public static TransformSequenceAlignment Reversed(TransformSequenceAlignment other)
{
TransformSequenceAlignment result = new TransformSequenceAlignment(other);
result.Reverse();
return(result);
}
/// <summary>
/// Returns sequence alignments that could join all of the input structures
/// </summary>
/// <param name="structures"></param>
/// <param name="chains">IChain indices for each structure that should be </param>
/// <returns></returns>
public static TransformSequenceAlignment[][] GetRepeatFilteredTransformAlignments(IStructure[] structures, int[][] chains)
{
TransformSequenceAlignment[][] result = new TransformSequenceAlignment[structures.Length - 1][];
for (int i = 0; i < structures.Length - 1; i++)
{
List <TransformSequenceAlignment> alignments = new List <TransformSequenceAlignment>();
foreach (int chainIndex1 in chains[i])
{
foreach (int chainIndex2 in chains[i + 1])
{
IChain chain1 = structures[i][chainIndex1];
IChain chain2 = structures[i + 1][chainIndex2];
// Shorten the
List <TransformSequenceAlignment> chainAlignments = GetRepeatFilteredTransformAlignments(structures[i], chainIndex1, false, structures[i + 1], chainIndex2, i != structures.Length - 2 && structures[i + 1].Count == 1, SS.Helix | SS.Extended);
foreach (TransformSequenceAlignment alignment in chainAlignments)
{
alignment.ChainIndex1 = chainIndex1;
alignment.ChainIndex2 = chainIndex2;
}
alignments.AddRange(chainAlignments);
}
}
result[i] = alignments.ToArray();
}
return(result);
}
public TransformSequenceAlignment(TransformSequenceAlignment other)
: this(other.ChainIndex1, other.Range1, other.ChainIndex2, other.Range2)
{
Align2 = other.Align2;
Align1 = other.Align1;
Centroid1 = other.Centroid1;
Centroid2 = other.Centroid2;
}
/// <summary>
/// Find splicing alignment ranges for two peptides that would retain a full secondary structure block for at least one of the two peptides. This prevents
/// short splice overlaps that remove some of the secondary structure on both sides of the alignment. Basically, the alignment must result in either:
/// 1) one secondary structure block being fully included in the other
/// 2) the N-terminal peptide being spliced has the end of its block fully in the resultant alignment, thus preserving the entire N-side block
/// 3) the C-terminal peptide being spliced has the start of its block fully in the resultant alignment, thus preserving the entire C-side block
/// </summary>
/// <param name="chain1"></param>
/// <param name="chain2"></param>
/// <param name="allowedTypes"></param>
/// <param name="minAlignmentLength"></param>
/// <returns></returns>
public static List <TransformSequenceAlignment> GetTransformAlignments(IChain chain1, IChain chain2, SS allowedTypes, int minAlignmentLength = DefaultMinAlignmentLength, float maxRmsd = DefaultRmsdThreshold)
{
List <TransformSequenceAlignment> alignments = new List <TransformSequenceAlignment>();
List <SSBlock> nBlocks = SecondaryStructure.GetPhiPsiSSBlocksOfType(chain1, allowedTypes, minAlignmentLength).Where(block => block.Length >= minAlignmentLength).ToList();
List <SSBlock> cBlocks = SecondaryStructure.GetPhiPsiSSBlocksOfType(chain2, allowedTypes, minAlignmentLength).Where(block => block.Length >= minAlignmentLength).ToList();
// Previously, calling this function with peptides A,B vs B,A returns different numbers of alignments. The original intent was for the first chain passed in to be at the
// N-terminus and the second at the C-terminus (post-fusion), so these post-fusion lengths were being calculated here and culled differently based on order.
foreach (SSBlock nBlock in nBlocks)
{
foreach (SSBlock cBlock in cBlocks)
{
for (int nAlignmentOfBlockC = nBlock.End - minAlignmentLength + 1; nAlignmentOfBlockC + cBlock.Length >= nBlock.Start + minAlignmentLength; nAlignmentOfBlockC--)
{
// Figure out the start and ends of the overlap region
int nStart = Math.Max(nBlock.Start, nAlignmentOfBlockC);
int nEnd = Math.Min(nBlock.End, nAlignmentOfBlockC + cBlock.Length - 1);
int alignmentLength = nEnd - nStart + 1;
int cStart = Math.Max(cBlock.Start, cBlock.Start + (nStart - nAlignmentOfBlockC));
int cEnd = cStart + alignmentLength - 1;
//Debug.WriteLine("Comparing {0}-{1} vs {2}-{3}", nStart, nEnd, cStart, cEnd);
Debug.Assert(nBlock.Start <= nStart && nEnd <= nBlock.End);
Debug.Assert(cBlock.Start <= cStart && cEnd <= cBlock.End);
Debug.Assert(nEnd - nStart == cEnd - cStart);
//bool cFullyIncluded = (cBlock.Start == cStart && cBlock.End == cEnd);
//bool nFullyIncluded = (nBlock.Start == nStart && nBlock.End == nEnd);
//if (!nFullyIncluded && !cFullyIncluded && cStart != cBlock.Start && nEnd != nBlock.End)
// continue;
Trace.Assert(nEnd - nStart + 1 >= minAlignmentLength);
float rmsd = float.NaN;
Matrix matrix = Rmsd.GetRmsdAndTransform(chain1, nStart, nEnd, chain2, cStart, cEnd, out rmsd);
bool fail = rmsd > maxRmsd;
#if DEBUG && false
float rmsd2 = float.NaN;
Matrix matrix2 = Rmsd.GetRmsdAndTransform(chain2, cStart, cEnd, chain1, nStart, nEnd, out rmsd2);
bool fail2 = rmsd2 > maxRmsd;
Trace.Assert(fail == fail2);
#endif
if (rmsd > maxRmsd)
{
continue;
}
TransformSequenceAlignment alignment = new TransformSequenceAlignment(nStart, nEnd, cStart, cEnd);
alignment.Centroid1 = Geometry.GetCenterNCAC(chain1[nStart, nEnd]);
alignment.Centroid2 = Geometry.GetCenterNCAC(chain2[cStart, cEnd]);
alignment.Align1 = matrix;
alignment.Align2 = Matrix.Invert(matrix);
alignments.Add(alignment);
}
}
}
return(alignments);
}
/// <summary>
/// Tests whether either N fused to C or C fused to N has a valid combination. If both are being tested, the function
/// returns whether either has a valid combination
/// </summary>
/// <param name="multiplicity"></param>
/// <param name="cn"></param>
/// <param name="other"></param>
/// <param name="alignment"></param>
/// <param name="ntermCnTest"></param>
/// <param name="ctermCnTest"></param>
/// <param name="minSubstructureLength"></param>
/// <returns></returns>
public static bool TestClashCn(int multiplicity, IStructure cn, IStructure other, TransformSequenceAlignment alignment, bool ntermCnTest = true, bool ctermCnTest = true, int minSubstructureLength = 0)
{
Trace.Assert(minSubstructureLength >= 0);
IChain cnChain = cn[alignment.ChainIndex1];
IChain otherChain = other[alignment.ChainIndex2];
if (ntermCnTest)
{
int finalOtherIndex = Math.Min(otherChain.Count - 1, alignment.Range2.End + minSubstructureLength - 1);
Trace.Assert(alignment.Range1.Start < cnChain.Count);
Trace.Assert(0 <= alignment.Range2.End && alignment.Range2.End < otherChain.Count && finalOtherIndex < otherChain.Count);
IChain copyCn = new Chain(cnChain[0, alignment.Range1.Start]);
IChain copyOther = new Chain(otherChain[alignment.Range2.End, finalOtherIndex], true);
copyOther.Transform(alignment.Align2);
if (!Clash.AnyContact(copyCn, copyOther, Clash.ContactType.MainchainMainchainClash))
{
copyCn.AddRange(copyOther);
AxisPattern <IChain> pattern = new AxisPattern <IChain>(Vector3.UnitZ, multiplicity, copyCn);
IChain[] neighbors = pattern[1, multiplicity - 1].ToArray();
//IChain[] pattern = CxUtilities.Pattern(copyCn, Vector3.UnitZ, multiplicity, new int[] { 0 }, true);
if (!Clash.AnyContact(new IChain[] { copyCn }, neighbors, Clash.ContactType.MainchainMainchainClash))
{
return(false);
}
}
}
if (ctermCnTest)
{
int firstOtherIndex = Math.Max(0, alignment.Range2.Start - minSubstructureLength + 1);
Trace.Assert(0 <= alignment.Range1.End && alignment.Range1.End < cnChain.Count);
Trace.Assert(0 <= firstOtherIndex && firstOtherIndex < otherChain.Count && alignment.Range2.Start < otherChain.Count);
IChain copyCn = new Chain(cnChain[alignment.Range1.End, cnChain.Count - 1]);
IChain copyOther = new Chain(otherChain[firstOtherIndex, alignment.Range2.Start], true);
copyOther.Transform(alignment.Align2);
if (!Clash.AnyContact(copyCn, copyOther, Clash.ContactType.MainchainMainchainClash))
{
copyCn.AddRange(copyOther);
AxisPattern <IChain> pattern = new AxisPattern <IChain>(Vector3.UnitZ, multiplicity, copyCn);
IChain[] neighbors = pattern[1, multiplicity - 1].ToArray();
//IChain[] pattern = CxUtilities.Pattern(copyCn, Vector3.UnitZ, multiplicity, new int[] { 0 }, true);
if (!Clash.AnyContact(new IChain[] { copyCn }, neighbors, Clash.ContactType.MainchainMainchainClash))
{
return(false);
}
}
}
return(true);
}