public static IEnumerable <FusionDesignInfo> GetSplices(IChain nPeptide, Range nAllowedSpliceRange, IChain cPeptide, Range cAllowedSpliceRange, int topX = DefaultTopX)
{
List <FusionDesignInfo> splices = new List <FusionDesignInfo>();
int minAlignmentLength = 8;
float maxRmsd = 0.25f;
// Find all alignments and remove those that are not between the desired ranges
// If this becomes a bottleneck, could specify allowed alignment ranges
List <SequenceAlignment> alignments = Fusion.GetAlignmentsPreservingFullSsBlocks(nPeptide, cPeptide, SS.Helix, minAlignmentLength, maxRmsd);
alignments.RemoveAll(a => !(nAllowedSpliceRange.Start <= a.Range1.Start && a.Range1.End <= nAllowedSpliceRange.End));
alignments.RemoveAll(a => !(cAllowedSpliceRange.Start <= a.Range2.Start && a.Range2.End <= cAllowedSpliceRange.End));
foreach (SequenceAlignment alignment in alignments)
{
Matrix alignmentTransform = Rmsd.GetRmsdTransformForResidues(nPeptide, alignment.Range1.Start, alignment.Range1.End, cPeptide, alignment.Range2.Start, alignment.Range2.End);
IChain copy1 = new Chain(nPeptide);
IChain copy2 = new Chain(cPeptide);
copy1.Transform(alignmentTransform);
IChain[] clashCheckPeptides = new IChain[] { copy1, copy2 };
if (Clash.GetInterSetBackboneClashes(clashCheckPeptides, new int[] { 0, alignment.Range2.End + 1 }, new int[] { alignment.Range1.Start - 1, copy2.Count - 1 }))
{
continue;
}
// Create the spliced peptide
IChain splicedPeptide = Fusion.GetChain(
new IChain[] { copy1, copy2 },
new SequenceAlignment[] { alignment },
new IEnumerable <int>[] { new int[] { }, new int[] { } });
// Save it
FusionDesignInfo spliceInfo = new FusionDesignInfo();
Range[] originalRanges = null;
Range[] finalRanges = null;
Fusion.GetIdentityRanges(clashCheckPeptides, new SequenceAlignment[] { alignment }, out originalRanges, out finalRanges);
spliceInfo.Peptide = splicedPeptide;
spliceInfo.OriginalChains = new IChain[] { nPeptide, cPeptide };
spliceInfo.PdbOutputChains = new IChain[] { splicedPeptide, copy1, copy2 };
spliceInfo.ImmutablePositions = new int[] { };
spliceInfo.IdentityRanges = finalRanges;
spliceInfo.OriginalRanges = originalRanges;
splices.Add(spliceInfo);
splices.Sort((a, b) => b.Score.CompareTo(a.Score));
if (splices.Count > topX)
{
splices.RemoveAt(topX);
}
}
return(splices);
}