void InitializeDesignablePositions()
{
List <int> designablePositions = new List <int>();
// Identify new contacts created between ranges (atomic contact or vector contact, i.e. potentially contacting), but not including the fusion region
// Identify any clashes involving the fusion region
{
for (int i = 0; i < IdentityRanges.Length - 1; i++)
{
List <int> newContactPositions = Clash.GetContactIndices(Peptide, new Range[] { IdentityRanges[i], IdentityRanges[i + 1] }, Clash.ContactType.VectorCACB | Clash.ContactType.Atomic);
Range spliceRange = new Range(IdentityRanges[i].End + 1, IdentityRanges[i + 1].Start - 1);
List <int> clashes = Clash.GetContactIndices(Peptide, new Range[] { IdentityRanges[i], IdentityRanges[i + 1], spliceRange }, Clash.ContactType.AtomicClash);
designablePositions.AddRange(newContactPositions);
designablePositions.AddRange(clashes);
designablePositions.AddRange(Enumerable.Range(spliceRange.Start, spliceRange.Length + 1));
}
}
// Identify broken contacts, i.e. those from within the identity region that interact with something
// past the splice region.
{
for (int i = 0; i < OriginalRanges.Length; i++)
{
List <Range> rangesForChain = new List <Range>();
Range rangeIncludingSplice = OriginalRanges[i];
if (i > 0)
{
rangeIncludingSplice.Start -= (IdentityRanges[i].Start - IdentityRanges[i - 1].End - 1);
}
if (i < OriginalRanges.Length - 1)
{
rangeIncludingSplice.End += (IdentityRanges[i + 1].Start - IdentityRanges[i].End - 1);
}
rangesForChain.Add(rangeIncludingSplice);
if (rangeIncludingSplice.Start > 0)
{
rangesForChain.Add(new Range(0, rangeIncludingSplice.Start - 1));
}
if (rangeIncludingSplice.End < OriginalChains[i].Count - 1)
{
rangesForChain.Add(new Range(rangeIncludingSplice.End + 1, OriginalChains[i].Count - 1));
}
List <int> brokenContacts = Clash.GetContactIndices(OriginalChains[i], rangesForChain.ToArray(), Clash.ContactType.SidechainSidechain | Clash.ContactType.IgnoreInvalidCoordinates);
foreach (int contactIndex in brokenContacts)
{
if (OriginalRanges[i].Contains(contactIndex))
{
int remappedIndex = contactIndex + IdentityRanges[i].Start - OriginalRanges[i].Start;
designablePositions.Add(remappedIndex);
Debug.Assert(0 <= remappedIndex && remappedIndex < Peptide.Count);
}
}
}
}
designablePositions.Sort();
designablePositions_ = designablePositions.Distinct().ToArray();
}
public static List <int> GetInterChainContactIndices(IStructure assembly, int chainIndex)
{
IChain a = assembly[chainIndex];
IChain[] others = assembly.Where(chain => chain != a).ToArray();
List <int> contacts = Clash.GetContactIndices(a, others);
return(contacts);
}
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 List <int> GetCnInterAsuContactIndices(IChain monomer, int multiplicity, Vector3 axis)
{
IChain[] oligomer = new IChain[multiplicity - 1];
for (int i = 0; i < multiplicity - 1; i++)
{
oligomer[i] = new Chain(monomer);
oligomer[i].RotateRadians(Vector3.Zero, Vector3.UnitZ, (float)((i + 1) * 2 * Math.PI / multiplicity));
}
List <int> contacts = Clash.GetContactIndices(monomer, oligomer);
return(contacts);
}