pyCADD.Demand package

Submodules

pyCADD.Demand.cli module

pyCADD.Demand.config module

class pyCADD.Demand.config.BaseQueryCfg(pdb_list)

Bases: object

get_query()

class pyCADD.Demand.config.BaseQueryPDB(uniprot_id: str)

Bases: object

get_query()

pyCADD.Demand.core module

class pyCADD.Demand.core.QueryClient(uniprot_id: str = None, pdb_list_file: str = None, pdbid_column: str = None)

Bases: object

clean_pdb_data(del_mutations: bool = True, del_ignore_lig: bool = True, cutoff: float = None)

清洗 pdb 数据:

• 去除Apo晶体

• 去除配体未结合于目标链的晶体

• 去除非WideType晶体(optional)

• 去除非配体的小分子(e.g. DMS, optional)

• 去除分辨率高于Cutoff的晶体(optional)

Parameters

del_mutationsbool

是否去除突变晶体

del_ignore_ligbool

是否去除非配体的小分子

generate_inputfile(path: str, _format: str = None)

为 Dock 模块生成输入文件 Parameters ———- path : str

输入文件路径

_formatstr

输入文件格式 (csv, ini, yml, yaml)

get_apo()

get_mutation_pdb()

识别突变晶体

get_mutations()

property pdb_save_dir

query()

查询 pdb 数据

property uniprot_save_dir

pyCADD.Demand.core.get_nested_value(data, keys)

pyCADD.Demand.core.parse_uniport(uniprot_file_path)

pyCADD.Demand.core.query_pdb(pdb_list, save_path=None, quert_cfg=None)

pyCADD.Demand.core.query_uniprot(uniprot_id: str, save_path: str = None)

pyCADD.Demand.core.query_uniprot_id_on_pdb(uniprot_id: str, save_path: str = None) → list

Module contents