UniProt ID to PDB ID and Chain

Usage

There is two method to use this program: call API or CLI

CLI

Run file, and input UniProtID, program will show a table of reuslt like:

+--------------+--------+-----------+
| UniProtKB_AC | PDB ID | PDB Chain |
+--------------+--------+-----------+
|    P02768    |  1AO6  |     A     |
|    P02768    |  1AO6  |     B     |
|    P02768    |  1BJ5  |     A     |
|    P02768    |  1BKE  |     A     |
+--------------+--------+-----------+

If you are first use, please import first:python uniprotToPdb.py -m import -f <filename>

File is provide by UniProt at UniProt FTP Server, download idmapping_selected.tab.gz

Import will take minutes or hours, be patience.

API

uniprotToPdb.importUniToPdb(fileName)

Input: fileName: id mapping file from UniProt

Action: import data to mysql

Class Method

There is one class: DBUniprotToPdb

uniprotToPdb.DBUniprotToPdb.query(uniprotId)

Input: uniprotId: UniProtKB_AC ID, like P12345

Return: selectRow, rowData:

• selectRow: row number of query
• rowData: A list of Dictionary, like [{'uniprotId':'P12345','pdbId':'100d','pdbChain':'A'},...]

Note: If record number larger than 100, please use DBUniprotToPdb.queryAll()

uniprotToPdb.DBUniProtToPdb.queryOne(uniprotId)

Input: uniprotId: UniProtKB_AC ID, like P12345

Return: selectRow, rowData:

• selectRow: should be 1
• rowData: A list of Dictionary, like [{'uniprotId':'P12345','pdbId':'100d','pdbChain':'A'}]

uniprotToPdb.DBUniProtToPdb.queryAll(uniprotId)

Input: uniprotId: UniProtKB_AC ID, like P12345

Return: selectRow, rowData:

• selectRow: row number of query
• rowData: A list of Dictionary, like [{'uniprotId':'P12345','pdbId':'100d','pdbChain':'A'},...]

Note: No limit to large query, use carefully.

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Dependencies

• tqdm
• PyMySQL
• PrettyTable

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Thanks

Thanks to UniProt.

The data from UniProt is shared under the Creative Commons Attribution 4.0 International (CC BY 4.0) License (https://creativecommons.org/licenses/by/4.0/).

License

Code is shared under GNU General Public License v3.0

Data is shared under the Creative Commons Attribution 4.0 International (CC BY 4.0) License