pharmastar 0.0.1a1

药理大师是一个具有多种功能的中药网络药理学分析工具，可进行经典的网络药理学及反向网络药理学分析。Pharmastar is a multi-functional traditional chinese medicine network pharmacology analysis tool for classical network pharmacology and reverse network pharmacology.

药理大师是一个开发中的具有多种功能的中药网络药理学分析工具，可进行经典的网络药理学及反向网络药理学分析。

Pharmastar is a multi-functional traditional chinese medicine network pharmacology analysis tool under development for classical network pharmacology and reverse network pharmacology.

• 中文

  • 使用

• English

  • Usage

中文

使用

基本使用

pharmastar.analysis中提供了进行网络药理学分析的pipeline函数。

• reverse函数: 反向网络药理学分析的pipeline函数。使用它仅需使用命令

from pharmastar import analysis
analysis.reverse(genes,
                 protein_chemical_links_filename,
                 score,
                 chemicals_filename,
                 chunksize,
                 swiss_filename,
                 drug_likeness_num,
                 try_num)

它需要一个必需形参genes，这是一个存储编码拟分析靶点的基因的Ensembl ID与其名称的字典，如{'9606.ENSP00000265022': 'DGKG'}。

它的可选形参有

• protein_chemical_links_filename: 字符串类型，从STITCH数据库中下载的protein_chemical.links.transfer的文件名，默认为9606.protein_chemical.links.transfer.v5.0.tsv；
• score: int类型，仅combined_score大于等于score的记录会被筛选出，默认为900；
• chemicals_filename: 字符串类型，从STITCH数据库中下载的chemicals数据集的文件名，默认为chemicals.v5.0.tsv.gz；
• param chunksize: int类型，遍历chemicals数据集时的chunksize，该值过大可能耗尽计算机的内存，默认为1000000；
• swiss_filename: SwissADME的分析结果（csv文件）的路径，默认为swissadme.csv；
• drug_likeness_num: int类型，筛选类药性指标时至少有多少个为Yes，默认为3；
• try_num: int类型，pubchempy重复尝试的次数，默认为3。

English

Pharmastar is a multi-functional traditional chinese medicine network pharmacology analysis tool for classical network pharmacology and reverse network pharmacology.

Usage

Basic usage

pharmastar.analysis provides pipeline function for network pharmacology analysis.

• reverse : pipeline function for reverse network pharmacology. To use it, please use command

from pharmastar import analysis
analysis.reverse(genes,
                 protein_chemical_links_filename,
                 score,
                 chemicals_filename,
                 chunksize,
                 swiss_filename,
                 drug_likeness_num,
                 try_num)

It needs a required parameter genes, which is a dictionary that stores the Ensembl ID(s) of the gene(s) encoding the target(s) to be analyzed along with their name(s), e.g. {'9606.ENSP00000265022': 'DGKG'}.

Its optional parameter includes

• protein_chemical_links_filename: dict, filename of the dataset protein_chemical.links.transfer from STITCH database, 9606.protein_chemical.links.transfer.v5.0.tsv by default;
• score: int, only when the combined_score is no less than it will be selected out, 900 by default;
• chemicals_filename: str, filename of the dataset chemicals from STITCH database, chemicals.v5.0.tsv.gz by default;
• param chunksize: int, chunksize of the traversal to the chemicals dataset，the computer's memory may be exhausted if it is too large, 1000000 by default;
• swiss_filename: pathway of the SwissADME result, swissadme.csv by default;
• drug_likeness_num: int, how many 'Yes' at least when processing ADME selection, 3 by default;
• try_num: int, the number of times pubchempy tries, 3 by default.