{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Pose & PDBinfo Layer\n",
"\n",
"@Author: 吴炜坤\n",
"\n",
"@email：weikun.wu@xtalpi.com/weikunwu@163.com\n",
"\n",
"PDBinfo是Pose和PDB中信息交换和储存的重要媒介。Pose通常是从PDB文件中衍生出来的，除了原子的坐标信息以外，PDB文件中包含了许多额外的信息，而这些信息是储存在PDBinfo中。比如温度因子数据(bfactor)、晶体解析数据(crystinfo)、原子的占用率(occupancy)等。使用PDBinfo可以实现Pose编号与PDB编号的转换以及Pose的序列信息获取等功能。如果Pose中的氨基酸发生了插入和删除，又或者其他的PDB相关信息发生了变化，更新的信息就需要从当前的Pose中获取并转换成PDBinfo的数据，因此PDBinfo和Pose是实时相互连通的两个信息储存器。"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### 一、PDB编号与Pose编号"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"在PDB文件中，每个氨基酸都有自己独立的编号，并且氨基酸的PDB编号是依赖于其所在的链ID，如1A，2A...120A，1B，2B...130B等，分别代表A链和B链上的氨基酸位置。\n",
"而在Pose的概念中，氨基酸的编号是忽略链的分隔，按照PDB文件中链编写的顺序，**从1开始递增**，由于缺乏直观的对应方式，在Pose中的氨基酸和PDB编号的处理往往是相当棘手的，但是现在可以通过PDB_info这个的功能来轻松解决编号转换的问题。"
]
},
{
"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=1748780196 seed_offset=0 real_seed=1748780196 thread_index=0\n",
"\u001b[0mbasic.random.init_random_generator: {0} \u001b[0mRandomGenerator:init: Normal mode, seed=1748780196 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 0.651955 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')\n",
"\n",
"# 获取PDBinfo对象:\n",
"pose_pdbinfo = pose.pdb_info()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"**编号转换的处理主要使用的是pdb_info中的pdb2pose和pose2pdb函数。**\n",
"- pdb2pose: 将pdb编号翻译成pose编号;\n",
"- pose2pdb: 将pose编号转换成pdb编号;"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"24\n"
]
}
],
"source": [
"# 获取PDB号为24A的氨基酸残基所在的Pose残基编号\n",
"pose_number = pose_pdbinfo.pdb2pose(chain='A', res=24)\n",
"print(pose_number)"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"24 A \n"
]
}
],
"source": [
"# 获取Pose残基编号为24的氨基酸残基所在的PDB号\n",
"pdb_number = pose_pdbinfo.pose2pdb(res=24)\n",
"print(pdb_number)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### 二、PDB链信息\n",
"由于Pose中链号也是从1号开始编，不同于PDB文件中链号信息以字母的形式进行储存。链中信息获取的方式有多种途径:\n",
"- 根据链的PDB chain ID获取Pose chain ID;\n",
"- 根据链的chain ID获取PDB chain ID;\n",
"- 根据氨基酸的Pose编号获取其所在的chain ID;\n",
"- Pose的链氨基酸序列信息;\n",
"- 获取链起始和末端氨基酸信息;"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'A:1-76 B:1-76'"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# 先来看看pdbinfo中链的基本信息:\n",
"pose_pdbinfo.short_desc()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"可见我们的这个pose中共有2条链，分别为A和B链，分别都有76个氨基酸"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"1 2\n"
]
}
],
"source": [
"# 根据链的PDB chain ID获取Pose chain ID;\n",
"from pyrosetta.rosetta.core.pose import get_chain_id_from_chain\n",
"chainA_pose_chain_id = get_chain_id_from_chain('A', pose)\n",
"chainB_pose_chain_id = get_chain_id_from_chain('B', pose)\n",
"print(chainA_pose_chain_id, chainB_pose_chain_id)"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"A B\n"
]
}
],
"source": [
"from pyrosetta.rosetta.core.pose import get_chain_from_chain_id\n",
"chain1_pdb_chain_id = get_chain_from_chain_id(1, pose)\n",
"chain2_pdb_chain_id = get_chain_from_chain_id(2, pose)\n",
"print(chain1_pdb_chain_id, chain2_pdb_chain_id)"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"A B\n"
]
}
],
"source": [
"# 根据某个氨基酸残基的Pose编号获取其所在的PDB链ID;\n",
"residue1_chain_id = pose_pdbinfo.chain(10)\n",
"residue82_chain_id = pose_pdbinfo.chain(82)\n",
"print(residue1_chain_id, residue82_chain_id)"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"1 76\n"
]
}
],
"source": [
"# 获取链的的起始和结尾的氨基酸Pose编号:\n",
"chain1_start_pose_id = pose.chain_begin(1) # 返回某链起始的rosetta index\n",
"chain1_end_pose_id = pose.chain_end(1) # 返回某链终止的rosetta index\n",
"print(chain1_start_pose_id, chain1_end_pose_id)"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'PSEEEEKRRAKQVAKEKILEQNPSSKVQVRRVQKQGNTIRVELEITENGKKTNITVEVEKQGNTFTVKRITETVGS'"
]
},
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# 获取链的序列信息:\n",
"pose.chain_sequence(1) # 返回某链的氨基酸序列"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### 三、PDB中晶体解析信息的提取\n",
"除了基本的编号信息以外，一些晶体相关的信息也可以轻松进行提取:"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"49.13"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# 提取第一个原子的bfactor信息\n",
"pose.pdb_info().bfactor(res=1, atom_index=1) # 返回温度因子信息"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"<CrystInfo>{0,0,0,90,90,90 : P 1}\n"
]
}
],
"source": [
"# 获取PDB的晶体信息\n",
"crystinfo = pose.pdb_info().crystinfo()\n",
"print(crystinfo)"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"1.0\n"
]
}
],
"source": [
"# 获取原子的occupancy\n",
"occupancy = pose.pdb_info().occupancy(res=1, atom_index=1)\n",
"print(occupancy)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### 练习\n",
"请写一个小程序，对残基中每一个原子的bfactor进行加和平均处理。"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### 进阶技巧. 氨基酸残基PDB LABEL\n",
"PyRosetta中的PDBinfo除了储存一些实验信息以外，还可以储存用户的自定义信息，比如用户可以通过pose的label系统对一些氨基酸打上PDB标签，在后续的氨基酸范围选取中快捷方便的操作。\n",
"进阶部分主要介绍:\n",
"- add_reslabel/get_reslabels/clear_reslabel/res_haslabel\n",
"- icode/set_resinfo"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### 1. 通过pdbinfo的add_reslabel函数对残基打标签:\n"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [],
"source": [
"# 打标签\n",
"pose_pdbinfo.add_reslabel(1, 'starts')\n",
"pose_pdbinfo.add_reslabel(2, 'haha')\n",
"pose_pdbinfo.add_reslabel(3, 'end')"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"vector1_std_string[starts]\n",
"vector1_std_string[haha]\n",
"vector1_std_string[end]\n"
]
},
{
"data": {
"text/plain": [
"True"
]
},
"execution_count": 14,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# 查标签\n",
"print(pose_pdbinfo.get_reslabels(1))\n",
"print(pose_pdbinfo.get_reslabels(2))\n",
"print(pose_pdbinfo.get_reslabels(3))\n",
"pose.dump_pdb('./data/reslabeled.pdb')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"在输出PDB文件之后，在文件的最下方可以看到以下的信息被记录:\n",
"- REMARK PDBinfo-LABEL: 1 starts\n",
"- REMARK PDBinfo-LABEL: 2 haha\n",
"- REMARK PDBinfo-LABEL: 3 end"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"False"
]
},
"execution_count": 15,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# 判断标签\n",
"pose_pdbinfo.res_haslabel(res=1, target_label='haha')"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {},
"outputs": [],
"source": [
"# 清除标签\n",
"pose_pdbinfo.clear_reslabel(1)\n",
"pose_pdbinfo.clear_reslabel(2)\n",
"pose_pdbinfo.clear_reslabel(3)"
]
},
{
"cell_type": "code",
"execution_count": 17,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"False"
]
},
"execution_count": 17,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# 判断标签还是否存在？\n",
"pose_pdbinfo.res_haslabel(res=1, target_label='starts')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### 2. 关于icode插入与管理\n",
"在PDB文件中，比如处理抗体结构时，一些特殊的PDB编号(含有insert code）, 如 1A 2B 3C等(此处的代码并非是链号)。\n",
"通过PDBinfo，用户也可以很方便的插入这些字符。"
]
},
{
"cell_type": "code",
"execution_count": 18,
"metadata": {},
"outputs": [],
"source": [
"# set_resinfo(res: int, chain_id: str, pdb_res: int, ins_code: str) -> None\n",
"pose_pdbinfo.set_resinfo(res=1, chain_id='A', pdb_res=1, ins_code='m')"
]
},
{
"cell_type": "code",
"execution_count": 19,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"m\n",
"Residue 1: PRO:NtermProteinFull (PRO, P):\n",
"Base: PRO\n",
" Properties: POLYMER PROTEIN CANONICAL_AA LOWER_TERMINUS ALIPHATIC METALBINDING ALPHA_AA L_AA\n",
" Variant types: LOWER_TERMINUS_VARIANT\n",
" Main-chain atoms: N CA C \n",
" Backbone atoms: N CA C O HA \n",
" Side-chain atoms: CB CG CD NV CAV 1HB 2HB 1HG 2HG 1HD 2HD 1H 2H \n",
"Atom Coordinates:\n",
" N : 35.432, -0.708, 7.647\n",
" CA : 35.959, 0.478, 8.332\n",
" C : 36.62, 1.469, 7.374\n",
" O : 36.946, 1.11, 6.24\n",
" CB : 36.987, -0.1, 9.317\n",
" CG : 37.119, -1.563, 8.97\n",
" CD : 35.846, -1.957, 8.305\n",
" NV : 35.4257, -0.707336, 7.64284 (virtual)\n",
" CAV : 35.8996, 0.441347, 8.25002 (virtual)\n",
" HA : 35.141, 0.97715, 8.8721\n",
" 1HB : 37.9438, 0.433685, 9.21849\n",
" 2HB : 36.6417, 0.0476102, 10.3509\n",
" 1HG : 37.9855, -1.72036, 8.31089\n",
" 2HG : 37.3003, -2.15428, 9.87969\n",
" 1HD : 36.0441, -2.75894, 7.57861\n",
" 2HD : 35.1232, -2.2907, 9.06406\n",
" 1H : 35.7595, -0.700397, 6.70024\n",
" 2H : 34.4274, -0.649029, 7.64284\n",
"Mirrored relative to coordinates in ResidueType: FALSE\n",
"\n"
]
}
],
"source": [
"# 查询某个残基的icode:\n",
"print(pose_pdbinfo.icode(res=1))\n",
"\n",
"# 打印1号氨基酸残基信息:\n",
"print(pose.residue(1))"
]
},
{
"cell_type": "code",
"execution_count": 20,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"True"
]
},
"execution_count": 20,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# 保存PDB\n",
"pose.dump_pdb('./data/insert_icode.pdb')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"使用文本编辑器打开后可以见，第一个氨基酸的残基编号发生了变化:从1变成了1m\n",
"```\n",
"ATOM 1 N PRO A 1m 35.432 -0.708 7.647 1.00 49.13 N \n",
"ATOM 2 CA PRO A 1m 35.959 0.478 8.332 1.00 38.65 C \n",
"ATOM 3 C PRO A 1m 36.620 1.469 7.374 1.00 28.53 C \n",
"ATOM 4 O PRO A 1m 36.946 1.110 6.240 1.00 28.02 O \n",
"ATOM 5 CB PRO A 1m 36.987 -0.100 9.317 1.00 32.04 C \n",
"ATOM 6 CG PRO A 1m 37.119 -1.563 8.970 1.00 40.69 C \n",
"ATOM 7 CD PRO A 1m 35.846 -1.957 8.305 1.00 42.21 C \n",
"ATOM 8 HA PRO A 1m 35.141 0.977 8.872 1.00 0.00 H \n",
"ATOM 9 1HB PRO A 1m 37.944 0.434 9.218 1.00 0.00 H \n",
"ATOM 10 2HB PRO A 1m 36.642 0.048 10.351 1.00 0.00 H \n",
"ATOM 11 1HG PRO A 1m 37.985 -1.720 8.311 1.00 0.00 H \n",
"ATOM 12 2HG PRO A 1m 37.300 -2.154 9.880 1.00 0.00 H \n",
"ATOM 13 1HD PRO A 1m 36.044 -2.759 7.579 1.00 0.00 H \n",
"ATOM 14 2HD PRO A 1m 35.123 -2.291 9.064 1.00 0.00 H \n",
"ATOM 15 1H PRO A 1m 35.759 -0.700 6.700 1.00 0.00 H \n",
"ATOM 16 2H PRO A 1m 34.427 -0.649 7.643 1.00 0.00 H\n",
"```"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
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