public void WriteProteinFragment(ref AtomParser.AtomCategory _atomCat, int _fragStart,
int _fragEnd, int _chainIndex, string _chainID, string _fileWithPath)
{
// this is complicated because the indices refer to alpha-carbon-only, while this function writes
// whole thing
AtomParser.ChainAtoms theChainAtoms = new ChainAtoms();
AtomParser.ChainAtoms onlyCAChainAtoms = new ChainAtoms();
theChainAtoms = _atomCat.ChainAtomList[_chainIndex];
onlyCAChainAtoms = _atomCat.CalphaAtomList()[_chainIndex];
string firstCAauthSeqID = onlyCAChainAtoms.CartnAtoms[_fragStart].authSeqId;
string lastCAauthSeqID = onlyCAChainAtoms.CartnAtoms[_fragEnd].authSeqId;
StreamWriter protWriter = new StreamWriter(_fileWithPath, false);
int atomCounter = new int();
atomCounter = 1;
bool writingInFragment = new bool();
bool hitLastCA = new bool();
writingInFragment = false;
hitLastCA = false;
for (int atomIndex = 0; atomIndex < theChainAtoms.CartnAtoms.Length; atomIndex++)
{
if (theChainAtoms.CartnAtoms[atomIndex].authSeqId == firstCAauthSeqID)
{
writingInFragment = true;
}
if (writingInFragment)
{
if (!hitLastCA)
{
if (theChainAtoms.CartnAtoms[atomIndex].authSeqId == lastCAauthSeqID)
{
hitLastCA = true;
}
}
else
{
if (theChainAtoms.CartnAtoms[atomIndex].authSeqId != lastCAauthSeqID) // hit the residue after the last residue in fragment
{
break;
}
}
protWriter.WriteLine(WriteSingleLine(theChainAtoms.CartnAtoms[atomIndex],
atomCounter, _chainID));
}
}
protWriter.Close();
return;
}
public void WriteCAOnlyFragment(ref AtomParser.AtomCategory _atomCat, int _fragStart,
int _fragEnd, int _chainIndex, string _chainID, string _fileWithPath)
{
AtomParser.ChainAtoms theChainAtoms = new ChainAtoms();
theChainAtoms = (_atomCat.CalphaAtomList())[_chainIndex];
StreamWriter protWriter = new StreamWriter(_fileWithPath, false);
int atomCounter = new int();
atomCounter = 1;
for (int atomIndex = _fragStart; atomIndex < _fragEnd; atomIndex++)
{
protWriter.WriteLine(WriteSingleLine(theChainAtoms.CartnAtoms[atomIndex],
atomCounter, _chainID));
}
protWriter.Close();
return;
}