Deprecated API

since biojava 5.0 this does not apply anymore. Chains contain either polymeric groups or non-polymeric groups

use Chain.getId() instead

use Chain.setId(String asymId) instead

use setStructure instead

use Structure.getPolyChainByPDB(String) instead

use Structure.getEntityById(int) instead

From BioJava 4.2, use getStructureIdentifier().toCanonical().getRanges()

Use StructureIdentifier.reduce(Structure) instead (v. 4.2.0)

use Chain.isWaterOnly() instead.

use Chain.isProtein() instead.