I recently got tripped up by the fact that AtomCache's constructor disables alignSeqRes and parseSecStruc specifically.

// we don't need this here
params.setAlignSeqRes(false);
// no secstruc either
params.setParseSecStruc(false);

The current default for FileParsingParams.alignSeqRes is true. I would have expected cache.setFileParsingParams(new FileParsingParams()) to reset a cache to its default state, but this is not true.

Would anyone object if I deleted the above two lines, making alignSeqRes=true the default?