就是本山人啦-CSDN博客

import numpy as npimport scipy as spimport randomimport torchfrom matplotlib import pyplot as pltfrom mpl_toolkits.mplot3d import Axes3Dxx = np.arange(-5,5,0.1)yy = np.arange(-5,5,0.1)X, Y = np.meshgrid(xx, yy)X = torch.tensor(X)Y = torch.tens

2021-12-17 16:47:35 993

原创 python 查看类的属性和方法

class A(): def __init__(self): self.a = 1 self.b = 2 def aa(self): print('i am ok')cl = A()print(cl.__dict__)# {'a': 1, 'b': 2}print(dir(cl))#[....'__subclasshook__', '__weakref__', 'a', 'aa', 'b']print(help(cl))

2021-11-30 18:47:19 3680

原创画单个分子

from rdkit import Chemfrom rdkit.Chem import Drawfrom rdkit.Chem.Draw.MolDrawing import MolDrawing, DrawingOptionssmiles = 'NC1=CCC(C2=CCC#CN2CC2OC3=CN2C(=O)C(=O)C3Nc2nc(C(F)(F)F)c(N=O)c(=O)[nH]2)C1=O'mol = Chem.MolFromSmiles(smiles)opts = DrawingOpt

2021-11-25 15:42:49 111

原创 itertools.combinations()测试

import itertoolsatoms = ['a','b','c','d','h']for atom1, atom2 in itertools.combinations(atoms, 2): print(atom1,atom2)output:a ba ca da hb cb db hc dc hd h

2021-11-23 09:20:34 174

原创 absl参数理解

from absl import app, flags, loggingimport sys#设置参数，第一个是参数名称，第二个是参数默认值，无默认值可取None，第三个是参数解释flags.DEFINE_string(‘str_1’, ‘hello’, ‘Input a string.’)flags.DEFINE_string(‘str_2’, ‘world’, ‘Input a string.’)flags.DEFINE_integer(‘num_1’, 0, ‘Input a integer

2021-11-11 15:06:33 1057

原创 anaconda安装早期tensorflow环境

#创建新环境conda create --n ‘your environment name’#激活环境conda activate ‘your environment name’#关闭环境conda deactivate#为了安装tensorflow早期版本conda install python=3.6conda install tensorflow==1.15conda install -c conda-forge rdkit...

2021-11-10 16:50:52 1396

原创 Ubantu ‘ZLIB_1.2.9‘ not found 错误处理

错误出现原因：你所安装软件软件的libz.so.1版本比较老，没有包含‘ZLIB_1.2.9’字体版本；你可以通过：strings libz.so.1 | grep ‘ZLIB*’ 命令查看你软件包含的字体版本，例如：ZLIB_1.2.0…解决方法：你可以使用：sudo find / -name “libz.so.1”命令来看着电脑的其他位置较新的‘libz.so.1’文件，然后把安装软件李的老文件给替换了就行。为了以防万一不要直接删除老文件，将它改名后保存。...

2021-10-25 16:49:26 1748

原创 windows环境创建mysql数据库

cd C:\Windows\System32open cmd.ext with administrator’s authoriitylog in mysql databasemysql -u root -ppassword: nonecreate databasecreate DATABASE ‘databse_name’;show all databasesshow databases;show basic info of ‘database_name’show crea

2021-10-21 11:57:25 724

原创生成复杂分子3D结构

from rdkit import Chemfrom rdkit.Chem import AllChemimport ossmiles = '[NH3+][C@@H](C(=O)N[C@@H](C(=O)N[C@@H](C(=O)N[C@H](C(=O)N[C@@H]1C(=O)N2[C@H](C(=O)N[C@@H](C(=O)N[C@@H](C(=O)N[C@@H](C(=O)N[C@H](C(=O)N[C@@H](C(=O)N[C@H](C(=O)N3[C@@H](C(=O)N[C@@H](

2021-09-22 10:46:56 670

原创将含有protein和ligands 的mol2文件转化成sdf文件

import osimport sysfrom rdkit import Chemdef split_mol2(mol_path, out_path): with open (mol_path,'r') as f: lines = f.readlines() if not os.path.exists(out_path): os.makedirs(out_path) path_protein = os.path.

2021-07-16 17:04:44 1284

原创测试rdkit分子结构输出

import rdkit from rdkit import Chemfrom rdkit.Chem import AllChemsmiles_1 = 'C[C@H]1[C@@H]2Cc3ccc(O)cc3[C@]1(C)CCN2C'#smiles_1 = 'N/C(F)(C)C\(=O)O'#smiles_1 = 'CC(C)(C)OC(=O)N[C@@](C)(Cc1ccccc1)C(=O)NC(Cc1ccccc1)C(=O)NCCCCCCCC(=O)O'smiles_2 = 'CC1C2

2021-07-14 09:43:51 512

原创测试symply

mport sympy as spimport mathfrom sympy import *import time import matplotlib.pyplot as pltdef get_R(a_x, a_y, a_z): #a_x, a_y, a_z

2021-07-14 09:41:13 108

原创 python 计算时间差

import timea = "Sat Mar 28 22:24:24 2016"print (time.mktime(time.strptime(a,"%a %b %d %H:%M:%S %Y")))b = '2021-04-19 03:32:29'print (time.mktime(time.strptime(b,"%Y-%m-%d %H:%M:%S")))c = '2021-04-20 03:32:29'bb = time.mktime(time.strptime(b,"%Y-%m-%

2021-07-06 15:01:17 116

原创 SDF 文件格式说明

XXXXXX #分子名称XXXXXX # 产生该文件的软件名称9 8 0 0 0 0 0 0 0999 V2000 #第一二参数分别代表原子数量和键的数量0.5369 0.9749 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 「1.4030 0.4749 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 02.2690 0.9749

2021-06-23 13:14:07 1842 1

原创根据中心原子切割分子碎片

class cut_fragment(): def __init__(self,center_atoms,mol): self.center_atoms = center_atoms self.mol = mol self.break_bond = [] self.connect_atom = self.center_atoms self.ssr = Chem.GetSymmSSSR(self.mol)

2021-04-15 14:38:53 142

原创筛选骨架差异较大分子

from rdkit import Chemfrom rdkit.Chem import AllChem, Drawfrom rdkit.Chem.Scaffolds import MurckoScaffoldfrom rdkit import DataStructsdef cal_mol_similar(m1,m2): core1 = MurckoScaffold.GetScaffoldForMol(m1) core2 = MurckoScaffold.GetScaffoldF

2021-04-14 14:46:51 153

原创 linux 打来文件后替换关键字命令：

linux 打来文件后替换关键字命令：gg 回到文档开头V 选择当前行G 回到末尾ggVG:s/“查找内容”/ “新内容”/ gc

2021-04-02 10:06:15 122

原创 Ubuntu 因为掉驱动而进不去主界面解决方案

Ubuntu 因为掉驱动而进不去主界面解决方案重装nvidia驱动cd /zfs/packagesudo systemctl stop lightdm.servicesudo ./NVIDIA-Linux-x86_64-418.56.runsudo systemctl start lightdm.service恢复down的节点sudo /usr/local/sbin/slurmd -n -19sudo scontrol update node=“your node name” state

2021-03-31 10:54:49 163

翻译创建git_hub命令

create your git_hub branchstep 1: git clone remote_pathstep 2: git remote add origin remote_pathstep 3: cd your downloaded folderstep 4: git branch -a # you will see all branchesstep 5: git checkout -b your_branch_namestep 6: git push origin your_b

2021-03-30 15:16:02 54

转载 RDkit: smiles 转化inche, inchikey

原网址链接：http://rdkit.org/docs/source/rdkit.Chem.inchi.htmlrdkit.Chem.inchi modulerdkit.Chem.inchi.MolToInchiAndAuxInfo(mol, options=’’, logLevel=None, treatWarningAsError=False)Returns the standard InChI string and InChI auxInfo for a moleculeKeyword arg

2021-02-06 17:58:05 2300

weixin_44853528的博客

原创修复: GLIBCXX_3.4.30‘ not found

原创本地部署二次开发的openmm库

原创 pybind11 error

原创提交本地项目到github仓库

原创 gromacs errors

原创在Linux 系统安装Gromacs

原创拆分 multiple mol2文件

原创画损失函数三维图