Version Compatibility

Reference examples tested with: BioPython 1.83+, numpy 1.26+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Structure Modification

"Extract a chain from a PDB file" → Remove/add atoms, residues, or chains; transform coordinates; modify B-factors and occupancies; build structures programmatically.

• Python: Bio.PDB.PDBIO() with Select subclass for filtering, Bio.PDB.Superimposer() for transforms

Transform coordinates, remove/add entities, modify properties, and build structures programmatically.

Required Imports