Version Compatibility

Reference examples tested with: BioPython 1.83+, scanpy 1.10+

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 I/O

"Read a PDB file" → Parse protein structure files (PDB, mmCIF, MMTF), download from RCSB PDB, and write structures to various formats.

• Python: Bio.PDB.PDBParser().get_structure('id', 'file.pdb'), Bio.PDB.MMCIFParser()

Parse, download, and write protein structure files in PDB, mmCIF, and MMTF formats.

Required Imports