通路、互作、蛋白与结构查询：参数与补充说明

用法和示例见功能教程。

各功能按作用、API、输入、输出、示例代码和结果说明介绍。运行前按说明准备凭据、本地文件与可选依赖；远程结果随数据库版本与查询时间变化。

获取已收录的 AlphaFold 蛋白质结构预测

dnakit.databases.alphafold_get_prediction(*, qualifier=None, uniprot_id=None, uniprot_accession=None, accession=None, sequence_checksum=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
qualifier	string	None	UniProt ACCESSION (e.g., 'P69905'). Do NOT use entry names like 'HBA_HUMAN'. Aliases: uniprot_id, uniprot_accession.
uniprot_id	string	None	Alias for qualifier: UniProt accession (e.g., 'P69905').
uniprot_accession	string	None	Alias for qualifier: UniProt accession (e.g., 'P69905').
accession	string	None	Alias for qualifier. UniProt accession (e.g., 'P04637') -- the same parameter name the UniProt_*_by_accession tools use.
sequence_checksum	string	None	Optional CRC64 checksum of the UniProt sequence.
verbose	bool	True	运行提示开关。

查询实验验证的蛋白质与遗传互作

dnakit.databases.bio_grid_get_interactions(*, gene_names=None, gene_name=None, organism=None, interaction_type=None, evidence_types=None, limit=None, throughput=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
gene_names	array	None	List of gene names or protein identifiers (e.g., ['TP53', 'BRCA1', 'MYC']). Accepts official gene symbols. {"items": {"type": "string"}, "minItems": 1}
gene_name	string	None	Alias for gene_names: single gene symbol (e.g., 'TP53'). Converted to gene_names list automatically.
organism	string	None	Organism name (e.g., 'Homo sapiens', 'Mus musculus') or NCBI taxonomy ID (e.g., '9606' for human, '10090' for mouse). Default: 9606 (human)
interaction_type	string	None	Type of interaction: 'physical' (protein-protein), 'genetic' (epistasis, synthetic lethality), 'both' (all interactions)
evidence_types	array	None	Filter by evidence types (e.g., ['Affinity Capture-MS', 'Two-hybrid'] for physical, ['Synthetic Lethality', 'Dosage Rescue'] for genetic). Leave empty for all evidence types. {"items": {"type": "string"}}
limit	integer	None	Maximum number of interactions to return (default: 100, max: 10000)
throughput	string	None	Filter by throughput: 'low' (low-throughput studies), 'high' (high-throughput screens), or leave empty for all
verbose	bool	True	运行提示开关。

运行前配置：BIOGRID_ACCESS_KEY。

检索病原体 B 细胞与 T 细胞表位

dnakit.databases.bvbrc_search_epitopes(*, taxon_id=None, protein_name=None, epitope_type=None, organism=None, limit=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
taxon_id	string | null	None	NCBI Taxonomy ID for the pathogen organism. Examples: '2697049' (SARS-CoV-2), '11320' (Influenza A), '1773' (M. tuberculosis).
protein_name	string | null	None	Target protein name to filter epitopes. Examples: 'Spike glycoprotein', 'Nucleocapsid protein', 'Replicase polyprotein 1ab'.
epitope_type	string | null	None	Type of epitope. Options: 'Linear peptide', 'Discontinuous peptide'. Most epitopes are linear peptides.
organism	string | null	None	Organism name keyword to search across epitope records. Example: 'coronavirus', 'influenza'.
limit	integer | null	None	Maximum number of results. Default: 25. Max: 100.
verbose	bool	True	运行提示开关。

查询基因或蛋白质的 GO 注释

dnakit.databases.go_get_annotations_for_gene(*, gene_id, rows=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
gene_id	string	必填	A gene identifier such as gene symbol (e.g., 'TP53') or database ID.
rows	integer	None	Maximum number of annotation rows to return. Default: 100. Raise it (e.g. 2000) for a heavily annotated gene such as TP53, which has 1812 annotation rows; lower it to keep responses small.
verbose	bool	True	运行提示开关。

按关键词检索 GO 术语

dnakit.databases.go_search_terms(*, query, verbose=True)

参数	类型	必填 / 默认值	说明与约束
query	string	必填	The keyword to search for, e.g., 'apoptosis' or 'kinase activity'.
verbose	bool	True	运行提示开关。

获取组织特异性蛋白互作网络

dnakit.databases.humanbase_ppi_analysis(*, gene_list=None, tissue=None, max_node=None, interaction=None, string_mode=None, genes=None, top_n=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
gene_list	array	None	List of gene names or symbols to analyze for protein-protein interactions. The gene name should be the official gene symbol, not the synonym. {"items": {"type": "string"}, "minItems": 1}
tissue	string	None	Tissue type for tissue-specific interactions. Use simple names like 'brain', 'heart', 'liver', 'kidney', 'lung', 'blood'. For v3 networks with more cell-type specificity, append '-v3' (e.g., 'brain-v3', 'liver-v3').
max_node	integer	None	Maximum number of nodes to retrieve in the interaction network. Warning: the more nodes, the more time it takes to retrieve the data. Default is 10 (~30 seconds).
interaction	string	None	Specific interaction type to filter by. Available types: 'co-expression', 'interaction', 'tf-binding', 'gsea-microrna-targets', 'gsea-perturbations'. If not specified, all types will be included.
string_mode	boolean	None	Whether to return the result in string mode. If True, the result will be a string of the network graph and the biological processes. If False, the result will be a NetworkX graph and a list of biological processes.
genes	array	None	Alias for gene_list. List of gene symbols to analyze. {"items": {"type": "string"}}
top_n	integer	None	Alias for max_node. Maximum number of network nodes to retrieve.
verbose	bool	True	运行提示开关。

查询免疫表位关联的抗原

dnakit.databases.iedb_get_epitope_antigens(*, structure_id, limit=None, offset=None, order=None, select=None, filters=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
structure_id	integer	必填	IEDB epitope structure ID (from iedb_search_epitopes).
limit	integer	None	Maximum number of rows to return.
offset	integer	None	Pagination offset.
order	string	None	Optional PostgREST order clause.
select	object | None	None	Optional projection list (comma-separated string or array of field names). {"anyOf": [{"type": "string"}, {"type": "array", "items": {"type": "string"}}]}
filters	object	None	Advanced PostgREST filters mapping column -> filter expression. {"additionalProperties": {"type": "string"}}
verbose	bool	True	运行提示开关。

查询免疫表位的 MHC 限制性关联

dnakit.databases.iedb_get_epitope_mhc(*, structure_id, limit=None, offset=None, order=None, select=None, filters=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
structure_id	integer	必填	IEDB epitope structure ID (from iedb_search_epitopes).
limit	integer	None	Maximum number of rows to return.
offset	integer	None	Pagination offset.
order	string	None	Optional PostgREST order clause.
select	object | None	None	Optional projection list (comma-separated string or array of field names). {"anyOf": [{"type": "string"}, {"type": "array", "items": {"type": "string"}}]}
filters	object	None	Advanced PostgREST filters mapping column -> filter expression. {"additionalProperties": {"type": "string"}}
verbose	bool	True	运行提示开关。

检索 B 细胞表位实验记录

dnakit.databases.iedb_search_bcell(*, limit=None, offset=None, order=None, select=None, filters=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
limit	integer	None	Maximum number of rows to return.
offset	integer	None	Pagination offset.
order	string	None	Optional PostgREST order clause.
select	object | None	None	Optional projection list (comma-separated string or array of field names). {"anyOf": [{"type": "string"}, {"type": "array", "items": {"type": "string"}}]}
filters	object	None	Advanced PostgREST filters mapping column -> filter expression. {"additionalProperties": {"type": "string"}}
verbose	bool	True	运行提示开关。

检索免疫表位及其结构编号

dnakit.databases.iedb_search_epitopes(*, sequence_contains=None, structure_type=None, limit=None, offset=None, order=None, select=None, filters=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
sequence_contains	string	None	Sequence fragment to search within linear_sequence using a contains match. Example: 'KVF' finds epitopes containing that motif.
structure_type	string	None	Filter by epitope structure type. Example: 'Linear peptide'.
limit	integer	None	Maximum number of rows to return.
offset	integer	None	Pagination offset.
order	string	None	Optional PostgREST order clause (e.g., 'structure_id.asc').
select	object | None	None	Optional projection list to reduce payload size. Provide a comma-separated string or an array of field names (e.g., ['structure_id','linear_sequence']). {"anyOf": [{"type": "string"}, {"type": "array", "items": {"type": "string"}}]}
filters	object	None	Advanced PostgREST filters mapping column -> filter expression (e.g., {"linear_sequence":"ilike.KVF"}). {"additionalProperties": {"type": "string"}}
verbose	bool	True	运行提示开关。

检索 MHC 相关实验记录

dnakit.databases.iedb_search_mhc(*, limit=None, offset=None, order=None, select=None, filters=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
limit	integer	None	Maximum number of rows to return.
offset	integer	None	Pagination offset.
order	string	None	Optional PostgREST order clause.
select	object | None	None	Optional projection list (comma-separated string or array of field names). {"anyOf": [{"type": "string"}, {"type": "array", "items": {"type": "string"}}]}
filters	object	None	Advanced PostgREST filters mapping column -> filter expression. {"additionalProperties": {"type": "string"}}
verbose	bool	True	运行提示开关。

检索 T 细胞免疫反应实验

dnakit.databases.iedb_search_tcell_assays(*, sequence=None, sequence_contains=None, mhc_class=None, qualitative_measure=None, limit=None, offset=None, select=None, filters=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
sequence	string	None	Exact peptide sequence to search (e.g., GILGFVFTL for influenza M1 epitope).
sequence_contains	string	None	Partial peptide sequence (substring match). Example: 'SIINFEKL'.
mhc_class	string	None	MHC class restriction (I or II).
qualitative_measure	string	None	Filter by assay result.
limit	integer	None	Maximum rows to return.
offset	integer	None	Pagination offset.
select	object | None	None	Columns to return (array of strings). Example: ['tcell_id','linear_sequence','mhc_restriction','qualitative_measure']. {"oneOf": [{"type": "string"}, {"type": "array", "items": {"type": "string"}}]}
filters	object	None	Advanced PostgREST filters (e.g., {"source_organism_iri":"eq.NCBITaxon:11320"}). {"additionalProperties": {"type": "string"}}
verbose	bool	True	运行提示开关。

查询免疫遗传学资源与基因命名规则

dnakit.databases.imgt_get_gene_info(*, operation=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
operation	string	None	提供方操作模式；默认值与允许值见本行约束。
verbose	bool	True	运行提示开关。

定位免疫球蛋白与 TCR 胚系基因检索入口

dnakit.databases.imgt_search_genes(*, operation=None, query=None, gene_type=None, species=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
operation	string	None	提供方操作模式；默认值与允许值见本行约束。
query	string	None	Search query (gene name)
gene_type	string	None	Gene type: IGHV, IGHD, IGHJ, IGKV, IGLV, TRAV, TRBV, etc.
species	string	None	Species name (default: Homo sapiens)
verbose	bool	True	运行提示开关。

按疾病与实验方法检索免疫学研究

dnakit.databases.imm_port_search_studies(*, query, condition_or_disease=None, assay_method=None, research_focus=None, species=None, limit=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
query	string	必填	Search keywords (e.g., 'influenza vaccine', 'COVID-19', 'T cell response', 'malaria')
condition_or_disease	string	None	Filter by disease/condition (e.g., 'influenza', 'malaria', 'HIV', 'dengue', 'tuberculosis'). Client-side substring match.
assay_method	string	None	Filter by assay method (e.g., 'Flow Cytometry', 'ELISPOT', 'RNA sequencing', 'ELISA', 'CyTOF', 'Luminex xMAP'). Client-side substring match.
research_focus	string	None	Filter by research focus (e.g., 'Vaccine Response', 'Infection Response', 'Immune Response', 'Transplantation', 'Autoimmune'). Client-side substring match.
species	string	None	Filter by species (e.g., 'Homo sapiens', 'Mus musculus'). Applied server-side.
limit	integer	None	Maximum number of studies to return (1-100, default 10)
verbose	bool	True	运行提示开关。

查询蛋白质复合物组成与功能

dnakit.databases.intact_get_complex_details(*, complex_ac, format=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
complex_ac	string	必填	Complex AC (Complex Accession) in format 'CPX-XXXXX' (e.g., 'CPX-915', 'CPX-10081'). Get complex ACs from intact_get_interactions_by_complex search results.
format	string	None	返回格式；允许值与服务默认值见当前接口说明。
verbose	bool	True	运行提示开关。

查询以指定蛋白质为中心的互作网络

dnakit.databases.intact_get_interaction_network(*, identifier=None, uniprot_id=None, protein_id=None, gene_symbol=None, gene_name=None, depth=None, limit=None, size=None, format=None, protein_name=None, protein=None, gene=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
identifier	string	None	IntAct identifier, UniProt ID, or gene name. Aliases: uniprot_id, protein_id, gene_symbol, gene_name.
uniprot_id	string	None	Alias for identifier: UniProt accession (e.g., 'P04637').
protein_id	string	None	Alias for identifier: protein identifier.
gene_symbol	string	None	Alias for identifier: gene symbol (e.g., 'BRCA1').
gene_name	string	None	Alias for identifier: gene name.
depth	integer	None	Network depth: 1 for direct interactions only, 2 for 2-hop network, etc. (default: 1)
limit	integer	None	Maximum number of interactions to return (default: 50, max: 200). Alias: size.
size	integer	None	Alias for limit. Maximum number of interactions to return (default: 50).
format	string	None	返回格式；允许值与服务默认值见当前接口说明。
protein_name	string	None	Alias for gene_symbol/identifier. Common protein name (e.g., MDM2, TP53).
protein	string	None	Alias for identifier. Gene symbol or protein name (e.g., 'TP53', 'BRCA1').
gene	string	None	DNAKit optional alias for gene_symbol
verbose	bool	True	运行提示开关。

查询指定蛋白质或基因的互作记录

dnakit.databases.intact_get_interactions(*, identifier, format=None, size=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
identifier	string	必填	IntAct identifier, UniProt ID, or gene name
format	string	None	Response format. Only 'json' is produced by this endpoint.
size	integer | null	None	Maximum number of interactions to return (default 25). IntAct entries commonly have far more -- the response reports the true total as 'hitCount', so raise 'size' to that value to retrieve them all.
verbose	bool	True	运行提示开关。

按关键词检索 IntAct 分子互作

dnakit.databases.intact_search_interactions(*, query, first=None, max=None, format=None, species=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
query	string	必填	Search query string (e.g., protein name, gene name, interaction type)
first	integer	None	First result index for pagination (default: 0)
max	integer	None	Maximum number of results to return (default: 25, max: 100)
format	string	None	返回格式；允许值与服务默认值见当前接口说明。
species	string	None	物种名或 Taxonomy ID；类型与支持值取决于当前接口。
verbose	bool	True	运行提示开关。

查询蛋白质关联的结构域与家族条目

dnakit.databases.inter_pro_get_entries_for_protein(*, accession, verbose=True)

参数	类型	必填 / 默认值	说明与约束
accession	string	必填	UniProt protein accession. Examples: 'P04637' (TP53, 9 entries), 'P00533' (EGFR), 'P01308' (Insulin), 'P38398' (BRCA1).
verbose	bool	True	运行提示开关。

查询蛋白质结构域与功能注释

dnakit.databases.inter_pro_get_protein_domains(*, protein_id=None, accession=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
protein_id	string	None	UniProt protein ID (e.g., P05067, Q9Y6K9)
accession	string	None	DNAKit optional alias for protein_id
verbose	bool	True	运行提示开关。

按关键词与物种检索 KEGG 基因

dnakit.databases.kegg_find_genes(*, keyword=None, organism=None, query=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
keyword	string	None	Search keyword for gene names or descriptions
organism	string	None	Organism code (e.g., 'hsa' for human, 'mmu' for mouse). Optional - searches all organisms if not specified
query	string	None	DNAKit optional alias for keyword
verbose	bool	True	运行提示开关。

查询 KEGG 基因序列、功能与通路

dnakit.databases.kegg_get_gene_info(*, gene_id, verbose=True)

参数	类型	必填 / 默认值	说明与约束
gene_id	string	必填	KEGG gene identifier (e.g., 'hsa:348', 'hsa:3480')
verbose	bool	True	运行提示开关。

查询基因参与的 KEGG 通路

dnakit.databases.kegg_get_gene_pathways(*, gene_id=None, gene_symbol=None, gene=None, organism=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
gene_id	string	None	KEGG gene identifier in organism:id format. Examples: 'hsa:7157' (human TP53), 'hsa:672' (human BRCA1), 'mmu:22059' (mouse Trp53). Use organism prefix: hsa=human, mmu=mouse, rno=rat, dme=fly, sce=yeast.
gene_symbol	string	None	Alias for gene_id: human gene symbol (e.g. 'TP53', 'BRCA1'). Auto-resolved to KEGG gene ID using organism='hsa'.
gene	string	None	Alias for gene_id: human gene symbol (e.g. 'TP53', 'EGFR').
organism	string	None	KEGG organism code for gene symbol resolution (default: 'hsa' for human). Used only when gene_symbol is provided instead of gene_id.
verbose	bool	True	运行提示开关。

列出 KEGG 通路中的成员基因

dnakit.databases.kegg_get_pathway_genes(*, pathway_id, verbose=True)

参数	类型	必填 / 默认值	说明与约束
pathway_id	string	必填	KEGG pathway identifier (e.g., 'hsa04115' for p53 signaling pathway, 'hsa04110' for cell cycle, 'hsa04210' for apoptosis). Use organism prefix: hsa=human, mmu=mouse.
verbose	bool	True	运行提示开关。

查询 KEGG 通路的基因、化合物与反应

dnakit.databases.kegg_get_pathway_info(*, pathway_id, verbose=True)

参数	类型	必填 / 默认值	说明与约束
pathway_id	string	必填	KEGG pathway identifier (e.g., 'hsa00010', 'path:hsa00010')
verbose	bool	True	运行提示开关。

按关键词检索 KEGG 通路

dnakit.databases.kegg_search_pathway(*, keyword, verbose=True)

参数	类型	必填 / 默认值	说明与约束
keyword	string	必填	Search keyword for pathway names or descriptions (e.g., 'diabetes', 'metabolism')
verbose	bool	True	运行提示开关。

按编号查询 NCBI 蛋白质记录摘要

dnakit.databases.ncbiprotein_get_summary(*, id, verbose=True)

参数	类型	必填 / 默认值	说明与约束
id	string	必填	NCBI Protein ID (GI number or accession). Can be a single ID or comma-separated list. Examples: '119395750' (keratin 1, NP_006112), '4507879' (TP53, NP_000537), '4503747' (EGFR, NP_005219). GI numbers can be obtained from NCBI Gene genomic info or from BLAST results.
verbose	bool	True	运行提示开关。

查询 PANTHER 跨物种直系同源基因

dnakit.databases.panther_ortholog(*, gene_id, organism=None, target_organism=None, ortholog_type=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
gene_id	string	必填	Gene identifier - UniProt accession, Ensembl ID, or gene symbol. Examples: 'P04637' (TP53), 'P38398' (BRCA1).
organism	integer | null	None	Source organism NCBI taxonomy ID. Default: 9606 (human).
target_organism	integer | null	None	Target organism NCBI taxonomy ID. Default: 10090 (mouse). Others: 10116 (rat), 7227 (fly), 6239 (worm).
ortholog_type	string | null	None	Ortholog type filter. Options: 'LDO' (least diverged ortholog, default), 'O' (all orthologs), 'P' (paralogs), 'X' (xenologs), 'LDX' (least diverged xenolog), 'all' (all types).
verbose	bool	True	运行提示开关。

读取 PDB 结构坐标文件文本

dnakit.databases.pdb_get_structure(*, pdb_id, format='cif', max_bytes=10000000, verbose=True)

参数	类型	必填 / 默认值	说明与约束
pdb_id	string	必填	PDB 结构编号，支持 4 字符编号或 pdb_ 加 8 字符编号。
format	string	'cif'	返回格式；允许值与服务默认值见当前接口说明。
max_bytes	integer	10000000	坐标文件大小上限，1–100000000 字节。
verbose	bool	True	运行提示开关。

映射 PDB 链与 UniProt 残基区间

dnakit.databases.pdbe_get_uniprot_mappings(*, pdb_id=None, uniprot_id=None, limit=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
pdb_id	string	None	PDB identifier (4-character code). Examples: '4hhb' (hemoglobin), '1cbs' (CRABP2), '6lu7' (SARS-CoV-2 main protease).
uniprot_id	string	None	UniProt accession；反向结构映射时不要同时传 pdb_id。
limit	integer	None	当前请求的返回数量上限；不是全库命中总数。
verbose	bool	True	运行提示开关。

按覆盖度与分辨率筛选蛋白质结构

dnakit.databases.pdbe_sifts_get_best_structures(*, uniprot_accession, limit=None, offset=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
uniprot_accession	string	必填	UniProt accession for the protein. Examples: 'P04637' (TP53), 'P00533' (EGFR), 'P38398' (BRCA1), 'P01308' (Insulin).
limit	integer | null	None	Maximum number of entries to return (default 50, max 500). Proteins such as P04637 (TP53) have hundreds of structure-chain entries; raise this or use 'offset' to reach past the first page.
offset	integer | null	None	Zero-based index of the first entry to return, for paging through the ranked list (e.g. offset=50 returns entries 51-100). Default: 0.
verbose	bool	True	运行提示开关。

查询蛋白质 Pfam 结构域与位置

dnakit.databases.pfam_get_protein_annotations(*, accession, verbose=True)

参数	类型	必填 / 默认值	说明与约束
accession	string	必填	UniProt protein accession. Examples: 'P04637' (TP53, 4 domains), 'P00533' (EGFR), 'P68431' (Histone H3.1), 'P38398' (BRCA1), 'P01308' (Insulin).
verbose	bool	True	运行提示开关。

查询植物通路的反应与注释

dnakit.databases.plant_reactome_get_pathway(*, pathway_id, verbose=True)

参数	类型	必填 / 默认值	说明与约束
pathway_id	string	必填	Plant Reactome stable identifier. Format: R-{species_code}-{number}. Examples: 'R-OSA-1119312' (Photorespiration in rice), 'R-OSA-1119519' (Calvin cycle in rice).
verbose	bool	True	运行提示开关。

列出植物通路数据库覆盖的物种

dnakit.databases.plant_reactome_list_species(*, verbose=True)

参数	类型	必填 / 默认值	说明与约束
verbose	bool	True	运行提示开关。

检索植物代谢与调控通路

dnakit.databases.plant_reactome_search_pathways(*, query, species=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
query	string	必填	Search query for plant pathways. Examples: 'photosynthesis', 'Calvin cycle', 'flavonoid biosynthesis', 'nitrogen fixation', 'auxin signaling'.
species	string | null	None	Species name to filter results. Examples: 'Oryza sativa', 'Arabidopsis thaliana', 'Zea mays'. Default: all species.
verbose	bool	True	运行提示开关。

查询蛋白质序列特征与修饰位点

dnakit.databases.proteins_api_get_features(*, accession, format=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
accession	string | array	必填	UniProt protein accession(s). Can be a single accession (e.g., 'P05067'), comma-separated string (e.g., 'P05067,P04637'), or list (e.g., ['P05067', 'P04637']). Use UniProt search or ebi_search_domain with domain='uniprot' to find valid accessions.
format	string	None	Response format. JSON is recommended for most use cases.
verbose	bool	True	运行提示开关。

按基因、蛋白名称或编号检索蛋白质

dnakit.databases.proteins_api_search(*, query=None, size=None, offset=None, format=None, gene_symbol=None, gene=None, reviewed=None, organism=None, taxid=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
query	string	None	Search query. Can be: gene name (e.g., 'BRCA1', 'TP53'), protein name (e.g., 'insulin', 'hemoglobin'), or UniProt accession (e.g., 'P05067'). The tool automatically determines the appropriate search parameter.
size	integer	None	Maximum number of results to return (default: 25, max: 100)
offset	integer	None	Offset for pagination (default: 0)
format	string	None	Response format. JSON is recommended for most use cases.
gene_symbol	string	None	Alias for query. Gene symbol to search (e.g., TP53, BRCA1).
gene	string	None	Alias for query. Gene name to search.
reviewed	boolean	None	If true, return only reviewed Swiss-Prot entries. If false or omitted, includes unreviewed TrEMBL entries.
organism	string	None	Restrict the search to an organism by NAME (e.g. 'Klebsiella pneumoniae', 'Escherichia coli'); use 'taxid' for numeric NCBI taxonomy ids. A purely numeric value here (e.g. '9606') is auto-corrected to a taxid lookup and the response reports it in 'normalization_note'. By default a gene/protein-name search is biased toward human (taxid 9606); set this for non-human proteins. If omitted and no human match is found, the search auto-widens to all organisms.
taxid	string	None	Restrict the search to an NCBI taxonomy id (e.g. '573' for Klebsiella pneumoniae, '562' for E. coli). Alternative to 'organism' for precise scoping.
verbose	bool	True	运行提示开关。

查询基因产物的 GO 注释与证据代码

dnakit.databases.quick_go_annotations_by_gene(*, gene_product_id, aspect=None, taxon_id=None, limit=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
gene_product_id	string	必填	Gene product identifier, typically a UniProtKB accession. Format: 'UniProtKB:P04637' (TP53), 'UniProtKB:P38398' (BRCA1), 'UniProtKB:P00533' (EGFR).
aspect	string | null	None	Filter by GO aspect: 'biological_process', 'molecular_function', or 'cellular_component'. Default: all aspects.
taxon_id	integer | null	None	Filter by NCBI taxonomy ID. Example: 9606 (human), 10090 (mouse).
limit	integer	None	Maximum number of annotations to return. Default: 25, max: 100.
verbose	bool	True	运行提示开关。

查询 PDB 结构实验方法与元数据

dnakit.databases.rcsbdata_get_entry(*, pdb_id=None, entry_id=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
pdb_id	string	None	PDB entry ID (4 characters). Examples: '4HHB' (hemoglobin), '1TUP' (p53-DNA complex), '1M17' (EGFR kinase), '6LU7' (SARS-CoV-2 main protease).
entry_id	string	None	Alias for pdb_id (the RCSB-native term; the REST endpoint is /core/entry/{id}). Provide either pdb_id or entry_id.
verbose	bool	True	运行提示开关。

以下参数组至少提供一组：pdb_id; entry_id。

检索 Reactome 通路、反应与生物实体

dnakit.databases.reactome_content_search(*, query, species=None, types=None, rows=None, start=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
query	string	必填	Search query. Examples: 'apoptosis', 'TP53', 'cell cycle', 'DNA repair', 'insulin signaling'.
species	string	None	Species name for filtering results. Default: 'Homo sapiens'. Other options: 'Mus musculus', 'Rattus norvegicus', 'Danio rerio', 'Drosophila melanogaster'.
types	string	None	Entity type to search. Options: 'Pathway', 'Reaction', 'Complex', 'Protein', 'SmallMolecule'. Default: 'Pathway'.
rows	integer | null	None	Number of results to return per page (1-1000). Omit to use Reactome's default page of 10. Queries often match far more than that ('DNA repair' in Homo sapiens matches 455 pathways), so raise this to see beyond the first page. Compare the returned 'count' against 'total_results' to know how much you are holding.
start	integer | null	None	Zero-based offset of the first result to return, for paging through large result sets. Use together with 'rows' (e.g. rows=50 with start=0, then start=50). Omit to start at the first result.
verbose	bool	True	运行提示开关。

查询生物反应的参与分子与复合物

dnakit.databases.reactome_get_participants(*, stId, verbose=True)

参数	类型	必填 / 默认值	说明与约束
stId	string	必填	Event Stable ID (reaction or pathway, e.g., 'R-HSA-111289'). To find reaction IDs, use Reactome_get_pathway_reactions with a pathway ID. To find pathway IDs, use Reactome_list_top_pathways.
verbose	bool	True	运行提示开关。

查询 Reactome 通路完整信息

dnakit.databases.reactome_get_pathway(*, stId, verbose=True)

参数	类型	必填 / 默认值	说明与约束
stId	string	必填	Pathway Stable ID (e.g., 'R-HSA-73817'). To find pathway IDs, use Reactome_list_top_pathways to get top-level pathways, or Reactome_map_uniprot_to_pathways if you have a UniProt protein ID.
verbose	bool	True	运行提示开关。

列出通路包含的反应与子通路

dnakit.databases.reactome_get_pathway_reactions(*, stId, verbose=True)

参数	类型	必填 / 默认值	说明与约束
stId	string	必填	Pathway Stable ID (e.g., 'R-HSA-73817'). To find pathway IDs, use Reactome_list_top_pathways to get top-level pathways, or Reactome_map_uniprot_to_pathways if you have a UniProt protein ID.
verbose	bool	True	运行提示开关。

将 UniProt 蛋白映射到 Reactome 通路

dnakit.databases.reactome_map_uniprot_to_pathways(*, uniprot_id=None, id=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
uniprot_id	string	None	UniProt protein accession (e.g., 'P04637' for TP53, 'P00533' for EGFR)
id	string	None	DNAKit optional alias for uniprot_id
verbose	bool	True	运行提示开关。

查询 STRING 蛋白质综合功能注释

dnakit.databases.string_get_functional_annotations(*, identifiers, species=None, category=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
identifiers	string	必填	Protein identifier (gene name or STRING ID). Examples: 'TP53', 'BRCA1', 'EGFR', '9606.ENSP00000269305'.
species	integer	None	NCBI taxonomy ID (default 9606 for human). Examples: 9606 (human), 10090 (mouse), 7227 (fly), 6239 (worm).
category	string	None	Filter by annotation category. Options: 'Process' (GO BP), 'Function' (GO MF), 'Component' (GO CC), 'KEGG', 'RCTM' (Reactome), 'WikiPathways', 'InterPro', 'Pfam', 'HPO', 'DISEASES', 'TISSUES', 'COMPARTMENTS', 'Keyword'. Leave null for all categories.
verbose	bool	True	运行提示开关。

查询蛋白质互作伙伴与置信度

dnakit.databases.string_get_interaction_partners(*, identifiers=None, species=None, limit=None, required_score=None, protein_ids=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
identifiers	string	None	Protein identifier (gene name or STRING ID). Examples: 'TP53', 'BRCA1', 'EGFR', '9606.ENSP00000269305'
species	integer	None	NCBI taxonomy ID (9606=human, 10090=mouse, 7227=fly, 6239=worm)
limit	integer	None	Maximum number of interaction partners to return
required_score	integer | null	None	Minimum combined STRING score (0-1000). 400=medium, 700=high, 900=highest confidence.
protein_ids	array | string	None	蛋白标识；输入列表或字符串类型见本行类型说明。 {"items": {"type": "string"}}
verbose	bool	True	运行提示开关。

构建查询蛋白及其邻居的互作网络

dnakit.databases.string_get_network(*, identifiers=None, species=None, limit=None, required_score=None, protein_ids=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
identifiers	string	None	Protein identifier(s). For multiple proteins, separate with '\r' (carriage return character). Examples: 'TP53', 'BRCA1\rBRCA2\rTP53', '9606.ENSP00000269305'
species	integer	None	NCBI taxonomy ID. Examples: 9606 (human), 10090 (mouse), 7227 (Drosophila), 6239 (C. elegans)
limit	integer	None	Maximum number of interaction partners to include (per protein). 0 = only interactions among input proteins.
required_score	integer | null	None	Minimum combined STRING score (0-1000). 400=medium, 700=high, 900=highest confidence. Default: 400.
protein_ids	array | string	None	蛋白标识；输入列表或字符串类型见本行类型说明。 {"items": {"type": "string"}}
verbose	bool	True	运行提示开关。

检验蛋白质集合的互作富集程度

dnakit.databases.string_ppi_enrichment(*, protein_ids, species=None, confidence_score=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
protein_ids	array	必填	List of protein identifiers (UniProt IDs, gene names, Ensembl IDs). Minimum 3 proteins required. {"items": {"type": "string"}, "minItems": 3}
species	integer	None	NCBI taxonomy ID (default: 9606 for human)
confidence_score	number	None	Minimum confidence score for counting interactions (0-1, default: 0.4)
verbose	bool	True	运行提示开关。

逐残基标注结合界面、口袋与溶剂暴露

dnakit.databases.structure_annotate_per_residue(*, operation=None, pdb_id=None, pdb_content=None, target_chain=None, partner_chains=None, ligand_resnames=None, distance_cutoff=None, core_rsa_cutoff=None, include_secondary_structure=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
operation	string	None	Operation type
pdb_id	string | null	None	4-character PDB ID (e.g. '6VJJ'). If provided, the structure is downloaded from RCSB. Exactly one of pdb_id or pdb_content must be supplied.
pdb_content	string | null	None	Raw PDB file content (string). Use when the structure is local (e.g. AlphaFold-predicted, in-memory).
target_chain	string	None	Chain ID of the protein to annotate (e.g. 'A').
partner_chains	array	None	Chain IDs that define the binding partner(s). Used to compute the interface. Empty list = no interface analysis (all dist_partner values null). {"items": {"type": "string"}, "default": []}
ligand_resnames	array	None	Three-letter residue names of bound ligands to define the ligand pocket (e.g. ['GNP', 'MG'] for GTP-analogue + magnesium). Searched across all chains. Empty list = no ligand-pocket analysis. {"items": {"type": "string"}, "default": []}
distance_cutoff	number	None	Distance cutoff in angstroms for interface and ligand-pocket classification.
core_rsa_cutoff	number	None	Relative solvent accessibility threshold below which a residue is classified as 'core'.
include_secondary_structure	boolean	None	If true and pdb_id is provided, fetch per-residue secondary structure (helix/strand/coil) from PDBe REST. Only meaningful for deposited PDB entries; ignored when pdb_content is supplied.
verbose	bool	True	运行提示开关。

提取 UniProt 蛋白质变异与相关注释

dnakit.databases.uni_prot_get_disease_variants_by_accession(*, accession, verbose=True)

参数	类型	必填 / 默认值	说明与约束
accession	string	必填	UniProtKB accession, e.g., P05067.
verbose	bool	True	运行提示开关。

按编号读取完整 UniProt 条目

dnakit.databases.uni_prot_get_entry_by_accession(*, accession, compact=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
accession	string	必填	UniProtKB entry accession, e.g., P05067.
compact	boolean	None	Return a bounded summary instead of the complete UniProtKB JSON entry. Defaults to true to avoid oversized LLM outputs. Set compact=false only when you explicitly need the raw UniProtKB JSON.
verbose	bool	True	运行提示开关。

提取蛋白质结构域、活性位点与序列特征

dnakit.databases.uni_prot_get_features_by_accession(*, accession, verbose=True)

参数	类型	必填 / 默认值	说明与约束
accession	string	必填	UniProtKB accession, e.g., 'P04637' (TP53) or 'P05067' (APP).
verbose	bool	True	运行提示开关。

提取 UniProt 蛋白质功能注释

dnakit.databases.uni_prot_get_function_by_accession(*, accession, verbose=True)

参数	类型	必填 / 默认值	说明与约束
accession	string	必填	UniProtKB accession, e.g., P05067.
verbose	bool	True	运行提示开关。

提取 UniProt 标准蛋白质序列

dnakit.databases.uni_prot_get_sequence_by_accession(*, accession, verbose=True)

参数	类型	必填 / 默认值	说明与约束
accession	string	必填	UniProtKB accession, e.g., P05067.
verbose	bool	True	运行提示开关。

按组合检索式查询 UniProt 蛋白质

dnakit.databases.uni_prot_search(*, query, organism=None, limit=None, min_length=None, max_length=None, fields=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
query	string	必填	Search query using UniProt syntax. Simple: 'MEIOB', 'insulin'. Field searches: 'gene:TP53', 'protein_name:insulin', 'taxonomy_id:9606', 'reviewed:true'. Ranges: 'length:[100 TO 500]', 'mass:[20000 TO 50000]'. Wildcards: 'gene:MEIOB*'. Boolean: 'gene:TP53 AND taxonomy_id:9606', 'tissue:brain OR tissue:liver', 'reviewed:true NOT fragment:true'. Use parentheses for grouping: '(taxonomy_id:9606 OR taxonomy_id:10090) AND gene:TP53'. Taxon scoping: use 'taxonomy_id:<taxid>' (matches the whole lineage, so strain-level entries under a species taxid are included) or 'organism_name:"..."'. A bare 'organism:' auto-converts, and 'organism_id:<taxid>' is rewritten to 'taxonomy_id:<taxid>' with a note in data.normalization_note, because organism_id matches only the exact organism node and misses strain-level entries.
organism	string	None	Optional organism filter. Use common names ('human', 'mouse', 'rat', 'yeast') or taxonomy ID ('9606'). Automatically combined with query using AND. Will not duplicate if organism is already in query.
limit	integer	None	Maximum number of results to return (default: 25, max: 500). Accepts string or integer.
min_length	integer	None	Minimum sequence length. Auto-converts to an open-ended length range query (min to unbounded).
max_length	integer	None	Maximum sequence length. Auto-converts to an open-ended length range query (unbounded to max).
fields	array	None	List of field names to return (e.g., ['accession','gene_primary','length','organism_name']). When specified, returns raw API response with requested fields. Common fields: accession, id, gene_names, gene_primary, protein_name, organism_name, organism_id, length, mass, sequence, reviewed, cc_function. See UniProt API docs for full list. Default (no fields): returns formatted response with accession, id, protein_name, gene_names, organism, length. {"items": {"type": "string"}}
verbose	bool	True	运行提示开关。

按通路标题检索 WikiPathways

dnakit.databases.wiki_pathways_search(*, query, organism=None, limit=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
query	string	必填	Text to search, e.g., p53
organism	string	None	Optional organism filter, e.g., 'Homo sapiens'
limit	integer	None	当前请求的返回数量上限；不是全库命中总数。
verbose	bool	True	运行提示开关。