{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Pose Operation\n",
"\n",
"@Author: 吴炜坤\n",
"\n",
"@email：weikun.wu@xtalpi.com weikunwu@163.com\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Pose中储存了非常多的信息，同时还提供了接口可以让用户方便的对其中的信息进行修改（采样）。\n",
"本章节将着重介绍Pose的基本操作方式。"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"PyRosetta-4 2021 [Rosetta PyRosetta4.conda.mac.cxx11thread.serialization.python37.Release 2021.31+release.c7009b3115c22daa9efe2805d9d1ebba08426a54 2021-08-07T10:04:12] retrieved from: http://www.pyrosetta.org\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 r292 2021.31+release.c7009b3115c c7009b3115c22daa9efe2805d9d1ebba08426a54 http://www.pyrosetta.org 2021-08-07T10:04:12\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=-1249606663 seed_offset=0 real_seed=-1249606663 thread_index=0\n",
"\u001b[0mbasic.random.init_random_generator: {0} \u001b[0mRandomGenerator:init: Normal mode, seed=-1249606663 RG_type=mt19937\n",
"\u001b[0mcore.chemical.GlobalResidueTypeSet: {0} \u001b[0mFinished initializing fa_standard residue type set. Created 983 residue types\n",
"\u001b[0mcore.chemical.GlobalResidueTypeSet: {0} \u001b[0mTotal time to initialize 0.695115 seconds.\n",
"\u001b[0mcore.import_pose.import_pose: {0} \u001b[0mFile './data/4R80.clean.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 SER:CtermProteinFull 76\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0m\u001b[1m[ WARNING ]\u001b[0m missing heavyatom: OXT on residue SER:CtermProteinFull 152\n"
]
}
],
"source": [
"# 首先依然是从PDB中读入Pose\n",
"from pyrosetta import init, pose_from_pdb\n",
"init()\n",
"pose = pose_from_pdb('./data/4R80.clean.pdb')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### 一、 Pose的创建和复制\n",
"前几节中提及过，pose是一个容器，理所当然我们可以创建一个空的容器，里面什么都不放。</br>\n",
"很多时候，我们需要创建空的Pose对象，便于保存当前pose的实例化状态，可作为可回溯点或初始状态，方便反复调用。"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"# 通过创建一个新的Pose\n",
"from pyrosetta import Pose\n",
"copy_pose1 = Pose()\n",
"copy_pose2 = None"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"此处通过两种方法，将已有的Pose信息放入新的容器里，一种是通过assign函数复制，一种是通过python赋值符号来赋值。"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"PDB file name: ./data/4R80.clean.pdb\n",
"Total residues: 152\n",
"Sequence: PSEEEEKRRAKQVAKEKILEQNPSSKVQVRRVQKQGNTIRVELEITENGKKTNITVEVEKQGNTFTVKRITETVGSPSEEEEKRRAKQVAKEKILEQNPSSKVQVRRVQKQGNTIRVELEITENGKKTNITVEVEKQGNTFTVKRITETVGS\n",
"Fold tree:\n",
"FOLD_TREE EDGE 1 76 -1 EDGE 1 77 1 EDGE 77 152 -1 \n",
"\n",
"\n",
"PDB file name: ./data/4R80.clean.pdb\n",
"Total residues: 152\n",
"Sequence: PSEEEEKRRAKQVAKEKILEQNPSSKVQVRRVQKQGNTIRVELEITENGKKTNITVEVEKQGNTFTVKRITETVGSPSEEEEKRRAKQVAKEKILEQNPSSKVQVRRVQKQGNTIRVELEITENGKKTNITVEVEKQGNTFTVKRITETVGS\n",
"Fold tree:\n",
"FOLD_TREE EDGE 1 76 -1 EDGE 1 77 1 EDGE 77 152 -1 \n"
]
}
],
"source": [
"# 方法1：通过assign复制新的构象\n",
"copy_pose1.assign(pose)\n",
"\n",
"# 方法2：通过python的直接赋值符号\n",
"copy_pose2 = pose\n",
"\n",
"print(copy_pose1)\n",
"print('\\n')\n",
"print(copy_pose2)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"可见，两种方式“看”起来里面都有了新的pose信息。但真的如此么？"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"copy_pose1 24 residue phi:-91.24043946940483\n",
"copy_pose2 24 residue phi:170.0\n"
]
}
],
"source": [
"# 尝试调整初始pose中的24号氨基酸phi值:\n",
"pose.set_phi(24, 170.0)\n",
"\n",
"# 查看对starting_pose以及starting_pose2的影响:\n",
"print(f'copy_pose1 24 residue phi:{copy_pose1.phi(24)}')\n",
"print(f'copy_pose2 24 residue phi:{copy_pose2.phi(24)}')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"结果表明:\n",
"- copy_pose2是用过python直接赋值的Pose并没有复制，而只是pose的一个\"超链接\"符，并没有进行\"复制\"的操作。\n",
"- copy_pose1通过assign的复制，原始的pose的任何调整都没有对copy_pose1造成任何的影响，可见其独立性。"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### 二、 链与氨基酸操作\n",
"先前章节中描述的都是对蛋白质的几何空间做参数的调整，而并不涉及到拓扑结构的改变。在PyRosetta中，对蛋白的结构域进行修改本质上就是对氨基酸的插入和删除。"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### 2.1 Pose中链的顺序交换"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[0mcore.import_pose.import_pose: {0} \u001b[0mFile './data/6LZ9_H_L.pdb' automatically determined to be of type PDB\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mFound disulfide between residues 21 94\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 21 CYS\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 94 CYS\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 21 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 94 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mFound disulfide between residues 141 206\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 141 CYS\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 206 CYS\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 141 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 206 CYD\n",
"PDB file name: ./data/6LZ9_H_L.pdb\n",
" Pose Range Chain PDB Range | #Residues #Atoms\n",
"\n",
"0001 -- 0081 H 0002 -- 0082 | 0081 residues; 01283 atoms\n",
"0082 -- 0082 H 0082A -- 0082A | 0001 residues; 00011 atoms\n",
"0083 -- 0083 H 0082B -- 0082B | 0001 residues; 00011 atoms\n",
"0084 -- 0084 H 0082C -- 0082C | 0001 residues; 00019 atoms\n",
"0085 -- 0102 H 0083 -- 0100 | 0018 residues; 00271 atoms\n",
"0103 -- 0103 H 0100A -- 0100A | 0001 residues; 00010 atoms\n",
"0104 -- 0104 H 0100B -- 0100B | 0001 residues; 00021 atoms\n",
"0105 -- 0105 H 0100C -- 0100C | 0001 residues; 00021 atoms\n",
"0106 -- 0106 H 0100D -- 0100D | 0001 residues; 00010 atoms\n",
"0107 -- 0107 H 0100E -- 0100E | 0001 residues; 00017 atoms\n",
"0108 -- 0119 H 0101 -- 0112 | 0012 residues; 00171 atoms\n",
"0120 -- 0223 L 0002 -- 0105 | 0104 residues; 01588 atoms\n",
" TOTAL | 0223 residues; 03433 atoms\n",
"\n"
]
}
],
"source": [
"# 链交换, 注意链号会变成AB.\n",
"from pyrosetta.rosetta.protocols.simple_moves import SwitchChainOrderMover\n",
"exchange_pose = pose_from_pdb('./data/6LZ9_H_L.pdb')\n",
"print(exchange_pose.pdb_info())"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[0mcore.scoring.ScoreFunctionFactory: {0} \u001b[0mSCOREFUNCTION: \u001b[32mref2015\u001b[0m\n",
"\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[0mprotocols.simple_moves.SwitchChainOrderMover: {0} \u001b[0mNumber of chains in pose: 2\n",
"\u001b[0mprotocols.simple_moves.SwitchChainOrderMover: {0} \u001b[0mNow at chain: 2\n",
"\u001b[0mprotocols.simple_moves.SwitchChainOrderMover: {0} \u001b[0mNow at chain: 1\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mFound disulfide between residues 22 87\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 22 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 87 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 22 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 87 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mFound disulfide between residues 125 198\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 125 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 198 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 125 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 198 CYD\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 0.181558 seconds to load from binary\n",
"\u001b[0mprotocols.simple_moves.SwitchChainOrderMover: {0} \u001b[0mNew pose's foldtree FOLD_TREE EDGE 1 104 -1 EDGE 1 105 1 EDGE 105 223 -1\n",
"PDB file name: \n",
" Pose Range Chain PDB Range | #Residues #Atoms\n",
"\n",
"0001 -- 0104 A 0001 -- 0104 | 0104 residues; 01588 atoms\n",
"0105 -- 0223 B 0105 -- 0223 | 0119 residues; 01845 atoms\n",
" TOTAL | 0223 residues; 03433 atoms\n",
"\n"
]
}
],
"source": [
"switch_chains = SwitchChainOrderMover()\n",
"switch_chains.chain_order(\"LH\")\n",
"switch_chains.apply(exchange_pose)\n",
"print(exchange_pose.pdb_info())"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"注意，这种方法虽然可以进行链交换，但是其中的PDB_info被强制更新为A链和B链了，如果需要保留原有的PDB信息系统，就不应该用这种快捷修改的方式！"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### 2.2 Pose中链的删除\n",
"Pose中的链是可以被整条删除的。（反之也可以添加）"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[0mprotocols.simple_moves.DeleteChainMover: {0} \u001b[0mRemoving chain 1 from pose with 2 chains\n",
"PDB file name: ./data/4R80.clean.pdb\n",
" Pose Range Chain PDB Range | #Residues #Atoms\n",
"\n",
"0001 -- 0076 B 0001 -- 0076 | 0076 residues; 01251 atoms\n",
" TOTAL | 0076 residues; 01251 atoms\n",
"\n"
]
}
],
"source": [
"# 链删除\n",
"from pyrosetta.rosetta.protocols.simple_moves import DeleteChainMover\n",
"delete_chain = DeleteChainMover()\n",
"delete_chain.chain_num(1)\n",
"delete_chain.apply(pose)\n",
"print(pose.pdb_info())"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"可见A链已经在Pose中消失，而B链还存在。"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### 2.3 Pose中链的索引分离\n",
"尽管pose的氨基酸编号是忽略多肽链的分隔的，pose中的链依然是根据多肽链的物理结构进行编号的，同理也是从1开始编号。\n",
"如一个蛋白中有2条链A和B，那么链编号结果即为1和2。其中A对应1号链，B对应2号链，与PDB的链顺序有关（当然A链的顺序如果在后面，那么B链就是1号链）。\n",
"Pose类中许多的方法可以很方便对链的增减进行操作, 以下2个举例进行说明:"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[0mcore.import_pose.import_pose: {0} \u001b[0mFile './data/6LZ9_H_L.pdb' automatically determined to be of type PDB\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mFound disulfide between residues 21 94\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 21 CYS\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 94 CYS\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 21 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 94 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mFound disulfide between residues 141 206\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 141 CYS\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 206 CYS\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 141 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 206 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mFound disulfide between residues 21 94\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 21 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 94 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 21 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 94 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mFound disulfide between residues 22 87\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 22 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 87 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 22 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 87 CYD\n"
]
},
{
"data": {
"text/plain": [
"vector1_std_shared_ptr_core_pose_Pose_t[0x7ff14f8106a8, 0x7ff14e6a6a18]"
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# 将Pose按照链的数量进行切割\n",
"pose = pose_from_pdb('./data/6LZ9_H_L.pdb')\n",
"pose_list = pose.split_by_chain()\n",
"pose_list"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"此处的pose_list中存放了2个数据，说明链已经被切割成2个独立的pose对象了。\n",
"\n",
"通过python的索引，可以获得具体的pose:"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mFound disulfide between residues 21 94\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 21 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 94 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 21 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 94 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mFound disulfide between residues 22 87\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 22 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 87 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 22 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 87 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mFound disulfide between residues 21 94\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 21 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 94 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 21 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 94 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mFound disulfide between residues 22 87\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 22 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 87 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 22 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 87 CYD\n",
"PDB file name: ./data/6LZ9_H_L.pdb\n",
" Pose Range Chain PDB Range | #Residues #Atoms\n",
"\n",
"0001 -- 0081 H 0002 -- 0082 | 0081 residues; 01283 atoms\n",
"0082 -- 0082 H 0082A -- 0082A | 0001 residues; 00011 atoms\n",
"0083 -- 0083 H 0082B -- 0082B | 0001 residues; 00011 atoms\n",
"0084 -- 0084 H 0082C -- 0082C | 0001 residues; 00019 atoms\n",
"0085 -- 0102 H 0083 -- 0100 | 0018 residues; 00271 atoms\n",
"0103 -- 0103 H 0100A -- 0100A | 0001 residues; 00010 atoms\n",
"0104 -- 0104 H 0100B -- 0100B | 0001 residues; 00021 atoms\n",
"0105 -- 0105 H 0100C -- 0100C | 0001 residues; 00021 atoms\n",
"0106 -- 0106 H 0100D -- 0100D | 0001 residues; 00010 atoms\n",
"0107 -- 0107 H 0100E -- 0100E | 0001 residues; 00017 atoms\n",
"0108 -- 0119 H 0101 -- 0112 | 0012 residues; 00171 atoms\n",
" TOTAL | 0119 residues; 01845 atoms\n",
"\n",
"PDB file name: ./data/6LZ9_H_L.pdb\n",
" Pose Range Chain PDB Range | #Residues #Atoms\n",
"\n",
"0001 -- 0104 L 0002 -- 0105 | 0104 residues; 01588 atoms\n",
" TOTAL | 0104 residues; 01588 atoms\n",
"\n"
]
}
],
"source": [
"# 获取只含有第一个链的pose\n",
"chain1_pose = pose.split_by_chain()[1] # 直接切片索引链号。\n",
"chain2_pose = pose.split_by_chain()[2] # 直接切片索引链号。\n",
"\n",
"# check\n",
"print(chain1_pose.pdb_info())\n",
"print(chain2_pose.pdb_info())"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### 2.4 Pose链的合并或延伸\n",
"除了索引操作，用户还可以通过一些简单的方式把链合并到一个pose中，此处使用append_pose_to_pose函数就可以达到目的。但需要注意，pose中的氨基酸、链的数量变化后，都需要对PDBinfo进行更新。否则PDBinfo的信息与Pose信息不对称。"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"**添加新的链**"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mFound disulfide between residues 21 94\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 21 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 94 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 21 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 94 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mFound disulfide between residues 141 206\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 141 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 206 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 141 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 206 CYD\n"
]
}
],
"source": [
"# 将chain2加载到chain1 pose的最后一个氨基酸的后面。\n",
"chain1_pose_last_residue = chain1_pose.total_residue()\n",
"chain1_pose.append_pose_by_jump(chain2_pose, jump_anchor_residue=chain1_pose_last_residue)\n",
"chain1_pose.update_residue_neighbors()\n",
"chain1_pose.update_pose_chains_from_pdb_chains()\n",
"chain1_pose.conformation().detect_disulfides()"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"PDB file name: ./data/6LZ9_H_L.pdb\n",
" Pose Range Chain PDB Range | #Residues #Atoms\n",
"\n",
"0001 -- 0081 H 0002 -- 0082 | 0081 residues; 01283 atoms\n",
"0082 -- 0082 H 0082A -- 0082A | 0001 residues; 00011 atoms\n",
"0083 -- 0083 H 0082B -- 0082B | 0001 residues; 00011 atoms\n",
"0084 -- 0084 H 0082C -- 0082C | 0001 residues; 00019 atoms\n",
"0085 -- 0102 H 0083 -- 0100 | 0018 residues; 00271 atoms\n",
"0103 -- 0103 H 0100A -- 0100A | 0001 residues; 00010 atoms\n",
"0104 -- 0104 H 0100B -- 0100B | 0001 residues; 00021 atoms\n",
"0105 -- 0105 H 0100C -- 0100C | 0001 residues; 00021 atoms\n",
"0106 -- 0106 H 0100D -- 0100D | 0001 residues; 00010 atoms\n",
"0107 -- 0107 H 0100E -- 0100E | 0001 residues; 00017 atoms\n",
"0108 -- 0119 H 0101 -- 0112 | 0012 residues; 00171 atoms\n",
"0120 -- 0223 L 0002 -- 0105 | 0104 residues; 01588 atoms\n",
" TOTAL | 0223 residues; 03433 atoms\n",
"\n",
"PDBinfo是否需要被更新:True\n"
]
}
],
"source": [
"print(chain1_pose.pdb_info())\n",
"\n",
"# 检查Pose的PDB_info是否是奇怪的:\n",
"print(f'PDBinfo是否需要被更新:{chain1_pose.pdb_info().obsolete()}')"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"PDBinfo是否需要被更新:False\n"
]
}
],
"source": [
"# update pdbinfo; 别忘了更新pdbinfo;\n",
"from pyrosetta.rosetta.core.pose import renumber_pdbinfo_based_on_conf_chains\n",
"renumber_pdbinfo_based_on_conf_chains(chain1_pose)\n",
"print(f'PDBinfo是否需要被更新:{chain1_pose.pdb_info().obsolete()}')"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [],
"source": [
"# 如果你非常确定，新的pose中不会有PDB的编号冲突等问题。可以直接修改obsolete的检查结果:\n",
"chain1_pose.pdb_info().obsolete(False)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"**合并为一条多肽链的case**"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[0mcore.import_pose.import_pose: {0} \u001b[0mFile './data/6LZ9_H_L.pdb' automatically determined to be of type PDB\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mFound disulfide between residues 21 94\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 21 CYS\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 94 CYS\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 21 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 94 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mFound disulfide between residues 141 206\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 141 CYS\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 206 CYS\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 141 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 206 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mFound disulfide between residues 21 94\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 21 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 94 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 21 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 94 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mFound disulfide between residues 22 87\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 22 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 87 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 22 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 87 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mFound disulfide between residues 21 94\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 21 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 94 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 21 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 94 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mFound disulfide between residues 22 87\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 22 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 87 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 22 CYD\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0mcurrent variant for 87 CYD\n",
"append之后的chain1_pose中的氨基酸总数:223\n",
"append之后chain的总数:1\n",
"PDB file name: ./data/6LZ9_H_L.pdb\n",
" Pose Range Chain PDB Range | #Residues #Atoms\n",
"\n",
"0001 -- 0223 H 0002 -- 0224 | 0223 residues; 03433 atoms\n",
" TOTAL | 0223 residues; 03433 atoms\n",
"\n"
]
}
],
"source": [
"# 链的延伸; 合并成一条链的意思;\n",
"from pyrosetta.rosetta.core.pose import append_pose_to_pose\n",
"pose = pose_from_pdb('./data/6LZ9_H_L.pdb')\n",
"chain1_pose = pose.split_by_chain()[1]\n",
"chain2_pose = pose.split_by_chain()[2]\n",
"\n",
"new_chain = False\n",
"combine_pose = Pose()\n",
"combine_pose.assign(chain1_pose)\n",
"append_pose_to_pose(combine_pose, chain2_pose, new_chain)\n",
"\n",
"# update pdbinfo; 别忘了更新pdbinfo;\n",
"renumber_pdbinfo_based_on_conf_chains(combine_pose)\n",
"\n",
"print(f'append之后的chain1_pose中的氨基酸总数:{combine_pose.total_residue()}')\n",
"combine_pose.sequence()\n",
"print(f'append之后chain的总数:{combine_pose.num_chains()}')\n",
"print(combine_pose.pdb_info())"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### 2.5 Pose中删除Region区域\n"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[0mcore.import_pose.import_pose: {0} \u001b[0mFile './data/4R80.clean.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 SER:CtermProteinFull 76\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0m\u001b[1m[ WARNING ]\u001b[0m missing heavyatom: OXT on residue SER:CtermProteinFull 152\n",
"删除前的PDB_info:\n",
"PDB file name: ./data/4R80.clean.pdb\n",
" Pose Range Chain PDB Range | #Residues #Atoms\n",
"\n",
"0001 -- 0076 A 0001 -- 0076 | 0076 residues; 01251 atoms\n",
"0077 -- 0152 B 0001 -- 0076 | 0076 residues; 01251 atoms\n",
" TOTAL | 0152 residues; 02502 atoms\n",
"\n",
"\u001b[0mprotocols.grafting.util: {0} \u001b[0mDeleting 50 residues from 1 to 50\n",
"删除后的PDB_info:\n",
"PDB file name: ./data/4R80.clean.pdb\n",
" Pose Range Chain PDB Range | #Residues #Atoms\n",
"\n",
"0001 -- 0026 A 0051 -- 0076 | 0026 residues; 00412 atoms\n",
"0027 -- 0102 B 0001 -- 0076 | 0076 residues; 01251 atoms\n",
" TOTAL | 0102 residues; 01663 atoms\n",
"\n"
]
}
],
"source": [
"pose = pose_from_pdb('./data/4R80.clean.pdb')\n",
"print('删除前的PDB_info:')\n",
"print(pose.pdb_info())\n",
"from pyrosetta.rosetta.protocols.grafting import delete_region\n",
"delete_region_mover = delete_region(pose, 1, 50) # 此处是pose number;\n",
"\n",
"# update pdbinfo; 别忘了更新pdbinfo;\n",
"renumber_pdbinfo_based_on_conf_chains(pose)\n",
"\n",
"# 打印查看信息, 一整个区域都被删除【比一个个氨基酸删除快得多】:\n",
"print('删除后的PDB_info:')\n",
"print(pose.pdb_info())"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"从pdb_info中可见，A链的1-50号氨基酸消失了。"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### 2.6 Pose中单独氨基酸的删减操作"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"除了对链的合并之外，我们还可以对链中的氨基酸进行添加、删除的操作！具体的过程是用户需要创建一个独立的氨基酸(residue object)，并将这个氨基酸加载到现有的构像中。\n",
"加载的方式可以是前置或后置，根据使用的函数不同而定。"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[0mcore.import_pose.import_pose: {0} \u001b[0mFile './data/4R80.clean.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 SER:CtermProteinFull 76\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0m\u001b[1m[ WARNING ]\u001b[0m missing heavyatom: OXT on residue SER:CtermProteinFull 152\n",
"原始氨基酸总数:152\n",
"原始氨基酸序列:PSEEEEKRRAKQVAKEKILEQNPSSKVQVRRVQKQGNTIRVELEITENGKKTNITVEVEKQGNTFTVKRITETVGSPSEEEEKRRAKQVAKEKILEQNPSSKVQVRRVQKQGNTIRVELEITENGKKTNITVEVEKQGNTFTVKRITETVGS\n",
"\n"
]
}
],
"source": [
"# 获取初始信息\n",
"from pyrosetta.rosetta.core.conformation import ResidueFactory\n",
"from pyrosetta.rosetta.core.chemical import ChemicalManager\n",
"\n",
"# print\n",
"pose = pose_from_pdb('./data/4R80.clean.pdb')\n",
"print(f'原始氨基酸总数:{pose.total_residue()}')\n",
"print(f'原始氨基酸序列:{pose.sequence()}\\n')"
]
},
{
"cell_type": "code",
"execution_count": 17,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Pose的残基数量:153\n",
"氨基酸序列:APSEEEEKRRAKQVAKEKILEQNPSSKVQVRRVQKQGNTIRVELEITENGKKTNITVEVEKQGNTFTVKRITETVGSPSEEEEKRRAKQVAKEKILEQNPSSKVQVRRVQKQGNTIRVELEITENGKKTNITVEVEKQGNTFTVKRITETVGS\n",
"\n"
]
}
],
"source": [
"# 通过ResidueFactory创建一个新的Residue(ALA)对象:\n",
"chm = ChemicalManager.get_instance()\n",
"rts = chm.residue_type_set(\"fa_standard\")\n",
"new_rsd = ResidueFactory.create_residue(rts.name_map('ALA')) # 创建一个residue object\n",
"\n",
"# 在第一个氨基酸前添加一个ALA\n",
"pose.prepend_polymer_residue_before_seqpos(new_rsd, 1, True) \n",
"\n",
"print(f'Pose的残基数量:{pose.total_residue()}')\n",
"print(f'氨基酸序列:{pose.sequence()}\\n')"
]
},
{
"cell_type": "code",
"execution_count": 18,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Pose的残基数量:154\n",
"氨基酸序列:APSEEEEKRRAKQVAKEKILEQNPSSKVQVRRVQKQGNTIRVELEITENGKKTNITVEVEKQGNTFTVKRITETVGSPSEEEEKRRAKQVAKEKILEQNPSSKVQVRRVQKQGNTIRVELEITENGKKTNITVEVEKQGNTFTVKRITETVGSA\n",
"\n"
]
}
],
"source": [
"# 向后添加氨基酸\n",
"last_residue = pose.total_residue()\n",
"pose.append_polymer_residue_after_seqpos(new_rsd, last_residue, True) # 在最后一个氨基酸后添加一个ALA\n",
"\n",
"print(f'Pose的残基数量:{pose.total_residue()}')\n",
"print(f'氨基酸序列:{pose.sequence()}\\n')"
]
},
{
"cell_type": "code",
"execution_count": 19,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"删除之后氨基酸总数:153\n",
"删除之后氨基酸序列:PSEEEEKRRAKQVAKEKILEQNPSSKVQVRRVQKQGNTIRVELEITENGKKTNITVEVEKQGNTFTVKRITETVGSPSEEEEKRRAKQVAKEKILEQNPSSKVQVRRVQKQGNTIRVELEITENGKKTNITVEVEKQGNTFTVKRITETVGSA\n",
"\n"
]
}
],
"source": [
"# 删除氨基酸\n",
"pose.delete_polymer_residue(1) # 删除第一个氨基酸\n",
"\n",
"print(f'删除之后氨基酸总数:{pose.total_residue()}')\n",
"print(f'删除之后氨基酸序列:{pose.sequence()}\\n')"
]
},
{
"cell_type": "code",
"execution_count": 20,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"删除之后氨基酸总数:148\n",
"删除之后氨基酸序列:EKRRAKQVAKEKILEQNPSSKVQVRRVQKQGNTIRVELEITENGKKTNITVEVEKQGNTFTVKRITETVGSPSEEEEKRRAKQVAKEKILEQNPSSKVQVRRVQKQGNTIRVELEITENGKKTNITVEVEKQGNTFTVKRITETVGSA\n",
"\n"
]
}
],
"source": [
"# 还可以范围性的删除氨基酸\n",
"pose.delete_residue_range_slow(1,5) # 删除第一个至第五个氨基酸\n",
"\n",
"print(f'删除之后氨基酸总数:{pose.total_residue()}')\n",
"print(f'删除之后氨基酸序列:{pose.sequence()}\\n')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"**对拓扑结构操作完后，千万记得PBDinfo更新!!**"
]
},
{
"cell_type": "code",
"execution_count": 21,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"PDBinfo是否需要被更新:False\n",
"PDB file name: ./data/4R80.clean.pdb\n",
" Pose Range Chain PDB Range | #Residues #Atoms\n",
"\n",
"0001 -- 0071 A 0006 -- 0076 | 0071 residues; 01177 atoms\n",
"0072 -- 0148 B 0001 -- 0077 | 0077 residues; 01260 atoms\n",
" TOTAL | 0148 residues; 02437 atoms\n",
"\n"
]
}
],
"source": [
"# 更新pdb_info; [别忘了!]\n",
"from pyrosetta.rosetta.core.pose import renumber_pdbinfo_based_on_conf_chains\n",
"\n",
"renumber_pdbinfo_based_on_conf_chains(pose) # 更新PDBinfo.\n",
"\n",
"# 检查PDBinfo是否正确: Returns true if PDBInfo is obsolete and needs updating\n",
"print(f'PDBinfo是否需要被更新:{pose.pdb_info().obsolete()}')\n",
"print(pose.pdb_info())"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### 2.7 Pose中连续region提取\n",
"在之前的章节里面我们提过，Pose中的每个氨基酸都是独立的构象，我们可以使用这个机制将Pose中一些连续的片段进行提取。"
]
},
{
"cell_type": "code",
"execution_count": 22,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[0mcore.import_pose.import_pose: {0} \u001b[0mFile './data/4R80.clean.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 SER:CtermProteinFull 76\n",
"\u001b[0mcore.conformation.Conformation: {0} \u001b[0m\u001b[1m[ WARNING ]\u001b[0m missing heavyatom: OXT on residue SER:CtermProteinFull 152\n",
"PDB file name: ./data/4R80.clean.pdb\n",
" Pose Range Chain PDB Range | #Residues #Atoms\n",
"\n",
"0001 -- 0076 A 0001 -- 0076 | 0076 residues; 01251 atoms\n",
"0077 -- 0152 B 0001 -- 0076 | 0076 residues; 01251 atoms\n",
" TOTAL | 0152 residues; 02502 atoms\n",
"\n"
]
}
],
"source": [
"# 读取pose\n",
"pose = pose_from_pdb('./data/4R80.clean.pdb')\n",
"print(pose.pdb_info())"
]
},
{
"cell_type": "code",
"execution_count": 23,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"P\n"
]
}
],
"source": [
"# 新建一个空的Pose\n",
"sub_region_pose = Pose()\n",
"\n",
"# 添加第一个氨基酸:\n",
"residue = pose.residue(1)\n",
"sub_region_pose.append_residue_by_jump(new_rsd=residue, jump_anchor_residue=1)\n",
"print(sub_region_pose.sequence())"
]
},
{
"cell_type": "code",
"execution_count": 24,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"PSEEE\n"
]
},
{
"data": {
"text/plain": [
"True"
]
},
"execution_count": 24,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# 添加第2-5个氨基酸:\n",
"for i in range(2, 6):\n",
" residue = pose.residue(i) # 索引原pose中的residue\n",
" last_residue_pose_id = sub_region_pose.total_residue() # 获取sub_region_pose中的最后一个氨基酸;\n",
" sub_region_pose.append_polymer_residue_after_seqpos(new_rsd=residue, seqpos=last_residue_pose_id, build_ideal_geometry=False) # 将氨基酸添加\n",
"print(sub_region_pose.sequence())\n",
"sub_region_pose.dump_pdb('./data/sub_region.pdb')"
]
},
{
"cell_type": "code",
"execution_count": 25,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"None\n"
]
}
],
"source": [
"# 这种非官方的操作方法，默认没有创建pdb_info!\n",
"print(sub_region_pose.pdb_info())"
]
},
{
"cell_type": "code",
"execution_count": 26,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"PDB file name: \n",
" Pose Range Chain PDB Range | #Residues #Atoms\n",
"\n",
"0001 -- 0005 A 0001 -- 0005 | 0005 residues; 00074 atoms\n",
" TOTAL | 0005 residues; 00074 atoms\n",
"\n"
]
}
],
"source": [
"# 通过AddPDBInfoMover可以创建对应的pdb_info给到当前的Pose\n",
"from pyrosetta.rosetta.protocols.simple_moves import AddPDBInfoMover\n",
"pdb_mover = AddPDBInfoMover()\n",
"pdb_mover.apply(sub_region_pose)\n",
"print(sub_region_pose.pdb_info())"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### 2.8 Pose中氨基酸类型的调整(突变)\n",
"除了具体的化学键数据的调整，在PyRosetta中进行氨基酸的类型调整也是很方便的"
]
},
{
"cell_type": "code",
"execution_count": 27,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"原始氨基酸类型:PRO:NtermProteinFull\n"
]
}
],
"source": [
"# 调整氨基酸的类型\n",
"from pyrosetta.toolbox import mutate_residue\n",
"print(f'原始氨基酸类型:{pose.residue(1).name()}')"
]
},
{
"cell_type": "code",
"execution_count": 28,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"突变氨基酸中...\n",
"\u001b[0mcore.scoring.ScoreFunctionFactory: {0} \u001b[0mSCOREFUNCTION: \u001b[32mref2015\u001b[0m\n",
"\u001b[0mcore.pack.task: {0} \u001b[0mPacker task: initialize from command line()\n",
"\u001b[0mcore.pack.pack_rotamers: {0} \u001b[0mbuilt 161 rotamers at 8 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[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"
]
}
],
"source": [
"print('突变氨基酸中...')\n",
"mutate_residue(pose, 1, 'C', 9.0) # 1 代表氨基酸突变的pose编号，9.0代表对氨基酸附近9埃范围内的氨基酸进行侧链优化，适应新的突变。"
]
},
{
"cell_type": "code",
"execution_count": 29,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"突变后氨基酸类型:CYS:NtermProteinFull\n"
]
}
],
"source": [
"print(f'突变后氨基酸类型:{pose.residue(1).name()}')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### 三、Pose中的自定义信息储存\n",
"Pose中含有让用户自定义写入任何信息的功能，比如在程序设计过程中，中间生成的临时数值或字符都可以写入到PoseExtraScore中，这些信息会随着Pose一并输出到PDB或则Silent文件中，在后续的分析和处理的过程中非常方便。"
]
},
{
"cell_type": "code",
"execution_count": 30,
"metadata": {},
"outputs": [],
"source": [
"# 给pose加入额外的信息: 比如filter计算的值就可以储存.\n",
"from pyrosetta.rosetta.core.pose import setPoseExtraScore, getPoseExtraScore\n",
"\n",
"setPoseExtraScore(pose, \"distance\", 1.0)\n",
"setPoseExtraScore(pose, \"angle\", 120.5)"
]
},
{
"cell_type": "code",
"execution_count": 31,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"1.0\n",
"120.5\n"
]
}
],
"source": [
"# 提取信息\n",
"print(getPoseExtraScore(pose, 'distance'))\n",
"print(getPoseExtraScore(pose, 'angle'))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### 练习\n",
"1. 尝试写一个程序，将Pose(单链)中某一个连续的结构域部分提取出来。\n",
"2. 尝试写一个程序，将Pose(单链)中某两个不同的连续结构域提取出来，并重新分为两条链。"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
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"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
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"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
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