no_design_pos, False)

design_tf = TaskFactory()
design_tf.push_back(design_taskop)

# 生成PackerTask
design_task = design_tf.create_task_and_apply_taskoperations(pose)
print(design_task)

#Packer_Task

Threads to request: ALL AVAILABLE

resid	pack?	design?	allowed_aas
1	TRUE	FALSE	ASP: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	FALSE	LEU
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	FALSE	VAL
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	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: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

In [8]:

# 初始化FastDesign:
fastdesign = FastDesign()
fastdesign.set_scorefxn(ref2015)
fastdesign.set_default_movemap() #使用默认的Movemap()
fastdesign.set_task_factory(design_tf)
fastdesign.apply(pose)
pose.dump_pdb('./data/fastdesign.pdb')

core.scoring.ScoreFunctionFactory: {0} SCOREFUNCTION: ref2015
protocols.denovo_design.movers.FastDesign: {0} #Packer_Task
protocols.denovo_design.movers.FastDesign: {0} 
protocols.denovo_design.movers.FastDesign: {0} Threads to request: ALL AVAILABLE
protocols.denovo_design.movers.FastDesign: {0} 
protocols.denovo_design.movers.FastDesign: {0} resid	pack?	design?	allowed_aas
protocols.denovo_design.movers.FastDesign: {0} 1	TRUE	FALSE	ASP:NtermProteinFull
protocols.denovo_design.movers.FastDesign: {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.movers.FastDesign: {0} 3	TRUE	FALSE	LEU
protocols.denovo_design.movers.FastDesign: {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.movers.FastDesign: {0} 5	TRUE	FALSE	LYS
protocols.denovo_design.movers.FastDesign: {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.movers.FastDesign: {0} 7	TRUE	FALSE	VAL
protocols.denovo_design.movers.FastDesign: {0} 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
protocols.denovo_design.movers.FastDesign: {0} 9	TRUE	FALSE	GLN
protocols.denovo_design.movers.FastDesign: {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.movers.FastDesign: {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.movers.FastDesign: {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.movers.FastDesign: {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.movers.FastDesign: {0} 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
protocols.relax.FastRelax: {0} CMD: repeat  -22.809  0  0  0.55
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -22.809  0  0  0.55
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -27.292  0  0  0.022
core.pack.pack_rotamers: {0} built 2580 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 PDInteractionGraph
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -33.9419  0  0  0.022
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -33.5386  0  0  0.02805
protocols.relax.FastRelax: {0} CMD: min  -33.5519  0.000789733  0.000789733  0.02805
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -33.5519  0.000789733  0.000789733  0.02805
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -25.7005  0.000789733  0.000789733  0.14575
core.pack.pack_rotamers: {0} built 2496 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 PDInteractionGraph
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -29.3306  0.000789733  0.000789733  0.14575
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -29.1736  0.000789733  0.000789733  0.154
protocols.relax.FastRelax: {0} CMD: min  -29.1777  0.00104836  0.00104836  0.154
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -29.1777  0.00104836  0.00104836  0.154
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -26.2553  0.00104836  0.00104836  0.30745
core.pack.pack_rotamers: {0} built 2430 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 PDInteractionGraph
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -26.4018  0.00104836  0.00104836  0.30745
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -26.1935  0.00104836  0.00104836  0.31955
protocols.relax.FastRelax: {0} CMD: min  -26.2022  0.00144815  0.00144815  0.31955
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -26.2022  0.00144815  0.00144815  0.31955
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -22.2381  0.00144815  0.00144815  0.55
core.pack.pack_rotamers: {0} built 2379 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 PDInteractionGraph
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -24.1411  0.00144815  0.00144815  0.55
protocols.relax.FastRelax: {0} CMD: min  -28.1179  0.140127  0.140127  0.55
protocols.relax.FastRelax: {0} MRP: 0  -28.1179  -28.1179  0.140127  0.140127
protocols.relax.FastRelax: {0} CMD: accept_to_best  -28.1179  0.140127  0.140127  0.55
protocols.relax.FastRelax: {0} CMD: endrepeat  -28.1179  0.140127  0.140127  0.55
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -28.1179  0.140127  0.140127  0.55
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -33.0957  0.140127  0.140127  0.022
core.pack.pack_rotamers: {0} built 2531 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 PDInteractionGraph
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -35.4398  0.140127  0.140127  0.022
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -35.0094  0.140127  0.140127  0.02805
protocols.relax.FastRelax: {0} CMD: min  -35.0213  0.139614  0.139614  0.02805
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -35.0213  0.139614  0.139614  0.02805
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -26.7146  0.139614  0.139614  0.14575
core.pack.pack_rotamers: {0} built 2429 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 PDInteractionGraph
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -31.3182  0.139614  0.139614  0.14575
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -31.1772  0.139614  0.139614  0.154
protocols.relax.FastRelax: {0} CMD: min  -31.1813  0.139846  0.139846  0.154
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -31.1813  0.139846  0.139846  0.154
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -28.5587  0.139846  0.139846  0.30745
core.pack.pack_rotamers: {0} built 2355 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 PDInteractionGraph
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -28.7355  0.139846  0.139846  0.30745
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -28.6147  0.139846  0.139846  0.31955
protocols.relax.FastRelax: {0} CMD: min  -28.6157  0.139874  0.139874  0.31955
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -28.6157  0.139874  0.139874  0.31955
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -26.3155  0.139874  0.139874  0.55
core.pack.pack_rotamers: {0} built 2283 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 PDInteractionGraph
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -26.458  0.139874  0.139874  0.55
protocols.relax.FastRelax: {0} CMD: min  -26.9144  0.0973955  0.0973955  0.55
protocols.relax.FastRelax: {0} MRP: 1  -26.9144  -28.1179  0.140127  0.140127
protocols.relax.FastRelax: {0} CMD: accept_to_best  -26.9144  0.0973955  0.0973955  0.55
protocols.relax.FastRelax: {0} CMD: endrepeat  -26.9144  0.0973955  0.0973955  0.55
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -26.9144  0.0973955  0.0973955  0.55
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -31.3626  0.0973955  0.0973955  0.022
core.pack.pack_rotamers: {0} built 2534 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 PDInteractionGraph
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -35.0507  0.0973955  0.0973955  0.022
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -34.7919  0.0973955  0.0973955  0.02805
protocols.relax.FastRelax: {0} CMD: min  -34.8058  0.0977755  0.0977755  0.02805
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -34.8058  0.0977755  0.0977755  0.02805
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -29.7448  0.0977755  0.0977755  0.14575
core.pack.pack_rotamers: {0} built 2427 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 PDInteractionGraph
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -31.4077  0.0977755  0.0977755  0.14575
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -31.2744  0.0977755  0.0977755  0.154
protocols.relax.FastRelax: {0} CMD: min  -31.2787  0.0978921  0.0978921  0.154
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -31.2787  0.0978921  0.0978921  0.154
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -28.8004  0.0978921  0.0978921  0.30745
core.pack.pack_rotamers: {0} built 2359 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 PDInteractionGraph
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -28.9509  0.0978921  0.0978921  0.30745
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -28.788  0.0978921  0.0978921  0.31955
protocols.relax.FastRelax: {0} CMD: min  -28.7896  0.0979167  0.0979167  0.31955
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -28.7896  0.0979167  0.0979167  0.31955
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -25.6866  0.0979167  0.0979167  0.55
core.pack.pack_rotamers: {0} built 2280 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 PDInteractionGraph
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -26.6963  0.0979167  0.0979167  0.55
protocols.relax.FastRelax: {0} CMD: min  -26.913  0.0955109  0.0955109  0.55
protocols.relax.FastRelax: {0} MRP: 2  -26.913  -28.1179  0.140127  0.140127
protocols.relax.FastRelax: {0} CMD: accept_to_best  -26.913  0.0955109  0.0955109  0.55
protocols.relax.FastRelax: {0} CMD: endrepeat  -26.913  0.0955109  0.0955109  0.55
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -26.913  0.0955109  0.0955109  0.55
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -31.3611  0.0955109  0.0955109  0.022
core.pack.pack_rotamers: {0} built 2532 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 PDInteractionGraph
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -35.0264  0.0955109  0.0955109  0.022
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -34.769  0.0955109  0.0955109  0.02805
protocols.relax.FastRelax: {0} CMD: min  -34.7829  0.0958909  0.0958909  0.02805
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -34.7829  0.0958909  0.0958909  0.02805
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -29.7486  0.0958909  0.0958909  0.14575
core.pack.pack_rotamers: {0} built 2425 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 PDInteractionGraph
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -31.388  0.0958909  0.0958909  0.14575
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -31.2539  0.0958909  0.0958909  0.154
protocols.relax.FastRelax: {0} CMD: min  -31.2583  0.0960147  0.0960147  0.154
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -31.2583  0.0960147  0.0960147  0.154
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -28.7637  0.0960147  0.0960147  0.30745
core.pack.pack_rotamers: {0} built 2357 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 PDInteractionGraph
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -28.9487  0.0960147  0.0960147  0.30745
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -28.7858  0.0960147  0.0960147  0.31955
protocols.relax.FastRelax: {0} CMD: min  -28.7875  0.0960447  0.0960447  0.31955
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -28.7875  0.0960447  0.0960447  0.31955
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -25.6852  0.0960447  0.0960447  0.55
core.pack.pack_rotamers: {0} built 2280 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 PDInteractionGraph
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -26.6957  0.0960447  0.0960447  0.55
protocols.relax.FastRelax: {0} CMD: min  -26.9132  0.095512  0.095512  0.55
protocols.relax.FastRelax: {0} MRP: 3  -26.9132  -28.1179  0.140127  0.140127
protocols.relax.FastRelax: {0} CMD: accept_to_best  -26.9132  0.095512  0.095512  0.55
protocols.relax.FastRelax: {0} CMD: endrepeat  -26.9132  0.095512  0.095512  0.55
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -26.9132  0.095512  0.095512  0.55
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -31.357  0.095512  0.095512  0.022
core.pack.pack_rotamers: {0} built 2532 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 PDInteractionGraph
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -35.0274  0.095512  0.095512  0.022
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -34.7696  0.095512  0.095512  0.02805
protocols.relax.FastRelax: {0} CMD: min  -34.7835  0.0958912  0.0958912  0.02805
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -34.7835  0.0958912  0.0958912  0.02805
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -29.7421  0.0958912  0.0958912  0.14575
core.pack.pack_rotamers: {0} built 2425 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 PDInteractionGraph
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -31.3872  0.0958912  0.0958912  0.14575
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -31.2531  0.0958912  0.0958912  0.154
protocols.relax.FastRelax: {0} CMD: min  -31.2575  0.0960121  0.0960121  0.154
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -31.2575  0.0960121  0.0960121  0.154
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -28.7652  0.0960121  0.0960121  0.30745
core.pack.pack_rotamers: {0} built 2357 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 PDInteractionGraph
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -28.9502  0.0960121  0.0960121  0.30745
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -28.7875  0.0960121  0.0960121  0.31955
protocols.relax.FastRelax: {0} CMD: min  -28.7892  0.0960411  0.0960411  0.31955
protocols.relax.FastRelax: {0} CMD: coord_cst_weight  -28.7892  0.0960411  0.0960411  0.31955
protocols.relax.FastRelax: {0} CMD: scale:fa_rep  -25.6913  0.0960411  0.0960411  0.55
core.pack.pack_rotamers: {0} built 2280 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 PDInteractionGraph
core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).
protocols.relax.FastRelax: {0} CMD: repack  -27.2444  0.0960411  0.0960411  0.55
protocols.relax.FastRelax: {0} CMD: min  -28.716  0.174474  0.174474  0.55
protocols.relax.FastRelax: {0} MRP: 4  -28.716  -28.716  0.174474  0.174474
protocols.relax.FastRelax: {0} CMD: accept_to_best  -28.716  0.174474  0.174474  0.55
protocols.relax.FastRelax: {0} CMD: endrepeat  -28.716  0.174474  0.174474  0.55
protocols::checkpoint: {0} Deleting checkpoints of FastRelax
protocols.denovo_design.movers.FastDesign: {0} 
------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 fa_atr                       1.000     -56.791     -56.791
 fa_rep                       0.550       8.173       4.495
 fa_sol                       1.000      61.636      61.636
 fa_intra_rep                 0.005      21.747       0.109
 fa_intra_sol_xover4          1.000       2.734       2.734
 lk_ball_wtd                  1.000      -1.989      -1.989
 fa_elec                      1.000     -31.585     -31.585
 pro_close                    1.250       0.000       0.000
 hbond_sr_bb                  1.000      -9.781      -9.781
 hbond_lr_bb                  1.000       0.000       0.000
 hbond_bb_sc                  1.000       0.000       0.000
 hbond_sc                     1.000      -3.564      -3.564
 dslf_fa13                    1.250       0.000       0.000
 omega                        0.400       1.037       0.415
 fa_dun                       0.700      24.695      17.287
 p_aa_pp                      0.600      -2.897      -1.738
 yhh_planarity                0.625       0.000       0.000
 ref                          1.000      -5.903      -5.903
 rama_prepro                  0.450      -8.982      -4.042
---------------------------------------------------
 Total weighted score:                      -28.716

Out[8]:

True

通过结构比对，我发现一些位点上的氨基酸类型发生了变化。

(图片来源: 晶泰科技团队)

练习:¶

【LayerDesign】找一个小于60个氨基酸的小蛋白质，通过PyMOL观察，将包埋在内部的氨基酸标记，只允许这些部分设计为疏水氨基酸，其余暴露在溶液中的部分只能设计为极性氨基酸，使用相关的ResidueSelector选择并创建相关TaskOperations，最后使用FastDesign进行设计，查看设计的结果。

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