/// <summary>
///
/// </summary>
/// <param name="buInterface"></param>
/// <param name="maxSeq1"></param>
/// <param name="minSeq1"></param>
/// <param name="maxSeq2"></param>
/// <param name="minSeq2"></param>
private void GetMaxMinContactSeqIDs(InterfaceChains buInterface, ref int maxSeq1, ref int minSeq1,
ref int maxSeq2, ref int minSeq2)
{
maxSeq1 = -1;
minSeq1 = 999999;
maxSeq2 = -1;
minSeq2 = 999999;
foreach (string seqString in buInterface.seqContactHash.Keys)
{
string[] seqIds = seqString.Split('_');
int seqId1 = ParseHelper.ConvertSeqToInt(seqIds[0]);
if (maxSeq1 < seqId1)
{
maxSeq1 = seqId1;
}
if (minSeq1 > seqId1)
{
minSeq1 = seqId1;
}
int seqId2 = ParseHelper.ConvertSeqToInt(seqIds[1]);
if (maxSeq2 < seqId2)
{
maxSeq2 = seqId2;
}
if (minSeq2 > seqId2)
{
minSeq2 = seqId2;
}
}
}
/// <summary>
/// atom coordinates for domains
/// A SCOP domain may have multiple segmentations
/// </summary>
/// <param name="chain"></param>
/// <param name="ranges"></param>
/// <returns></returns>
private AtomInfo[] GetDomainAtoms(ChainAtoms chain, string rangeString)
{
AtomInfo[] domainAtoms = null;
List <AtomInfo> domainAtomList = new List <AtomInfo> ();
int startPos = -1;
int endPos = -1;
int seqId = -1;
string[] ranges = rangeString.Split(';');
foreach (string range in ranges)
{
if (range == "-")
{
domainAtoms = chain.CartnAtoms;
}
else
{
string[] posFields = range.Split('-');
startPos = ParseHelper.ConvertSeqToInt(posFields[0]);
endPos = ParseHelper.ConvertSeqToInt(posFields[1]);
foreach (AtomInfo atom in chain.CartnAtoms)
{
seqId = ParseHelper.ConvertSeqToInt(atom.seqId);
if (seqId >= startPos && seqId <= endPos)
{
domainAtomList.Add(atom);
}
}
}
}
return(domainAtomList.ToArray());
}
/// <summary>
///
/// </summary>
/// <param name="chain"></param>
/// <param name="domainStart"></param>
/// <param name="domainEnd"></param>
/// <returns></returns>
private AtomInfo[] GetDomainAtoms(AtomInfo[] chainAtoms, int domainStart, int domainEnd)
{
List <AtomInfo> domainAtomsList = new List <AtomInfo> ();
int seqId = -1;
foreach (AtomInfo atom in chainAtoms)
{
seqId = ParseHelper.ConvertSeqToInt(atom.seqId);
if (seqId <= domainEnd && seqId >= domainStart)
{
domainAtomsList.Add(atom);
}
}
return(domainAtomsList.ToArray());
}
/// <summary>
/// the atoms of the domain
/// </summary>
/// <param name="chainAtoms">atomic coordinate for the chain</param>
/// <param name="domainRange">domain range</param>
/// <returns>all atomic coordinates for the domain</returns>
private AtomInfo[] GetDomainAtoms(AtomInfo[] chainAtoms, Range[] domainRange)
{
List <AtomInfo> domainAtomList = new List <AtomInfo> ();
int atomSeqId = -1;
foreach (AtomInfo atom in chainAtoms)
{
atomSeqId = ParseHelper.ConvertSeqToInt(atom.seqId);
if (IsSeqIdInRange(atomSeqId, domainRange))
{
domainAtomList.Add(atom);
}
}
return(domainAtomList.ToArray());
}
/// <summary>
///
/// </summary>
/// <param name="buInterface"></param>
/// <param name="domainStart1"></param>
/// <param name="domainEnd1"></param>
/// <param name="domainStart2"></param>
/// <param name="domainEnd2"></param>
/// <returns></returns>
private bool AreDomainsInteracted(InterfaceChains buInterface, int domainStart1, int domainEnd1,
int domainStart2, int domainEnd2)
{
int numOfResidueContacts = 0;
int numOfAtomContacts = 0;
int seqId1 = -1;
int seqId2 = -1;
bool hasEnoughResiduePairs = false;
bool hasContacts = false;
foreach (string seqString in buInterface.seqDistHash.Keys)
{
string[] seqIds = seqString.Split('_');
seqId1 = ParseHelper.ConvertSeqToInt(seqIds[0]);
seqId2 = ParseHelper.ConvertSeqToInt(seqIds[1]);
if (seqId1 >= domainStart1 && seqId1 <= domainEnd1 &&
seqId2 >= domainStart2 && seqId2 <= domainEnd2)
{
numOfResidueContacts++;
if (numOfResidueContacts >= AppSettings.parameters.contactParams.numOfResidueContacts)
{
hasEnoughResiduePairs = true;
break;
}
}
}
foreach (string seqString in buInterface.seqContactHash.Keys)
{
string[] seqIds = seqString.Split('_');
seqId1 = ParseHelper.ConvertSeqToInt(seqIds[0]);
seqId2 = ParseHelper.ConvertSeqToInt(seqIds[1]);
if (seqId1 >= domainStart1 && seqId1 <= domainEnd1 &&
seqId2 >= domainStart2 && seqId2 <= domainEnd2)
{
numOfAtomContacts++;
hasContacts = true;
// break;
}
}
// if (hasContacts && hasEnoughResiduePairs)
if ((hasContacts && hasEnoughResiduePairs) ||
numOfAtomContacts >= AppSettings.parameters.contactParams.domainNumOfAtomContacts)
{
return(true);
}
return(false);
}
/// <summary>
/// the domain in the chain
/// </summary>
/// <param name="chain"></param>
/// <param name="startPos"></param>
/// <param name="endPos"></param>
/// <returns></returns>
private AtomInfo[] GetDomainAtoms(AtomInfo[] chain, int startPos, int endPos)
{
List <AtomInfo> atomList = new List <AtomInfo> ();
int seqId = -1;
foreach (AtomInfo atom in chain)
{
seqId = ParseHelper.ConvertSeqToInt(atom.seqId);
if (seqId <= endPos && seqId >= startPos)
{
atomList.Add(atom);
}
}
AtomInfo[] domain = new AtomInfo[atomList.Count];
atomList.CopyTo(domain);
return(domain);
}
/// <summary>
/// the domain in the chain
/// </summary>
/// <param name="chain"></param>
/// <param name="startPos"></param>
/// <param name="endPos"></param>
/// <returns></returns>
private AtomInfo[] GetDomainAtoms(AtomInfo[] chain, Range[] ranges)
{
List <AtomInfo> atomList = new List <AtomInfo> ();
int seqId = -1;
foreach (AtomInfo atom in chain)
{
seqId = ParseHelper.ConvertSeqToInt(atom.seqId);
foreach (Range range in ranges)
{
if (seqId <= range.endPos && seqId >= range.startPos)
{
atomList.Add(atom);
break;
}
}
}
AtomInfo[] domain = new AtomInfo[atomList.Count];
atomList.CopyTo(domain);
return(domain);
}
