{
"cells": [
{
"cell_type": "markdown",
"id": "destroyed-catholic",
"metadata": {},
"source": [
"## TaskOperation & PackTask\n",
"\n",
"@Author: 吴炜坤\n",
"\n",
"@email：weikun.wu@xtalpi.com/weikunwu@163.com"
]
},
{
"cell_type": "markdown",
"id": "promising-budapest",
"metadata": {},
"source": [
"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:\n",
"- Repacking: 该位点处Rotamer类型只能是同一种氨基酸;\n",
"- Design: 该位点上Rotamer类型可以是多种氨酸;\n",
"- Fixed: 该位点Rotamer不允许发生变化。"
]
},
{
"cell_type": "markdown",
"id": "cosmetic-nothing",
"metadata": {},
"source": [
"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”。"
]
},
{
"cell_type": "markdown",
"id": "objective-sport",
"metadata": {},
"source": [
"### 一、PackerTask与TaskFactory"
]
},
{
"cell_type": "markdown",
"id": "maritime-security",
"metadata": {},
"source": [
"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。\n",
"\n",
"<center><img src=\"./img/PackerTask.jpg\" width = \"700\" height = \"200\" align=center /></center>\n",
"(图片来源: 晶泰科技团队)"
]
},
{
"cell_type": "code",
"execution_count": 1,
"id": "matched-northwest",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"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\n",
"(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\n",
"\u001b[0mcore.init: {0} \u001b[0mChecking for fconfig files in pwd and ./rosetta/flags\n",
"\u001b[0mcore.init: {0} \u001b[0mRosetta version: PyRosetta4.conda.mac.cxx11thread.serialization.python37.Release r288 2021.26+release.b308454c455 b308454c455dd04f6824cc8b23e54bbb9be2cdd7 http://www.pyrosetta.org 2021-07-02T13:01:54\n",
"\u001b[0mcore.init: {0} \u001b[0mcommand: PyRosetta -ex1 -ex2aro -database /opt/miniconda3/lib/python3.7/site-packages/pyrosetta/database\n",
"\u001b[0mbasic.random.init_random_generator: {0} \u001b[0m'RNG device' seed mode, using '/dev/urandom', seed=-778071707 seed_offset=0 real_seed=-778071707 thread_index=0\n",
"\u001b[0mbasic.random.init_random_generator: {0} \u001b[0mRandomGenerator:init: Normal mode, seed=-778071707 RG_type=mt19937\n",
"\u001b[0mcore.chemical.GlobalResidueTypeSet: {0} \u001b[0mFinished initializing fa_standard residue type set. Created 984 residue types\n",
"\u001b[0mcore.chemical.GlobalResidueTypeSet: {0} \u001b[0mTotal time to initialize 0.684034 seconds.\n",
"\u001b[0mcore.import_pose.import_pose: {0} \u001b[0mFile './data/helix.pdb' automatically determined to be of type PDB\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0m\u001b[1m[ WARNING ]\u001b[0m missing heavyatom: OXT on residue GLY:CtermProteinFull 14\n"
]
}
],
"source": [
"# 初始化PyRosetta并读取一段螺旋结构的PDB。\n",
"from pyrosetta import *\n",
"init()\n",
"pose = pose_from_pdb('./data/helix.pdb')"
]
},
{
"cell_type": "markdown",
"id": "stuffed-procurement",
"metadata": {},
"source": [
"**PackerTask需要从TaskFactory中进行自动生成。**"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "powered-management",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"#Packer_Task\n",
"\n",
"Threads to request: ALL AVAILABLE\n",
"\n",
"resid\tpack?\tdesign?\tallowed_aas\n",
"1\tTRUE\tTRUE\tALA: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\n",
"2\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"3\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"4\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"5\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"6\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"7\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"8\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"9\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"10\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"11\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"12\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"13\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"14\tTRUE\tTRUE\tALA: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\n",
"\n"
]
}
],
"source": [
"# 从TaskFactory生成packer_task\n",
"from pyrosetta.rosetta.core.pack.task import TaskFactory\n",
"tf = TaskFactory()\n",
"packer_task = tf.create_packer_task(pose)\n",
"print(packer_task)"
]
},
{
"cell_type": "markdown",
"id": "intellectual-camping",
"metadata": {},
"source": [
"从上述结果可见，默认生成的Packer_Task包含三种数据:\n",
"- 残基位点编号信息\n",
"- 每个位点上，Rotamer的3种基本状态\n",
"- 每个位点上，被允许氨基酸Rotamer类型"
]
},
{
"cell_type": "markdown",
"id": "gross-equity",
"metadata": {},
"source": [
"**并且默认的PackerTask是运行每个位点都包含20种氨基酸的Rotamer**"
]
},
{
"cell_type": "markdown",
"id": "compressed-middle",
"metadata": {},
"source": [
"### 二、什么是TaskOperations?\n",
"\n",
"TaskOperations直译的意思即为\"任务操作元件\", **TaskOperations被TaskFactory加载并创建PackerTask。**"
]
},
{
"cell_type": "markdown",
"id": "electric-stranger",
"metadata": {},
"source": [
"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。"
]
},
{
"cell_type": "markdown",
"id": "fatty-swiss",
"metadata": {},
"source": [
"<center><img src=\"./img/taskop_turnoff.png\" width = \"500\" height = \"200\" align=center /></center>\n",
"(图片来源: jadolfbr@gmail.com提供的ppt)"
]
},
{
"cell_type": "markdown",
"id": "oriental-saskatchewan",
"metadata": {},
"source": [
"小结: \n",
"* TaskOperations的三层自由度级别: Design/Repack/No_repack;\n",
"* 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;\n",
"* 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。"
]
},
{
"cell_type": "markdown",
"id": "separated-marble",
"metadata": {},
"source": [
"### 三、TaskOperations的分类"
]
},
{
"cell_type": "markdown",
"id": "suffering-adobe",
"metadata": {},
"source": [
"TaskOperation从构建逻辑上来分类共计有两种类型:\n",
"\n",
"* Residue Level TaskOperations: 根据Selector设定选择范围内位点的Rotamer自由度(手动挡);\n",
"* Specialized Operations: 根据预设好逻辑，对位点进行全局Rotamer操作(自动挡);"
]
},
{
"cell_type": "markdown",
"id": "periodic-transition",
"metadata": {},
"source": [
"#### 3.1 Residue Level TaskOperations的使用示例"
]
},
{
"cell_type": "markdown",
"id": "saved-roberts",
"metadata": {},
"source": [
"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**。\n",
"\n",
"**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。**"
]
},
{
"cell_type": "markdown",
"id": "described-baptist",
"metadata": {},
"source": [
"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："
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "fluid-teaching",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"#Packer_Task\n",
"\n",
"Threads to request: ALL AVAILABLE\n",
"\n",
"resid\tpack?\tdesign?\tallowed_aas\n",
"1\tTRUE\tFALSE\tASP:NtermProteinFull\n",
"2\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"3\tTRUE\tFALSE\tLEU\n",
"4\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"5\tTRUE\tFALSE\tLYS\n",
"6\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"7\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"8\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"9\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"10\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"11\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"12\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"13\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"14\tTRUE\tTRUE\tALA: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\n",
"\n"
]
}
],
"source": [
"from pyrosetta.rosetta.core.pack.task.operation import RestrictToRepackingRLT, OperateOnResidueSubset\n",
"from pyrosetta.rosetta.core.select.residue_selector import ResidueIndexSelector\n",
"# 选择氨基酸范围\n",
"select_pos3 = ResidueIndexSelector('1,3,5')\n",
"\n",
"# 使用OperateOnResidueSubset生成TaskOperations\n",
"packing_taskop = OperateOnResidueSubset(RestrictToRepackingRLT(), select_pos3, False)\n",
"\n",
"# 将TaskOperations加载至TaskFactory中\n",
"pack_tf = TaskFactory()\n",
"pack_tf.push_back(packing_taskop)\n",
"\n",
"# 生成PackerTask\n",
"packer_task = pack_tf.create_task_and_apply_taskoperations(pose)\n",
"print(packer_task)"
]
},
{
"cell_type": "markdown",
"id": "mental-endorsement",
"metadata": {},
"source": [
"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。"
]
},
{
"cell_type": "markdown",
"id": "approximate-level",
"metadata": {},
"source": [
"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:\n",
"- RestrictToRepackingRLT: 将Rotamer自由度设置为repacking\n",
"- PreventRepackingRLT: 将Rotamer自由度设置为no_repack\n",
"- 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\n",
"- RestrictAbsentCanonicalAASRLT: 将Rotamer自由度限定在给定的氨基酸类型列表。\n",
"- 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\n",
"- 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)。\n",
"- 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。 \n",
"\n",
"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。"
]
},
{
"cell_type": "markdown",
"id": "given-hobby",
"metadata": {},
"source": [
"#### 思考\n",
"如果将OperateOnResidueSubset中的False转变为True，PackerTask会发生什么变化？"
]
},
{
"cell_type": "markdown",
"id": "taken-rolling",
"metadata": {},
"source": [
"#### 3.2 Specialized Operations的使用示例"
]
},
{
"cell_type": "markdown",
"id": "identical-history",
"metadata": {},
"source": [
"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。"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "lined-prayer",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"#Packer_Task\n",
"\n",
"Threads to request: ALL AVAILABLE\n",
"\n",
"resid\tpack?\tdesign?\tallowed_aas\n",
"1\tTRUE\tFALSE\tASP:NtermProteinFull\n",
"2\tTRUE\tFALSE\tGLU\n",
"3\tTRUE\tFALSE\tLEU\n",
"4\tTRUE\tFALSE\tGLN\n",
"5\tTRUE\tFALSE\tLYS\n",
"6\tTRUE\tFALSE\tTRP\n",
"7\tTRUE\tFALSE\tVAL\n",
"8\tTRUE\tFALSE\tGLU\n",
"9\tTRUE\tFALSE\tGLN\n",
"10\tTRUE\tFALSE\tALA\n",
"11\tTRUE\tFALSE\tGLU\n",
"12\tTRUE\tFALSE\tARG\n",
"13\tTRUE\tFALSE\tASN\n",
"14\tTRUE\tFALSE\tGLY:CtermProteinFull\n",
"\n"
]
}
],
"source": [
"from pyrosetta.rosetta.core.pack.task.operation import RestrictToRepacking\n",
"\n",
"# 将TaskOperations加载至TaskFactory中\n",
"pack_tf = TaskFactory()\n",
"pack_tf.push_back(RestrictToRepacking())\n",
"\n",
"# 生成PackerTask\n",
"packer_task = pack_tf.create_task_and_apply_taskoperations(pose)\n",
"print(packer_task)"
]
},
{
"cell_type": "markdown",
"id": "funny-nylon",
"metadata": {},
"source": [
"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。"
]
},
{
"cell_type": "markdown",
"id": "convenient-virginia",
"metadata": {
"tags": []
},
"source": [
"### 四、Pack Rotamer相关Mover"
]
},
{
"cell_type": "markdown",
"id": "recovered-survivor",
"metadata": {},
"source": [
"#### 4.1 PackRotamersMover"
]
},
{
"cell_type": "markdown",
"id": "grateful-patio",
"metadata": {},
"source": [
"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。"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "adjusted-chemical",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[0mcore.scoring.etable: {0} \u001b[0mStarting energy table calculation\n",
"\u001b[0mcore.scoring.etable: {0} \u001b[0msmooth_etable: changing atr/rep split to bottom of energy well\n",
"\u001b[0mcore.scoring.etable: {0} \u001b[0msmooth_etable: spline smoothing lj etables (maxdis = 6)\n",
"\u001b[0mcore.scoring.etable: {0} \u001b[0msmooth_etable: spline smoothing solvation etables (max_dis = 6)\n",
"\u001b[0mcore.scoring.etable: {0} \u001b[0mFinished calculating energy tables.\n",
"\u001b[0mbasic.io.database: {0} \u001b[0mDatabase file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\n",
"\u001b[0mbasic.io.database: {0} \u001b[0mDatabase file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\n",
"\u001b[0mbasic.io.database: {0} \u001b[0mDatabase file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\n",
"\u001b[0mbasic.io.database: {0} \u001b[0mDatabase file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\n",
"\u001b[0mbasic.io.database: {0} \u001b[0mDatabase file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\n",
"\u001b[0mbasic.io.database: {0} \u001b[0mDatabase file opened: scoring/score_functions/rama/fd/all.ramaProb\n",
"\u001b[0mbasic.io.database: {0} \u001b[0mDatabase file opened: scoring/score_functions/rama/fd/prepro.ramaProb\n",
"\u001b[0mbasic.io.database: {0} \u001b[0mDatabase file opened: scoring/score_functions/omega/omega_ppdep.all.txt\n",
"\u001b[0mbasic.io.database: {0} \u001b[0mDatabase file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\n",
"\u001b[0mbasic.io.database: {0} \u001b[0mDatabase file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\n",
"\u001b[0mbasic.io.database: {0} \u001b[0mDatabase file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\n",
"\u001b[0mbasic.io.database: {0} \u001b[0mDatabase file opened: scoring/score_functions/P_AA_pp/P_AA\n",
"\u001b[0mbasic.io.database: {0} \u001b[0mDatabase file opened: scoring/score_functions/P_AA_pp/P_AA_n\n",
"\u001b[0mcore.scoring.P_AA: {0} \u001b[0mshapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\n",
"\u001b[0mbasic.io.database: {0} \u001b[0mDatabase file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\n",
"\u001b[0mcore.import_pose.import_pose: {0} \u001b[0mFile './data/helix.pdb' automatically determined to be of type PDB\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0m\u001b[1m[ WARNING ]\u001b[0m missing heavyatom: OXT on residue GLY:CtermProteinFull 14\n",
"\u001b[0mbasic.io.database: {0} \u001b[0mDatabase file opened: scoring/score_functions/elec_cp_reps.dat\n",
"\u001b[0mcore.scoring.elec.util: {0} \u001b[0mRead 40 countpair representative atoms\n",
"\u001b[0mcore.pack.dunbrack.RotamerLibrary: {0} \u001b[0mshapovalov_lib_fixes_enable option is true.\n",
"\u001b[0mcore.pack.dunbrack.RotamerLibrary: {0} \u001b[0mshapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\n",
"\u001b[0mcore.pack.dunbrack.RotamerLibrary: {0} \u001b[0mBinary rotamer library selected: /opt/miniconda3/lib/python3.7/site-packages/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\n",
"\u001b[0mcore.pack.dunbrack.RotamerLibrary: {0} \u001b[0mUsing Dunbrack library binary file '/opt/miniconda3/lib/python3.7/site-packages/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\n",
"\u001b[0mcore.pack.dunbrack.RotamerLibrary: {0} \u001b[0mDunbrack 2010 library took 0.182942 seconds to load from binary\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 182 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating DensePDInteractionGraph\n",
"\u001b[0mbasic.thread_manager.RosettaThreadManager: {?} \u001b[0mCreating a thread pool of 1 threads.\n",
"\u001b[0mbasic.thread_manager.RosettaThreadPool: {?} \u001b[0mLaunched 0 new threads.\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n"
]
},
{
"data": {
"text/plain": [
"True"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"from pyrosetta.rosetta.protocols.minimization_packing import PackRotamersMover\n",
"from pyrosetta import create_score_function\n",
"pack_mover = PackRotamersMover()\n",
"ref2015 = create_score_function('ref2015')\n",
"pose = pose_from_pdb('./data/helix.pdb')\n",
"\n",
"# 不需要导入PackTask，只需要输入TaskFactory即可。\n",
"pack_mover.task_factory(pack_tf)\n",
"pack_mover.score_function(ref2015)\n",
"\n",
"# 执行repacking\n",
"pack_mover.apply(pose)\n",
"pose.dump_pdb('./data/repacked.pdb')"
]
},
{
"cell_type": "markdown",
"id": "operational-ridge",
"metadata": {},
"source": [
"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。\n",
"<center><img src=\"./img/repacking_conf.png\" width = \"600\" height = \"200\" align=center /></center>\n",
"(图片来源: 晶泰科技团队)"
]
},
{
"cell_type": "markdown",
"id": "private-fetish",
"metadata": {},
"source": [
"#### 4.2 FastRelax"
]
},
{
"cell_type": "markdown",
"id": "classical-andorra",
"metadata": {},
"source": [
"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。"
]
},
{
"cell_type": "markdown",
"id": "brutal-absolute",
"metadata": {},
"source": [
"一张图看懂FastRelax在做什么:"
]
},
{
"cell_type": "markdown",
"id": "marked-prize",
"metadata": {},
"source": [
"<center><img src=\"./img/FastRelax.jpg\" width = \"600\" height = \"200\" align=center /></center>\n",
"(图片来源: 晶泰科技团队)"
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "invalid-sweet",
"metadata": {
"scrolled": true,
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[0mprotocols.relax.RelaxScriptManager: {0} \u001b[0mReading relax scripts list from database.\n",
"\u001b[0mcore.scoring.ScoreFunctionFactory: {0} \u001b[0mSCOREFUNCTION: \u001b[32mref2015\u001b[0m\n",
"\u001b[0mprotocols.relax.RelaxScriptManager: {0} \u001b[0mLooking for MonomerRelax2019.txt\n",
"\u001b[0mprotocols.relax.RelaxScriptManager: {0} \u001b[0m================== Reading script file: /opt/miniconda3/lib/python3.7/site-packages/pyrosetta/database/sampling/relax_scripts/MonomerRelax2019.txt ==================\n",
"\u001b[0mprotocols.relax.RelaxScriptManager: {0} \u001b[0mrepeat %%nrepeats%%\n",
"\u001b[0mprotocols.relax.RelaxScriptManager: {0} \u001b[0mcoord_cst_weight 1.0\n",
"\u001b[0mprotocols.relax.RelaxScriptManager: {0} \u001b[0mscale:fa_rep 0.040\n",
"\u001b[0mprotocols.relax.RelaxScriptManager: {0} \u001b[0mrepack\n",
"\u001b[0mprotocols.relax.RelaxScriptManager: {0} \u001b[0mscale:fa_rep 0.051\n",
"\u001b[0mprotocols.relax.RelaxScriptManager: {0} \u001b[0mmin 0.01\n",
"\u001b[0mprotocols.relax.RelaxScriptManager: {0} \u001b[0mcoord_cst_weight 0.5\n",
"\u001b[0mprotocols.relax.RelaxScriptManager: {0} \u001b[0mscale:fa_rep 0.265\n",
"\u001b[0mprotocols.relax.RelaxScriptManager: {0} \u001b[0mrepack\n",
"\u001b[0mprotocols.relax.RelaxScriptManager: {0} \u001b[0mscale:fa_rep 0.280\n",
"\u001b[0mprotocols.relax.RelaxScriptManager: {0} \u001b[0mmin 0.01\n",
"\u001b[0mprotocols.relax.RelaxScriptManager: {0} \u001b[0mcoord_cst_weight 0.0\n",
"\u001b[0mprotocols.relax.RelaxScriptManager: {0} \u001b[0mscale:fa_rep 0.559\n",
"\u001b[0mprotocols.relax.RelaxScriptManager: {0} \u001b[0mrepack\n",
"\u001b[0mprotocols.relax.RelaxScriptManager: {0} \u001b[0mscale:fa_rep 0.581\n",
"\u001b[0mprotocols.relax.RelaxScriptManager: {0} \u001b[0mmin 0.01\n",
"\u001b[0mprotocols.relax.RelaxScriptManager: {0} \u001b[0mcoord_cst_weight 0.0\n",
"\u001b[0mprotocols.relax.RelaxScriptManager: {0} \u001b[0mscale:fa_rep 1\n",
"\u001b[0mprotocols.relax.RelaxScriptManager: {0} \u001b[0mrepack\n",
"\u001b[0mprotocols.relax.RelaxScriptManager: {0} \u001b[0mmin 0.00001\n",
"\u001b[0mprotocols.relax.RelaxScriptManager: {0} \u001b[0maccept_to_best\n",
"\u001b[0mprotocols.relax.RelaxScriptManager: {0} \u001b[0mendrepeat\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repeat -16.7505 0 0 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -16.7505 0 0 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -22.4175 0 0 0.022\n",
"\u001b[0mcore.pack.task: {0} \u001b[0mPacker task: initialize from command line()\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 201 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating DensePDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -24.6338 0 0 0.022\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -24.4608 0 0 0.02805\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -24.4789 0.000592829 0.000592829 0.02805\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -24.4789 0.000592829 0.000592829 0.02805\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -21.09 0.000592829 0.000592829 0.14575\n",
"\u001b[0mcore.pack.task: {0} \u001b[0mPacker task: initialize from command line()\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 194 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating DensePDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -21.3231 0.000592829 0.000592829 0.14575\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -21.1753 0.000592829 0.000592829 0.154\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -21.1948 0.000882851 0.000882851 0.154\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -21.1948 0.000882851 0.000882851 0.154\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -18.4693 0.000882851 0.000882851 0.30745\n",
"\u001b[0mcore.pack.task: {0} \u001b[0mPacker task: initialize from command line()\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 194 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating DensePDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -19.3676 0.000882851 0.000882851 0.30745\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -19.2377 0.000882851 0.000882851 0.31955\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -19.2466 0.00116297 0.00116297 0.31955\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -19.2466 0.00116297 0.00116297 0.31955\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -16.7738 0.00116297 0.00116297 0.55\n",
"\u001b[0mcore.pack.task: {0} \u001b[0mPacker task: initialize from command line()\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 194 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating DensePDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -16.2946 0.00116297 0.00116297 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -20.9544 0.271541 0.271541 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mMRP: 0 -20.9544 -20.9544 0.271541 0.271541\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: accept_to_best -20.9544 0.271541 0.271541 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: endrepeat -20.9544 0.271541 0.271541 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -20.9544 0.271541 0.271541 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -25.4018 0.271541 0.271541 0.022\n",
"\u001b[0mcore.pack.task: {0} \u001b[0mPacker task: initialize from command line()\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 207 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating DensePDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -26.771 0.271541 0.271541 0.022\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -26.6961 0.271541 0.271541 0.02805\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -26.7002 0.27138 0.27138 0.02805\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -26.7002 0.27138 0.27138 0.02805\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -25.2457 0.27138 0.27138 0.14575\n",
"\u001b[0mcore.pack.task: {0} \u001b[0mPacker task: initialize from command line()\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 200 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating DensePDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -25.2457 0.27138 0.27138 0.14575\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -25.1438 0.27138 0.27138 0.154\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -25.1559 0.270886 0.270886 0.154\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -25.1559 0.270886 0.270886 0.154\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -23.2676 0.270886 0.270886 0.30745\n",
"\u001b[0mcore.pack.task: {0} \u001b[0mPacker task: initialize from command line()\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 196 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating DensePDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -23.2676 0.270886 0.270886 0.30745\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -23.1187 0.270886 0.270886 0.31955\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -23.1555 0.269967 0.269967 0.31955\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -23.1555 0.269967 0.269967 0.31955\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -20.3431 0.269967 0.269967 0.55\n",
"\u001b[0mcore.pack.task: {0} \u001b[0mPacker task: initialize from command line()\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 195 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating DensePDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -20.3651 0.269967 0.269967 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -22.809 0.263703 0.263703 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mMRP: 1 -22.809 -22.809 0.263703 0.263703\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: accept_to_best -22.809 0.263703 0.263703 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: endrepeat -22.809 0.263703 0.263703 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -22.809 0.263703 0.263703 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -27.292 0.263703 0.263703 0.022\n",
"\u001b[0mcore.pack.task: {0} \u001b[0mPacker task: initialize from command line()\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 210 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating DensePDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -27.4217 0.263703 0.263703 0.022\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -27.3649 0.263703 0.263703 0.02805\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -27.3682 0.263861 0.263861 0.02805\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -27.3682 0.263861 0.263861 0.02805\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -26.2615 0.263861 0.263861 0.14575\n",
"\u001b[0mcore.pack.task: {0} \u001b[0mPacker task: initialize from command line()\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 205 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating DensePDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -26.2615 0.263861 0.263861 0.14575\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -26.1839 0.263861 0.263861 0.154\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -26.1858 0.263953 0.263953 0.154\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -26.1858 0.263953 0.263953 0.154\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -24.7424 0.263953 0.263953 0.30745\n",
"\u001b[0mcore.pack.task: {0} \u001b[0mPacker task: initialize from command line()\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 201 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating DensePDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -24.7524 0.263953 0.263953 0.30745\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -24.6407 0.263953 0.263953 0.31955\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -24.6416 0.263979 0.263979 0.31955\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -24.6416 0.263979 0.263979 0.31955\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -22.513 0.263979 0.263979 0.55\n",
"\u001b[0mcore.pack.task: {0} \u001b[0mPacker task: initialize from command line()\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 200 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating DensePDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -22.513 0.263979 0.263979 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -22.8052 0.264081 0.264081 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mMRP: 2 -22.8052 -22.809 0.263703 0.263703\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: accept_to_best -22.8052 0.264081 0.264081 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: endrepeat -22.8052 0.264081 0.264081 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -22.8052 0.264081 0.264081 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -27.2738 0.264081 0.264081 0.022\n",
"\u001b[0mcore.pack.task: {0} \u001b[0mPacker task: initialize from command line()\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 210 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating DensePDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -27.3953 0.264081 0.264081 0.022\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -27.3397 0.264081 0.264081 0.02805\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -27.343 0.264247 0.264247 0.02805\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -27.343 0.264247 0.264247 0.02805\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -26.2609 0.264247 0.264247 0.14575\n",
"\u001b[0mcore.pack.task: {0} \u001b[0mPacker task: initialize from command line()\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 205 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating DensePDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -26.2608 0.264247 0.264247 0.14575\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -26.185 0.264247 0.264247 0.154\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -26.1868 0.264353 0.264353 0.154\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -26.1868 0.264353 0.264353 0.154\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -24.7752 0.264353 0.264353 0.30745\n",
"\u001b[0mcore.pack.task: {0} \u001b[0mPacker task: initialize from command line()\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 201 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating DensePDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -24.7752 0.264353 0.264353 0.30745\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -24.6639 0.264353 0.264353 0.31955\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -24.6648 0.264378 0.264378 0.31955\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -24.6648 0.264378 0.264378 0.31955\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -22.5448 0.264378 0.264378 0.55\n",
"\u001b[0mcore.pack.task: {0} \u001b[0mPacker task: initialize from command line()\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 200 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating DensePDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -22.571 0.264378 0.264378 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -22.8064 0.262966 0.262966 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mMRP: 3 -22.8064 -22.809 0.263703 0.263703\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: accept_to_best -22.8064 0.262966 0.262966 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: endrepeat -22.8064 0.262966 0.262966 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -22.8064 0.262966 0.262966 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -27.2757 0.262966 0.262966 0.022\n",
"\u001b[0mcore.pack.task: {0} \u001b[0mPacker task: initialize from command line()\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 210 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating DensePDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -27.4014 0.262966 0.262966 0.022\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -27.3455 0.262966 0.262966 0.02805\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -27.3489 0.263132 0.263132 0.02805\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -27.3489 0.263132 0.263132 0.02805\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -26.2614 0.263132 0.263132 0.14575\n",
"\u001b[0mcore.pack.task: {0} \u001b[0mPacker task: initialize from command line()\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 205 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating DensePDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -26.2614 0.263132 0.263132 0.14575\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -26.1851 0.263132 0.263132 0.154\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -26.1869 0.263236 0.263236 0.154\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -26.1869 0.263236 0.263236 0.154\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -24.7684 0.263236 0.263236 0.30745\n",
"\u001b[0mcore.pack.task: {0} \u001b[0mPacker task: initialize from command line()\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 201 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating DensePDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -24.7684 0.263236 0.263236 0.30745\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -24.6566 0.263236 0.263236 0.31955\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -24.6576 0.263258 0.263258 0.31955\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -24.6576 0.263258 0.263258 0.31955\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -22.5273 0.263258 0.263258 0.55\n",
"\u001b[0mcore.pack.task: {0} \u001b[0mPacker task: initialize from command line()\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 200 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating DensePDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -22.5578 0.263258 0.263258 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -22.806 0.263123 0.263123 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mMRP: 4 -22.806 -22.809 0.263703 0.263703\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: accept_to_best -22.806 0.263123 0.263123 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: endrepeat -22.806 0.263123 0.263123 0.55\n",
"\u001b[0mprotocols::checkpoint: {0} \u001b[0mDeleting checkpoints of FastRelax\n"
]
},
{
"data": {
"text/plain": [
"True"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# FastRelax\n",
"from pyrosetta.rosetta.protocols.relax import FastRelax\n",
"fastrelax = FastRelax()\n",
"fastrelax.set_scorefxn(ref2015)\n",
"fastrelax.set_default_movemap() #使用默认的Movemap()\n",
"fastrelax.apply(pose)\n",
"pose.dump_pdb('./data/fastrelaxed.pdb')"
]
},
{
"cell_type": "markdown",
"id": "consecutive-optics",
"metadata": {},
"source": [
"<center><img src=\"./img/fastrelaxed.png\" width = \"600\" height = \"200\" align=center /></center>\n",
"(图片来源: 晶泰科技团队)"
]
},
{
"cell_type": "markdown",
"id": "champion-harvey",
"metadata": {},
"source": [
"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。"
]
},
{
"cell_type": "markdown",
"id": "working-provision",
"metadata": {},
"source": [
"#### 4.3 FastDesign"
]
},
{
"cell_type": "markdown",
"id": "beneficial-content",
"metadata": {},
"source": [
"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。"
]
},
{
"cell_type": "code",
"execution_count": 7,
"id": "smart-roads",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"#Packer_Task\n",
"\n",
"Threads to request: ALL AVAILABLE\n",
"\n",
"resid\tpack?\tdesign?\tallowed_aas\n",
"1\tTRUE\tFALSE\tASP:NtermProteinFull\n",
"2\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"3\tTRUE\tFALSE\tLEU\n",
"4\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"5\tTRUE\tFALSE\tLYS\n",
"6\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"7\tTRUE\tFALSE\tVAL\n",
"8\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"9\tTRUE\tFALSE\tGLN\n",
"10\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"11\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"12\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"13\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"14\tTRUE\tTRUE\tALA: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\n",
"\n"
]
}
],
"source": [
"# 设置FastDesign的蓝图。\n",
"from pyrosetta.rosetta.protocols.denovo_design.movers import FastDesign\n",
"\n",
"# 将TaskOperations加载至TaskFactory中\n",
"# 选择氨基酸范围\n",
"no_design_pos = ResidueIndexSelector('1,3,5,7,9')\n",
"\n",
"# 使用OperateOnResidueSubset生成TaskOperations\n",
"design_taskop = OperateOnResidueSubset(RestrictToRepackingRLT(), no_design_pos, False)\n",
"\n",
"design_tf = TaskFactory()\n",
"design_tf.push_back(design_taskop)\n",
"\n",
"# 生成PackerTask\n",
"design_task = design_tf.create_task_and_apply_taskoperations(pose)\n",
"print(design_task)"
]
},
{
"cell_type": "code",
"execution_count": 8,
"id": "computational-medicaid",
"metadata": {
"scrolled": true,
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[0mcore.scoring.ScoreFunctionFactory: {0} \u001b[0mSCOREFUNCTION: \u001b[32mref2015\u001b[0m\n",
"\u001b[0mprotocols.denovo_design.movers.FastDesign: {0} \u001b[0m#Packer_Task\n",
"\u001b[0mprotocols.denovo_design.movers.FastDesign: {0} \u001b[0m\n",
"\u001b[0mprotocols.denovo_design.movers.FastDesign: {0} \u001b[0mThreads to request: ALL AVAILABLE\n",
"\u001b[0mprotocols.denovo_design.movers.FastDesign: {0} \u001b[0m\n",
"\u001b[0mprotocols.denovo_design.movers.FastDesign: {0} \u001b[0mresid\tpack?\tdesign?\tallowed_aas\n",
"\u001b[0mprotocols.denovo_design.movers.FastDesign: {0} \u001b[0m1\tTRUE\tFALSE\tASP:NtermProteinFull\n",
"\u001b[0mprotocols.denovo_design.movers.FastDesign: {0} \u001b[0m2\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"\u001b[0mprotocols.denovo_design.movers.FastDesign: {0} \u001b[0m3\tTRUE\tFALSE\tLEU\n",
"\u001b[0mprotocols.denovo_design.movers.FastDesign: {0} \u001b[0m4\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"\u001b[0mprotocols.denovo_design.movers.FastDesign: {0} \u001b[0m5\tTRUE\tFALSE\tLYS\n",
"\u001b[0mprotocols.denovo_design.movers.FastDesign: {0} \u001b[0m6\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"\u001b[0mprotocols.denovo_design.movers.FastDesign: {0} \u001b[0m7\tTRUE\tFALSE\tVAL\n",
"\u001b[0mprotocols.denovo_design.movers.FastDesign: {0} \u001b[0m8\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"\u001b[0mprotocols.denovo_design.movers.FastDesign: {0} \u001b[0m9\tTRUE\tFALSE\tGLN\n",
"\u001b[0mprotocols.denovo_design.movers.FastDesign: {0} \u001b[0m10\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"\u001b[0mprotocols.denovo_design.movers.FastDesign: {0} \u001b[0m11\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"\u001b[0mprotocols.denovo_design.movers.FastDesign: {0} \u001b[0m12\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"\u001b[0mprotocols.denovo_design.movers.FastDesign: {0} \u001b[0m13\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n",
"\u001b[0mprotocols.denovo_design.movers.FastDesign: {0} \u001b[0m14\tTRUE\tTRUE\tALA: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\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repeat -22.809 0 0 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -22.809 0 0 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -27.292 0 0 0.022\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 2580 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating PDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -33.9419 0 0 0.022\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -33.5386 0 0 0.02805\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -33.5519 0.000789733 0.000789733 0.02805\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -33.5519 0.000789733 0.000789733 0.02805\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -25.7005 0.000789733 0.000789733 0.14575\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 2496 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating PDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -29.3306 0.000789733 0.000789733 0.14575\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -29.1736 0.000789733 0.000789733 0.154\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -29.1777 0.00104836 0.00104836 0.154\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -29.1777 0.00104836 0.00104836 0.154\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -26.2553 0.00104836 0.00104836 0.30745\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 2430 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating PDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -26.4018 0.00104836 0.00104836 0.30745\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -26.1935 0.00104836 0.00104836 0.31955\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -26.2022 0.00144815 0.00144815 0.31955\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -26.2022 0.00144815 0.00144815 0.31955\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -22.2381 0.00144815 0.00144815 0.55\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 2379 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating PDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -24.1411 0.00144815 0.00144815 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -28.1179 0.140127 0.140127 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mMRP: 0 -28.1179 -28.1179 0.140127 0.140127\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: accept_to_best -28.1179 0.140127 0.140127 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: endrepeat -28.1179 0.140127 0.140127 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -28.1179 0.140127 0.140127 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -33.0957 0.140127 0.140127 0.022\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 2531 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating PDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -35.4398 0.140127 0.140127 0.022\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -35.0094 0.140127 0.140127 0.02805\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -35.0213 0.139614 0.139614 0.02805\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -35.0213 0.139614 0.139614 0.02805\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -26.7146 0.139614 0.139614 0.14575\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 2429 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating PDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -31.3182 0.139614 0.139614 0.14575\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -31.1772 0.139614 0.139614 0.154\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -31.1813 0.139846 0.139846 0.154\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -31.1813 0.139846 0.139846 0.154\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -28.5587 0.139846 0.139846 0.30745\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 2355 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating PDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -28.7355 0.139846 0.139846 0.30745\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -28.6147 0.139846 0.139846 0.31955\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -28.6157 0.139874 0.139874 0.31955\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -28.6157 0.139874 0.139874 0.31955\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -26.3155 0.139874 0.139874 0.55\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 2283 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating PDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -26.458 0.139874 0.139874 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -26.9144 0.0973955 0.0973955 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mMRP: 1 -26.9144 -28.1179 0.140127 0.140127\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: accept_to_best -26.9144 0.0973955 0.0973955 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: endrepeat -26.9144 0.0973955 0.0973955 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -26.9144 0.0973955 0.0973955 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -31.3626 0.0973955 0.0973955 0.022\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 2534 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating PDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -35.0507 0.0973955 0.0973955 0.022\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -34.7919 0.0973955 0.0973955 0.02805\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -34.8058 0.0977755 0.0977755 0.02805\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -34.8058 0.0977755 0.0977755 0.02805\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -29.7448 0.0977755 0.0977755 0.14575\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 2427 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating PDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -31.4077 0.0977755 0.0977755 0.14575\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -31.2744 0.0977755 0.0977755 0.154\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -31.2787 0.0978921 0.0978921 0.154\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -31.2787 0.0978921 0.0978921 0.154\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -28.8004 0.0978921 0.0978921 0.30745\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 2359 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating PDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -28.9509 0.0978921 0.0978921 0.30745\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -28.788 0.0978921 0.0978921 0.31955\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -28.7896 0.0979167 0.0979167 0.31955\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -28.7896 0.0979167 0.0979167 0.31955\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -25.6866 0.0979167 0.0979167 0.55\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 2280 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating PDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -26.6963 0.0979167 0.0979167 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -26.913 0.0955109 0.0955109 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mMRP: 2 -26.913 -28.1179 0.140127 0.140127\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: accept_to_best -26.913 0.0955109 0.0955109 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: endrepeat -26.913 0.0955109 0.0955109 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -26.913 0.0955109 0.0955109 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -31.3611 0.0955109 0.0955109 0.022\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 2532 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating PDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -35.0264 0.0955109 0.0955109 0.022\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -34.769 0.0955109 0.0955109 0.02805\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -34.7829 0.0958909 0.0958909 0.02805\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -34.7829 0.0958909 0.0958909 0.02805\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -29.7486 0.0958909 0.0958909 0.14575\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 2425 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating PDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -31.388 0.0958909 0.0958909 0.14575\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -31.2539 0.0958909 0.0958909 0.154\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -31.2583 0.0960147 0.0960147 0.154\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -31.2583 0.0960147 0.0960147 0.154\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -28.7637 0.0960147 0.0960147 0.30745\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 2357 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating PDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -28.9487 0.0960147 0.0960147 0.30745\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -28.7858 0.0960147 0.0960147 0.31955\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -28.7875 0.0960447 0.0960447 0.31955\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -28.7875 0.0960447 0.0960447 0.31955\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -25.6852 0.0960447 0.0960447 0.55\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 2280 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating PDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -26.6957 0.0960447 0.0960447 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -26.9132 0.095512 0.095512 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mMRP: 3 -26.9132 -28.1179 0.140127 0.140127\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: accept_to_best -26.9132 0.095512 0.095512 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: endrepeat -26.9132 0.095512 0.095512 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -26.9132 0.095512 0.095512 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -31.357 0.095512 0.095512 0.022\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 2532 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating PDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -35.0274 0.095512 0.095512 0.022\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -34.7696 0.095512 0.095512 0.02805\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -34.7835 0.0958912 0.0958912 0.02805\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -34.7835 0.0958912 0.0958912 0.02805\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -29.7421 0.0958912 0.0958912 0.14575\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 2425 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating PDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -31.3872 0.0958912 0.0958912 0.14575\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -31.2531 0.0958912 0.0958912 0.154\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -31.2575 0.0960121 0.0960121 0.154\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -31.2575 0.0960121 0.0960121 0.154\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -28.7652 0.0960121 0.0960121 0.30745\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 2357 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating PDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -28.9502 0.0960121 0.0960121 0.30745\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -28.7875 0.0960121 0.0960121 0.31955\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -28.7892 0.0960411 0.0960411 0.31955\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: coord_cst_weight -28.7892 0.0960411 0.0960411 0.31955\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: scale:fa_rep -25.6913 0.0960411 0.0960411 0.55\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 2280 rotamers at 14 positions.\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mRequesting all available threads for interaction graph computation.\n",
"\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: {0} \u001b[0mInstantiating PDInteractionGraph\n",
"\u001b[0mcore.pack.rotamer_set.RotamerSets: {0} \u001b[0mCompleted interaction graph pre-calculation in 1 available threads (1 had been requested).\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: repack -27.2444 0.0960411 0.0960411 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: min -28.716 0.174474 0.174474 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mMRP: 4 -28.716 -28.716 0.174474 0.174474\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: accept_to_best -28.716 0.174474 0.174474 0.55\n",
"\u001b[0mprotocols.relax.FastRelax: {0} \u001b[0mCMD: endrepeat -28.716 0.174474 0.174474 0.55\n",
"\u001b[0mprotocols::checkpoint: {0} \u001b[0mDeleting checkpoints of FastRelax\n",
"\u001b[0mprotocols.denovo_design.movers.FastDesign: {0} \u001b[0m\n",
"------------------------------------------------------------\n",
" Scores Weight Raw Score Wghtd.Score\n",
"------------------------------------------------------------\n",
" fa_atr 1.000 -56.791 -56.791\n",
" fa_rep 0.550 8.173 4.495\n",
" fa_sol 1.000 61.636 61.636\n",
" fa_intra_rep 0.005 21.747 0.109\n",
" fa_intra_sol_xover4 1.000 2.734 2.734\n",
" lk_ball_wtd 1.000 -1.989 -1.989\n",
" fa_elec 1.000 -31.585 -31.585\n",
" pro_close 1.250 0.000 0.000\n",
" hbond_sr_bb 1.000 -9.781 -9.781\n",
" hbond_lr_bb 1.000 0.000 0.000\n",
" hbond_bb_sc 1.000 0.000 0.000\n",
" hbond_sc 1.000 -3.564 -3.564\n",
" dslf_fa13 1.250 0.000 0.000\n",
" omega 0.400 1.037 0.415\n",
" fa_dun 0.700 24.695 17.287\n",
" p_aa_pp 0.600 -2.897 -1.738\n",
" yhh_planarity 0.625 0.000 0.000\n",
" ref 1.000 -5.903 -5.903\n",
" rama_prepro 0.450 -8.982 -4.042\n",
"---------------------------------------------------\n",
" Total weighted score: -28.716\n"
]
},
{
"data": {
"text/plain": [
"True"
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# 初始化FastDesign:\n",
"fastdesign = FastDesign()\n",
"fastdesign.set_scorefxn(ref2015)\n",
"fastdesign.set_default_movemap() #使用默认的Movemap()\n",
"fastdesign.set_task_factory(design_tf)\n",
"fastdesign.apply(pose)\n",
"pose.dump_pdb('./data/fastdesign.pdb')"
]
},
{
"cell_type": "markdown",
"id": "swedish-violation",
"metadata": {},
"source": [
"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。\n",
"<center><img src=\"./img/fastdesign.png\" width = \"500\" height = \"200\" align=center /></center>\n",
"(图片来源: 晶泰科技团队)"
]
},
{
"cell_type": "markdown",
"id": "historic-payroll",
"metadata": {},
"source": [
"### 练习:\n",
"1. 【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。"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "norman-footwear",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.10"
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