{
"cells": [
{
"cell_type": "markdown",
"id": "mature-restriction",
"metadata": {},
"source": [
"## Resfile System"
]
},
{
"cell_type": "markdown",
"id": "monthly-september",
"metadata": {},
"source": [
"@Author: 吴炜坤\n",
"\n",
"@email：weikun.wu@xtalpi.com/weikunwu@163.com"
]
},
{
"cell_type": "markdown",
"id": "intelligent-associate",
"metadata": {},
"source": [
"Resfile是控制Packer的外部输入文件，用于告诉Rosetta Packer如何对结构中的每一个氨基酸侧链自由度进行定义。Resfile以文件的形式被ReadResfile函数读取并生成对应的TaskOperation。用户可以很方便地在外部进行快速的定义，而不需要写出复杂的selector+RLT的方式。但Resfile系统的缺点是每个文件的定义都需要人去处理，无法自动化完成任务。"
]
},
{
"cell_type": "code",
"execution_count": 1,
"id": "understanding-satin",
"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=-867162182 seed_offset=0 real_seed=-867162182 thread_index=0\n",
"\u001b[0mbasic.random.init_random_generator: {0} \u001b[0mRandomGenerator:init: Normal mode, seed=-867162182 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 0.668191 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\n",
"from pyrosetta import init, pose_from_pdb\n",
"from pyrosetta.rosetta.core.pack.task.operation import ReadResfile\n",
"from pyrosetta.rosetta.core.pack.task import TaskFactory\n",
"init()\n",
"pose = pose_from_pdb('./data/helix.pdb')"
]
},
{
"cell_type": "markdown",
"id": "crucial-scratch",
"metadata": {},
"source": [
"### 一、Resfile的基本格式"
]
},
{
"cell_type": "markdown",
"id": "attempted-consistency",
"metadata": {},
"source": [
"在Resfile中，我们使用的编号策略是: PDB Numbering, 并且大小写敏感。通常一个Resfile的格式包括两部分:HEADER & BODYs.\n",
"\n",
"每个部分的作用:\n",
"- HEADER: **控制全局**如何进行Rotamer搜索方式；\n",
"- BODY: 记录明确指定的**特定位置或范围**氨基酸Rotamer搜索方式；\n"
]
},
{
"cell_type": "markdown",
"id": "possible-novel",
"metadata": {},
"source": [
"Resfile实例:"
]
},
{
"cell_type": "markdown",
"id": "together-nutrition",
"metadata": {},
"source": [
"<center><img src=\"./img/Resfile_format.jpg\" width = \"600\" height = \"200\" align=center /></center>\n",
"(图片来源: 晶泰科技团队)"
]
},
{
"cell_type": "markdown",
"id": "sealed-badge",
"metadata": {},
"source": [
"### 二、HEADER的语法与编写"
]
},
{
"cell_type": "markdown",
"id": "artificial-skiing",
"metadata": {},
"source": [
"#### 2.1 全局自由度控制"
]
},
{
"cell_type": "markdown",
"id": "least-cleaner",
"metadata": {},
"source": [
"这部分语法实现的是除BODY部分中出现的氨基酸位点进行自由度控制，控制可以设置为Design/Repacking/No_repack三种基本状态。以下列举所有的语法:\n",
"- ALLAA ......... # 允许设计为20种氨基酸\n",
"- ALLAAxc ......... # 允许设计为**非半胱氨酸**以外的所有氨基酸\n",
"- POLAR ......... # 允许设计极性氨基酸(DEHKNQRST)\n",
"- APOLAR ......... # 允许设计非极性氨基酸(ACFGILMPVWY)\n",
"- NOTAA ......... # 不允许设计为特定的氨基酸列表。(列表连续编写无空格)\n",
"- PIKAA ......... # 只允许设计为特定的氨基酸列表。(列表连续编写无空格)\n",
"- NATAA ......... # Repack当前氨基酸类型，只允许构象变化。\n",
"- NATRO ......... # NoRepack不允许构象变化。\n",
"- PROPERTY ......... # 只允许设计为有以下性质的氨基酸"
]
},
{
"cell_type": "markdown",
"id": "major-finance",
"metadata": {},
"source": [
"PROPERTY一般常用可选:\n",
"- METAL: 金属离子\n",
"- POLAR: 极性氨基酸\n",
"- HYDROPHOBIC: 疏水氨基酸\n",
"- CHARGED: 带电氨基酸\n",
"- NEGATIVE_CHARGE: 带负电氨基酸\n",
"- POSITIVE_CHARGE: 带正电氨基酸\n",
"- AROMATIC: 芳香族氨基酸"
]
},
{
"cell_type": "markdown",
"id": "academic-gather",
"metadata": {},
"source": [
"编写一个NATRO相关的Resfile的demo:\n",
"```\n",
"NATRO\n",
"START\n",
"```"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "genetic-spank",
"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\tFALSE\tFALSE\t\n",
"2\tFALSE\tFALSE\t\n",
"3\tFALSE\tFALSE\t\n",
"4\tFALSE\tFALSE\t\n",
"5\tFALSE\tFALSE\t\n",
"6\tFALSE\tFALSE\t\n",
"7\tFALSE\tFALSE\t\n",
"8\tFALSE\tFALSE\t\n",
"9\tFALSE\tFALSE\t\n",
"10\tFALSE\tFALSE\t\n",
"11\tFALSE\tFALSE\t\n",
"12\tFALSE\tFALSE\t\n",
"13\tFALSE\tFALSE\t\n",
"14\tFALSE\tFALSE\t\n",
"\n"
]
}
],
"source": [
"# restrict to baestype list\n",
"resfile_type = ReadResfile('./data/NATRO.resfile')\n",
"\n",
"# 将TaskOperations加载至TaskFactory中\n",
"pack_tf = TaskFactory()\n",
"pack_tf.push_back(resfile_type)\n",
"\n",
"# 生成PackerTask\n",
"packer_task = pack_tf.create_task_and_apply_taskoperations(pose)\n",
"print(packer_task)"
]
},
{
"cell_type": "markdown",
"id": "considered-lounge",
"metadata": {},
"source": [
"#### 练习\n",
"尝试写更多的Resfile并读取到上述的代码中，比较不同语法之间的差异。"
]
},
{
"cell_type": "markdown",
"id": "exempt-dating",
"metadata": {},
"source": [
"#### 2.2 Rotamer采样丰度的设置:\n",
"\n",
"Rosetta Pack采样Rotamer时是离散的，默认只会采纳每个格点的中心富集的构象，我们可以通过Extra Rotamer相关控制手段来增加Rotamer的采样，默认扩充采样时，采集Rotamer时会额外考虑平均$\\chi$的+/-1个标准差的构象。这种Extra Rotamer相关控制仅对**包埋**的残基有效！\n",
"\n",
"只要在Resfile中HEADER中使用Extra Rotamer Commands字段即可，目前针对不同的氨基酸有四种编写方式:\n",
"\n",
"1. EX \\<chi-id> LEVEL \\<level-value> 语法\n",
"\n",
" - EX \\<chi-id> 代表指定对侧链中第几个$\\chi$角进行扩大采样, 如EX 1 EX 2 代表同时对$\\chi_{1}$角和$\\chi_{2}$角扩大采样\n",
" - LEVEL \\<level-value> 代表如何允许的$\\chi$角标准差范围，如果缺省这部分的参数默认为+/-1个标准差\n",
"\n",
"2. EX ARO \\<chi-id> LEVEL \\<level-value> 语法\n",
" - EX ARO \\<chi-id> 代表指定对侧链中第几个$\\chi$角进行扩大采样, **但范围仅限于芳香族氨基酸(FHWY)！**\n",
" - LEVEL \\<level-value> 代表如何允许的$\\chi$角标准差范围，如果缺省这部分的参数默认为+/-1个标准差\n",
"\n",
"3. EX_CUTOFF \\<number of neighbors> 语法\n",
" - Rosetta默认不会对处于蛋白表面的氨基酸进行额外Rotamer采集，除非用户显式地设置(EX_CUTOFF >=0等)，来改变“包埋”氨基酸的判断条件。默认为统计当前氨基酸10埃范围内残基数量，当数量大于设定的阈值时，认为是\"包埋\"的氨基酸，进行额外的Rotamer采样。因此通常EX_CUTOFF被显式地设置为0(默认值为18)，来考虑所有的氨基酸位点都做Rotamer。\n",
"\n",
"4. USE_INPUT_SC 语法\n",
" - 第一轮Packer时考虑初始输入的侧链Rotamer构象"
]
},
{
"cell_type": "markdown",
"id": "toxic-avatar",
"metadata": {},
"source": [
"LEVEL参数目前有7个级别:\n",
"- 0 ...... no extra chi angles\n",
"- 1 ...... sample at 1 standard deviation\n",
"- 2 ...... sample at 1/2 standard deviation\n",
"- 3 ...... sample at two full standard deviations\n",
"- 4 ...... sample at two 1/2 standard deviations\n",
"- 5 ...... sample at four 1/2 standard deviations\n",
"- 6 ...... sample at three 1/3 standard deviations\n",
"- 7 ...... sample at six 1/4 standard deviations"
]
},
{
"cell_type": "markdown",
"id": "sticky-retention",
"metadata": {},
"source": [
"以下举一个控制Rotamer丰度的Resfile例子:\n",
"```\n",
"NATRO\n",
"EX 1 EX 2\n",
"START\n",
"```"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "random-sucking",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"start\n",
"1 A NATRO EX ARO 1 EX ARO 2\n",
"2 A NATRO EX ARO 1 EX ARO 2\n",
"3 A NATRO EX ARO 1 EX ARO 2\n",
"4 A NATRO EX ARO 1 EX ARO 2\n",
"5 A NATRO EX ARO 1 EX ARO 2\n",
"6 A NATRO EX ARO 1 EX ARO 2\n",
"7 A NATRO EX ARO 1 EX ARO 2\n",
"8 A NATRO EX ARO 1 EX ARO 2\n",
"9 A NATRO EX ARO 1 EX ARO 2\n",
"10 A NATRO EX ARO 1 EX ARO 2\n",
"11 A NATRO EX ARO 1 EX ARO 2\n",
"12 A NATRO EX ARO 1 EX ARO 2\n",
"13 A NATRO EX ARO 1 EX ARO 2\n",
"14 A NATRO EX ARO 1 EX ARO 2\n",
"\n"
]
}
],
"source": [
"# restrict to baestype list\n",
"resfile_type = ReadResfile('./data/EX1EX2.resfile')\n",
"\n",
"# 将TaskOperations加载至TaskFactory中\n",
"pack_tf = TaskFactory()\n",
"pack_tf.push_back(resfile_type)\n",
"\n",
"# 生成PackerTask\n",
"packer_task = pack_tf.create_task_and_apply_taskoperations(pose)\n",
"\n",
"# 查看每个残基的Rotamer采样级别:\n",
"print(packer_task.task_string(pose))"
]
},
{
"cell_type": "markdown",
"id": "several-sunglasses",
"metadata": {},
"source": [
"可见所有位点的Rotamer都会额外采集$\\chi_{1}$和$\\chi_{2}$角。**（上述结果存在显示错误，我们并没有设置ARO，其实是没有设置ARO的。因此不影响实际的运行效果）**"
]
},
{
"cell_type": "markdown",
"id": "aboriginal-constitution",
"metadata": {},
"source": [
"除了全局控制，我们可以还可在HEADER中特定地给一些氨基酸设置额外Rotamer采集：\n",
"```\n",
"1. EX 1 EX 2\n",
"\n",
"2. EX ARO 2\n",
"\n",
"3. EX 1 LEVEL 7\n",
"\n",
"4. EX 1 EX ARO 1 LEVEL 4\n",
"```"
]
},
{
"cell_type": "markdown",
"id": "closed-actress",
"metadata": {},
"source": [
"#### 练习\n",
"思考上述语法的具体含义。"
]
},
{
"cell_type": "markdown",
"id": "defined-trainer",
"metadata": {},
"source": [
"### 三、BODY的语法与编写"
]
},
{
"cell_type": "markdown",
"id": "internal-blond",
"metadata": {},
"source": [
"BODY部分用于指明特定位点或范围的氨基酸Rotamer自由度。指定的形式一共有4种。\n",
"- 特定单个位点指定\n",
"- 指定位点范围\n",
"- 指定链范围\n",
"- 多重指定"
]
},
{
"cell_type": "markdown",
"id": "recorded-bottle",
"metadata": {},
"source": [
"#### 3.1 位点指定\n",
"第一列为氨基酸的PDB编号(允许有insert code)。第二列为PDB链编号，第三列为COMMAND项。\n",
"\n",
"基本语法: \n",
"```\n",
"<PDBNUM>[<ICODE>] <CHAIN> <COMMANDS>\n",
"```"
]
},
{
"cell_type": "markdown",
"id": "wired-shareware",
"metadata": {},
"source": [
"注: ICODE是指PDB中存在特殊插入编号字符时使用，如抗体等有特殊编号的系统，和PDBNUM连续编写如35A，35B等。正常的PDBNUM应该只有数字。"
]
},
{
"cell_type": "markdown",
"id": "reserved-miniature",
"metadata": {},
"source": [
"使用举例:\n",
"```\n",
"NATRO\n",
"EX 1 EX 2\n",
"START\n",
"\n",
"3 A ALLAA # 3号位允许设计为20种氨基酸\n",
"4 A APOLAR # 4号位只允许在非极性氨基酸范围\n",
"```"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "necessary-depression",
"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\tFALSE\tFALSE\t\n",
"2\tFALSE\tFALSE\t\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,PHE,GLY,ILE,LEU,MET,PRO,VAL,TRP,TYR\n",
"5\tFALSE\tFALSE\t\n",
"6\tFALSE\tFALSE\t\n",
"7\tFALSE\tFALSE\t\n",
"8\tFALSE\tFALSE\t\n",
"9\tFALSE\tFALSE\t\n",
"10\tFALSE\tFALSE\t\n",
"11\tFALSE\tFALSE\t\n",
"12\tFALSE\tFALSE\t\n",
"13\tFALSE\tFALSE\t\n",
"14\tFALSE\tFALSE\t\n",
"\n"
]
}
],
"source": [
"# restrict to baestype list\n",
"resfile_type = ReadResfile('./data/position_mut.resfile')\n",
"\n",
"# 将TaskOperations加载至TaskFactory中\n",
"pack_tf = TaskFactory()\n",
"pack_tf.push_back(resfile_type)\n",
"\n",
"# 生成PackerTask\n",
"packer_task = pack_tf.create_task_and_apply_taskoperations(pose)\n",
"print(packer_task)"
]
},
{
"cell_type": "markdown",
"id": "worth-mechanics",
"metadata": {
"tags": []
},
"source": [
"#### 3.2 位点范围进行指定\n",
"范围氨基酸指定格式:\n",
"```\n",
"<PDBNUM>[<ICODE>] - <PDBNUM>[<ICODE>] <CHAIN> <COMMANDS>\n",
"```"
]
},
{
"cell_type": "markdown",
"id": "expanded-section",
"metadata": {},
"source": [
"使用举例:\n",
"```\n",
"NATRO\n",
"EX 1 EX 2\n",
"START\n",
"\n",
"1 - 5 A APOLAR # A链1-5号位只允许在非极性氨基酸范围\n",
"```"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "induced-memorabilia",
"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,PHE:NtermProteinFull,GLY:NtermProteinFull,ILE:NtermProteinFull,LEU:NtermProteinFull,MET:NtermProteinFull,PRO:NtermProteinFull,VAL:NtermProteinFull,TRP:NtermProteinFull,TYR:NtermProteinFull\n",
"2\tTRUE\tTRUE\tALA,CYS,PHE,GLY,ILE,LEU,MET,PRO,VAL,TRP,TYR\n",
"3\tTRUE\tTRUE\tALA,CYS,PHE,GLY,ILE,LEU,MET,PRO,VAL,TRP,TYR\n",
"4\tTRUE\tTRUE\tALA,CYS,PHE,GLY,ILE,LEU,MET,PRO,VAL,TRP,TYR\n",
"5\tTRUE\tTRUE\tALA,CYS,PHE,GLY,ILE,LEU,MET,PRO,VAL,TRP,TYR\n",
"6\tFALSE\tFALSE\t\n",
"7\tFALSE\tFALSE\t\n",
"8\tFALSE\tFALSE\t\n",
"9\tFALSE\tFALSE\t\n",
"10\tFALSE\tFALSE\t\n",
"11\tFALSE\tFALSE\t\n",
"12\tFALSE\tFALSE\t\n",
"13\tFALSE\tFALSE\t\n",
"14\tFALSE\tFALSE\t\n",
"\n"
]
}
],
"source": [
"# restrict to baestype list\n",
"resfile_type = ReadResfile('./data/range_mut.resfile')\n",
"\n",
"# 将TaskOperations加载至TaskFactory中\n",
"pack_tf = TaskFactory()\n",
"pack_tf.push_back(resfile_type)\n",
"\n",
"# 生成PackerTask\n",
"packer_task = pack_tf.create_task_and_apply_taskoperations(pose)\n",
"print(packer_task)"
]
},
{
"cell_type": "markdown",
"id": "traditional-reconstruction",
"metadata": {},
"source": [
"#### 3.3 链为单位进行指定\n",
"链单位指定基本格式:\n",
"```\n",
"* <CHAIN> <COMMANDS>\n",
"```"
]
},
{
"cell_type": "markdown",
"id": "conscious-backing",
"metadata": {},
"source": [
"使用举例:\n",
"```\n",
"NATRO\n",
"EX 1 EX 2\n",
"START\n",
"\n",
"* A PROPERTY HYDROPHOBIC # A链所有位点可设计为疏水的天然氨基酸\n",
"```"
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "compatible-respondent",
"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\tPHE:NtermProteinFull,ILE:NtermProteinFull,LEU:NtermProteinFull,MET:NtermProteinFull,VAL:NtermProteinFull,TRP:NtermProteinFull,TYR:NtermProteinFull\n",
"2\tTRUE\tTRUE\tPHE,ILE,LEU,MET,VAL,TRP,TYR\n",
"3\tTRUE\tTRUE\tPHE,ILE,LEU,MET,VAL,TRP,TYR\n",
"4\tTRUE\tTRUE\tPHE,ILE,LEU,MET,VAL,TRP,TYR\n",
"5\tTRUE\tTRUE\tPHE,ILE,LEU,MET,VAL,TRP,TYR\n",
"6\tTRUE\tTRUE\tPHE,ILE,LEU,MET,VAL,TRP,TYR\n",
"7\tTRUE\tTRUE\tPHE,ILE,LEU,MET,VAL,TRP,TYR\n",
"8\tTRUE\tTRUE\tPHE,ILE,LEU,MET,VAL,TRP,TYR\n",
"9\tTRUE\tTRUE\tPHE,ILE,LEU,MET,VAL,TRP,TYR\n",
"10\tTRUE\tTRUE\tPHE,ILE,LEU,MET,VAL,TRP,TYR\n",
"11\tTRUE\tTRUE\tPHE,ILE,LEU,MET,VAL,TRP,TYR\n",
"12\tTRUE\tTRUE\tPHE,ILE,LEU,MET,VAL,TRP,TYR\n",
"13\tTRUE\tTRUE\tPHE,ILE,LEU,MET,VAL,TRP,TYR\n",
"14\tTRUE\tTRUE\tPHE:CtermProteinFull,ILE:CtermProteinFull,LEU:CtermProteinFull,MET:CtermProteinFull,VAL:CtermProteinFull,TRP:CtermProteinFull,TYR:CtermProteinFull\n",
"\n",
"start\n",
"\n"
]
}
],
"source": [
"# restrict to baestype list\n",
"resfile_type = ReadResfile('./data/chain_range.resfile')\n",
"\n",
"# 将TaskOperations加载至TaskFactory中\n",
"pack_tf = TaskFactory()\n",
"pack_tf.push_back(resfile_type)\n",
"\n",
"# 生成PackerTask\n",
"packer_task = pack_tf.create_task_and_apply_taskoperations(pose)\n",
"print(packer_task)\n",
"\n",
"# 查看每个残基的Rotamer采样级别:\n",
"print(packer_task.task_string(pose))"
]
},
{
"cell_type": "markdown",
"id": "personalized-brisbane",
"metadata": {},
"source": [
"#### 3.4 非标准氨基酸的指定\n",
"当在BODY中想引入非标准氨基酸时，需要特殊的格式进行指定(2019年版本的Rosetta支持该语法)\n",
"```\n",
"<PDBNUM>[<ICODE>] <CHAIN> <COMMANDS> X[ncaa]\n",
"```"
]
},
{
"cell_type": "markdown",
"id": "proof-winner",
"metadata": {},
"source": [
"不同的地方在于COMMANDs部分: 非标准氨基酸加入前必须加入\"X[ncaa]\" ncaa=非标准氨基酸的三字母缩写\n",
"\n",
"使用举例:\n",
"```\n",
"NATRO\n",
"EX 1 EX 2\n",
"START\n",
"\n",
"5 A PIKAA X[B36]X[A20] # 5号引入单点非标准氨基酸B36以及A20非标准氨基酸\n",
"```"
]
},
{
"cell_type": "code",
"execution_count": 7,
"id": "selective-jumping",
"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\tFALSE\tFALSE\t\n",
"2\tFALSE\tFALSE\t\n",
"3\tFALSE\tFALSE\t\n",
"4\tFALSE\tFALSE\t\n",
"5\tTRUE\tTRUE\tB36,A20\n",
"6\tFALSE\tFALSE\t\n",
"7\tFALSE\tFALSE\t\n",
"8\tFALSE\tFALSE\t\n",
"9\tFALSE\tFALSE\t\n",
"10\tFALSE\tFALSE\t\n",
"11\tFALSE\tFALSE\t\n",
"12\tFALSE\tFALSE\t\n",
"13\tFALSE\tFALSE\t\n",
"14\tFALSE\tFALSE\t\n",
"\n"
]
}
],
"source": [
"from pyrosetta.rosetta.core.pack.palette import CustomBaseTypePackerPalette\n",
"# restrict to baestype list\n",
"resfile_type = ReadResfile('./data/ncaa.resfile')\n",
"\n",
"# 先在CustomBaseTypePackerPalette引入NCAA列表\n",
"pp = CustomBaseTypePackerPalette()\n",
"pp.add_type('B36')\n",
"pp.add_type('A20')\n",
"\n",
"# 将TaskOperations加载至TaskFactory中\n",
"pack_tf = TaskFactory()\n",
"pack_tf.set_packer_palette(pp) ## 加载Palette到TaskFactory中;\n",
"pack_tf.push_back(resfile_type)\n",
"\n",
"# 生成PackerTask\n",
"packer_task = pack_tf.create_task_and_apply_taskoperations(pose)\n",
"print(packer_task)"
]
},
{
"cell_type": "markdown",
"id": "growing-raleigh",
"metadata": {},
"source": [
"#### 3.5 多重逻辑指定\n",
"在Resfile中，如果BODY部分指定发生了重叠，有两种处理方式:\n",
"\n",
"- 如果BODY是同一种指定级别，**按照交集逻辑**进行处理，**无交集时为空集**。\n",
"- 不同指定级别时，单位点指定的优先级高于范围级指定的优先级"
]
},
{
"cell_type": "markdown",
"id": "genetic-diary",
"metadata": {},
"source": [
"使用举例:\n",
"```\n",
"NATRO\n",
"EX 1 EX 2\n",
"START\n",
"\n",
"1 - 5 A APOLAR # A链1-5号位只允许在非极性氨基酸范围内进行Rotamer搜索\n",
"3 - 5 A POLAR # A链3-5号位只允许在极性氨基酸范围内进行Rotamer搜索\n",
"```"
]
},
{
"cell_type": "code",
"execution_count": 8,
"id": "spatial-qatar",
"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,PHE:NtermProteinFull,GLY:NtermProteinFull,ILE:NtermProteinFull,LEU:NtermProteinFull,MET:NtermProteinFull,PRO:NtermProteinFull,VAL:NtermProteinFull,TRP:NtermProteinFull,TYR:NtermProteinFull\n",
"2\tTRUE\tTRUE\tALA,CYS,PHE,GLY,ILE,LEU,MET,PRO,VAL,TRP,TYR\n",
"3\tFALSE\tFALSE\t\n",
"4\tFALSE\tFALSE\t\n",
"5\tFALSE\tFALSE\t\n",
"6\tFALSE\tFALSE\t\n",
"7\tFALSE\tFALSE\t\n",
"8\tFALSE\tFALSE\t\n",
"9\tFALSE\tFALSE\t\n",
"10\tFALSE\tFALSE\t\n",
"11\tFALSE\tFALSE\t\n",
"12\tFALSE\tFALSE\t\n",
"13\tFALSE\tFALSE\t\n",
"14\tFALSE\tFALSE\t\n",
"\n"
]
}
],
"source": [
"# restrict to baestype list\n",
"resfile_type = ReadResfile('./data/multi-logic.resfile')\n",
"\n",
"# 将TaskOperations加载至TaskFactory中\n",
"pack_tf = TaskFactory()\n",
"pack_tf.push_back(resfile_type)\n",
"\n",
"# 生成PackerTask\n",
"packer_task = pack_tf.create_task_and_apply_taskoperations(pose)\n",
"print(packer_task)"
]
},
{
"cell_type": "markdown",
"id": "surprised-spread",
"metadata": {},
"source": [
"同一指定级别，3-5号氨基酸自由度为空集。"
]
},
{
"cell_type": "markdown",
"id": "acceptable-baking",
"metadata": {},
"source": [
"另外一种情况: \n",
"\n",
"使用举例:\n",
"```\n",
"NATRO\n",
"EX 1 EX 2\n",
"START\n",
"\n",
"1 - 5 A APOLAR # A链1-5号位只允许在非极性氨基酸范围内进行Rotamer搜索\n",
"3 A POLAR # A链3号氨基酸设计为极性氨基酸范围\n",
"```"
]
},
{
"cell_type": "code",
"execution_count": 9,
"id": "sharing-steal",
"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,PHE:NtermProteinFull,GLY:NtermProteinFull,ILE:NtermProteinFull,LEU:NtermProteinFull,MET:NtermProteinFull,PRO:NtermProteinFull,VAL:NtermProteinFull,TRP:NtermProteinFull,TYR:NtermProteinFull\n",
"2\tTRUE\tTRUE\tALA,CYS,PHE,GLY,ILE,LEU,MET,PRO,VAL,TRP,TYR\n",
"3\tTRUE\tTRUE\tASP,GLU,HIS,HIS_D,LYS,ASN,GLN,ARG,SER,THR\n",
"4\tTRUE\tTRUE\tALA,CYS,PHE,GLY,ILE,LEU,MET,PRO,VAL,TRP,TYR\n",
"5\tTRUE\tTRUE\tALA,CYS,PHE,GLY,ILE,LEU,MET,PRO,VAL,TRP,TYR\n",
"6\tFALSE\tFALSE\t\n",
"7\tFALSE\tFALSE\t\n",
"8\tFALSE\tFALSE\t\n",
"9\tFALSE\tFALSE\t\n",
"10\tFALSE\tFALSE\t\n",
"11\tFALSE\tFALSE\t\n",
"12\tFALSE\tFALSE\t\n",
"13\tFALSE\tFALSE\t\n",
"14\tFALSE\tFALSE\t\n",
"\n"
]
}
],
"source": [
"# restrict to baestype list\n",
"resfile_type = ReadResfile('./data/multi-logic2.resfile')\n",
"\n",
"# 将TaskOperations加载至TaskFactory中\n",
"pack_tf = TaskFactory()\n",
"pack_tf.push_back(resfile_type)\n",
"\n",
"# 生成PackerTask\n",
"packer_task = pack_tf.create_task_and_apply_taskoperations(pose)\n",
"print(packer_task)"
]
},
{
"cell_type": "markdown",
"id": "south-migration",
"metadata": {},
"source": [
"得到的结果: 3号设计为极性氨酸，1-2，4-5号氨基酸设计为非极性氨基酸。因为单位点优先级高于氨基酸范围指定。"
]
},
{
"cell_type": "markdown",
"id": "prepared-serve",
"metadata": {},
"source": [
"再举一个例子:\n",
"```\n",
"NATRO\n",
"EX 1 EX 2\n",
"START\n",
"\n",
"* A POLAR # A链所有氨基酸设计为极性氨酸\n",
"1 - 5 A APOLAR # A链1-5号位只允许在非极性氨基酸范围内进行Rotamer搜索\n",
"```"
]
},
{
"cell_type": "code",
"execution_count": 10,
"id": "apart-protein",
"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,PHE:NtermProteinFull,GLY:NtermProteinFull,ILE:NtermProteinFull,LEU:NtermProteinFull,MET:NtermProteinFull,PRO:NtermProteinFull,VAL:NtermProteinFull,TRP:NtermProteinFull,TYR:NtermProteinFull\n",
"2\tTRUE\tTRUE\tALA,CYS,PHE,GLY,ILE,LEU,MET,PRO,VAL,TRP,TYR\n",
"3\tTRUE\tTRUE\tALA,CYS,PHE,GLY,ILE,LEU,MET,PRO,VAL,TRP,TYR\n",
"4\tTRUE\tTRUE\tALA,CYS,PHE,GLY,ILE,LEU,MET,PRO,VAL,TRP,TYR\n",
"5\tTRUE\tTRUE\tALA,CYS,PHE,GLY,ILE,LEU,MET,PRO,VAL,TRP,TYR\n",
"6\tTRUE\tTRUE\tASP,GLU,HIS,HIS_D,LYS,ASN,GLN,ARG,SER,THR\n",
"7\tTRUE\tTRUE\tASP,GLU,HIS,HIS_D,LYS,ASN,GLN,ARG,SER,THR\n",
"8\tTRUE\tTRUE\tASP,GLU,HIS,HIS_D,LYS,ASN,GLN,ARG,SER,THR\n",
"9\tTRUE\tTRUE\tASP,GLU,HIS,HIS_D,LYS,ASN,GLN,ARG,SER,THR\n",
"10\tTRUE\tTRUE\tASP,GLU,HIS,HIS_D,LYS,ASN,GLN,ARG,SER,THR\n",
"11\tTRUE\tTRUE\tASP,GLU,HIS,HIS_D,LYS,ASN,GLN,ARG,SER,THR\n",
"12\tTRUE\tTRUE\tASP,GLU,HIS,HIS_D,LYS,ASN,GLN,ARG,SER,THR\n",
"13\tTRUE\tTRUE\tASP,GLU,HIS,HIS_D,LYS,ASN,GLN,ARG,SER,THR\n",
"14\tTRUE\tTRUE\tASP:CtermProteinFull,GLU:CtermProteinFull,HIS:CtermProteinFull,HIS_D:CtermProteinFull,LYS:CtermProteinFull,ASN:CtermProteinFull,GLN:CtermProteinFull,ARG:CtermProteinFull,SER:CtermProteinFull,THR:CtermProteinFull\n",
"\n"
]
}
],
"source": [
"# restrict to baestype list\n",
"resfile_type = ReadResfile('./data/multi-logic3.resfile')\n",
"\n",
"# 将TaskOperations加载至TaskFactory中\n",
"pack_tf = TaskFactory()\n",
"pack_tf.push_back(resfile_type)\n",
"\n",
"# 生成PackerTask\n",
"packer_task = pack_tf.create_task_and_apply_taskoperations(pose)\n",
"print(packer_task)"
]
},
{
"cell_type": "markdown",
"id": "informational-bolivia",
"metadata": {},
"source": [
"得到的结果: 1-5号设计为非极性氨酸，其余氨基酸设计为极性氨基酸。因为氨基酸范围指定优先级大于链范围指定。"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "bright-niagara",
"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"
}
},
"nbformat": 4,
"nbformat_minor": 5
}