public static void calculateScores ( MultipleAlignment alignment ) throws StructureException { // Put RMSD List < Atom [ ] > trans = MultipleAlignmentTools . transformAtoms ( alignment ) ; alignment . putScore ( RMSD , getRMSD ( trans ) ) ; // Put AvgTM-Score List < Integer > lengths = new ArrayList < Integer > ( alignment . size ( ) ) ; for ( Atom [ ] atoms : alignment . getAtomArrays ( ) ) { lengths . add ( atoms . length ) ; } alignment . putScore ( AVGTM_SCORE , getAvgTMScore ( trans , lengths ) ) ; }
Calculates and puts the RMSD and the average TM - Score of the MultipleAlignment .