PyBioMed学习

【1】介绍：

1、PyBioMed是一个Python库，专为生物信息学研究设计，它结合了化学、生物和计算科学的知识，提供了一系列方便的功能用于处理生物大分子数据，如蛋白质、核酸和小分子化合物等。这个库支持结构分析、序列比对、药效预测、分子绘图等多种生物信息学任务，并且易于集成到Python的数据科学工作流程中。

2、文档：Getting Started with PyBioMed — PyBioMed 1 documentation

【2】安装：

ps:参考实验遇到的问题03_python2下载openbabel wheel-CSDN博客

1、下载软件包PyBioMed/PyBioMed/download/PyBioMed_package_zip at master · gadsbyfly/PyBioMed (github.com)

https://github.com/gadsbyfly/PyBioMed/blob/master/PyBioMed/download/PyBioMed_package_zip

下载软件包

extract here,cd 文件夹

2、需要先安装rdkit 和 openbabel  

conda install -c openbabel openbabel
 
conda install -c conda-forge rdkit

 3、安装pybiomed

cd 文件夹
python setup.py install 

 【3】pyprotein

1、介绍

PyProtein is a tool used for protein feature calculation. PyProtein calculates structural and physicochemical features of proteins and peptides from amino acid sequence. These sequence-derived structural and physicochemical features have been widely used in the development of machine learning models for predicting protein structural and functional classes, post-translational modification, subcellular locations and peptides of specific properties. There are two ways to calculate protein descriptors in the PyProtein module. One is to directly use the corresponding methods, the other one is firstly to construct a PyProtein class and then run their methods to obtain the protein descriptors. It should be noted that the output is a dictionary form, whose keys and values represent the descriptor name and the descriptor value, respectively. The user could clearly understand the meaning of each descriptor.

2、计算

【参考学习】：PyBioMed:一个用于化学物质、蛋白质和DNA及其相互作用的各种分子表示的Python文库-CSDN博客

（1）AAC：氨基酸组成

 from PyBioMed.PyProtein import AAComposition
>>> protein="ADGCGVGEGTGQGPMCNCMCMKWVYADEDAADLESDSFADEDASLESDSFPWSNQRVFCSFADEDAS"
>>> AAC=AAComposition.CalculateAAComposition(protei