PDB2SQL¶
This module is based on sqlite3
.
- class pdb2sql.pdb2sqlcore.pdb2sql(pdbfile, tablename='atom', **kwargs)[source]¶
Create a SQL database with PDB data.
Notes
Only “ATOM” data of PDB is parsed, other items e.g. HETATM are not ignored.
Examples
>>> db = pdb2sql.pdb2sql('3CRO.pdb')
Process PDB¶
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Read pdb file or data to a list. |
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Export a PDB file. |
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Convert SQL data to PDB formatted lines. |
Get SQL Data¶
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Exectute simple SQL query to extract values. |
Get SQL column names. |
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Get the chain IDs. |
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Get the residue sequence. |
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Shortcut to get the xyz coordinates. |
Set SQL data¶
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Update the database with given values. |
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Add an new column to the ATOM table with same value for each row. |
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Update a single column. |
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Update the xyz coordinates. |
Print SQL data¶
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Print out SQL ATOM table. |
Print out SQL column names. |