public static Selection GetCnInterAsuContacts(IStructure cnAsymmetricUnit, int multiplicity, Vector3 axis)
{
AxisPattern <IStructure> pattern = new AxisPattern <IStructure>(axis, multiplicity, cnAsymmetricUnit);
IStructure[] others = pattern[1, multiplicity - 1].ToArray(); // CxUtilities.Pattern(cnAsymmetricUnit, axis, multiplicity, new int[] { 0 }, true);
Selection selection = Clash.GetContactSelectionInFocusSet(new IStructure[] { cnAsymmetricUnit }, others);
return(selection);
}
public static Selection GetCnInterAsuContacts(IStructure cnAsymmetricUnit, int multiplicity, Line axis, Clash.ContactType contactType = Clash.ContactType.Atomic)
{
IStructure mirror = cnAsymmetricUnit.GetMirroredElement(true, null);
AxisPattern <IStructure> pattern = new AxisPattern <IStructure>(axis.Point, axis.Direction, multiplicity, mirror, new int[] { 0 });
IStructure[] others = pattern.ToArray();//[1, multiplicity - 1].ToArray(); // CxUtilities.Pattern(cnAsymmetricUnit, axis, multiplicity, new int[] { 0 }, true);
Selection selection = Clash.GetContactSelectionInFocusSet(new IStructure[] { cnAsymmetricUnit }, others, contactType);
return(selection);
}
public static List <int> GetCnInterAsuContactIndices(IStructure cnAsymmetricUnit, int chainIndex, int multiplicity, Vector3 axis)
{
Trace.Assert(0 <= chainIndex && chainIndex < cnAsymmetricUnit.Count);
AxisPattern <IStructure> pattern = new AxisPattern <IStructure>(axis, multiplicity, cnAsymmetricUnit);
IStructure[] others = pattern[1, multiplicity - 1].ToArray();// CxUtilities.Pattern(cnAsymmetricUnit, axis, multiplicity, new int[] { 0 }, true);
List <int> interAsuContacts = Clash.GetContactIndices(cnAsymmetricUnit[chainIndex], others.SelectMany(str => str).ToArray());
return(interAsuContacts);
}
public static bool[][] GetCnInterAsuContactBools(IStructure asu, int multiplicity, Vector3 axis)
{
asu = (IStructure)asu.DeepCopy();
IStructure mirror = asu.GetMirroredElement(true, null);
AxisPattern <IStructure> pattern = new AxisPattern <IStructure>(axis, multiplicity, mirror, new int[] { 0 });
IStructure[] neighbors = pattern.ToArray();
//IStructure[] neighbors = CxUtilities.Pattern(asu, axis, multiplicity, new int[] { 0 }, true);
Selection contactAas = Clash.GetContactSelectionInFocusSet(new IStructure[] { asu }, neighbors, Clash.ContactType.Atomic);
bool[][] contacts = asu.Select(chain => chain.Select(aa => contactAas.Aas.Contains(aa)).ToArray()).ToArray();
return(contacts);
}
/// <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);
}