- alignDNA
- alignRNA
- areResNumbersAligned
- createPurelyNonPolyEntities
Given all chains of all models find entities for the nonpolymers and water
chains within them, assig
- findEntitiesFromAlignment
- findNonPolyEntityWithDescription
- findPolyEntities
Utility method that employs some heuristics to find the EntityInfos for the
polymeric chains given i
- findUniqueEntities
Utility method to obtain a list of unique entities from the chainIds2entities
map
- getDNASequence
Returns the DNASequence or null if one can't be created
- getNumGaps
- getNumGapsQuery
- getNumGapsTarget