public static new Monomer validateAndAllocate(Chain chain, string group3, int seqcode, int firstAtomIndex, int lastAtomIndex, int[] specialAtomIndexes, Atom[] atoms)
{
sbyte[] offsets = scanForOffsets(firstAtomIndex, specialAtomIndexes, interestingAminoAtomIDs);
if (offsets == null)
{
return(null);
}
if (specialAtomIndexes[JmolConstants.ATOMID_CARBONYL_OXYGEN] < 0)
{
int carbonylOxygenIndex = specialAtomIndexes[JmolConstants.ATOMID_O1];
System.Console.Out.WriteLine("I see someone who does not have a carbonyl oxygen");
if (carbonylOxygenIndex < 0)
{
return(null);
}
offsets[1] = (sbyte)(carbonylOxygenIndex - firstAtomIndex);
}
if (!isBondedCorrectly(firstAtomIndex, offsets, atoms))
{
return(null);
}
AminoMonomer aminoMonomer = new AminoMonomer(chain, group3, seqcode, firstAtomIndex, lastAtomIndex, offsets);
return(aminoMonomer);
}
public static Monomer[] getAminoMonomers(Group[] groups, int firstGroupIndex)
{
AminoMonomer previous = null;
int count = 0;
for (int i = firstGroupIndex; i < groups.Length; ++i, ++count)
{
Group group = groups[i];
if (!(group is AminoMonomer))
{
break;
}
AminoMonomer current = (AminoMonomer)group;
if (current.polymer != null)
{
break;
}
if (!current.isConnectedAfter(previous))
{
break;
}
previous = current;
}
if (count == 0)
{
return(null);
}
Monomer[] monomers = new Monomer[count];
for (int j = 0; j < count; ++j)
{
monomers[j] = (AminoMonomer)groups[firstGroupIndex + j];
}
return(monomers);
}
public virtual void calcProteinMainchainHydrogenBonds(BitArray bsA, BitArray bsB)
{
Point3f carbonPoint;
Point3f oxygenPoint;
for (int i = 0; i < monomerCount; ++i)
{
AminoMonomer residue = (AminoMonomer)monomers[i];
mainchainHbondOffsets[i] = 0;
/****************************************************************
* This does not acount for the first nitrogen in the chain
* is there some way to predict where it's hydrogen is?
* mth 20031219
****************************************************************/
if (i > 0 && residue.GroupID != JmolConstants.GROUPID_PROLINE)
{
Point3f nitrogenPoint = residue.NitrogenAtomPoint;
aminoHydrogenPoint.add(nitrogenPoint, vectorPreviousOC);
bondAminoHydrogen(i, aminoHydrogenPoint, bsA, bsB);
}
carbonPoint = residue.CarbonylCarbonAtomPoint;
oxygenPoint = residue.CarbonylOxygenAtomPoint;
vectorPreviousOC.sub(carbonPoint, oxygenPoint);
vectorPreviousOC.scale(1 / vectorPreviousOC.length());
}
}
public virtual void calcSheetUnitVectors()
{
if (widthUnitVector == null)
{
Vector3f vectorCO = new Vector3f();
Vector3f vectorCOSum = new Vector3f();
AminoMonomer amino = (AminoMonomer)aminoPolymer.monomers[monomerIndex];
vectorCOSum.sub(amino.CarbonylOxygenAtomPoint, amino.CarbonylCarbonAtomPoint);
for (int i = monomerCount; --i > 0;)
{
amino = (AminoMonomer)aminoPolymer.monomers[i];
vectorCO.sub(amino.CarbonylOxygenAtomPoint, amino.CarbonylCarbonAtomPoint);
//UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1042'"
if (vectorCOSum.angle(vectorCO) < (float)System.Math.PI / 2)
{
vectorCOSum.add(vectorCO);
}
else
{
vectorCOSum.sub(vectorCO);
}
}
heightUnitVector = vectorCO; // just reuse the same temp vector;
heightUnitVector.cross(axisUnitVector, vectorCOSum);
heightUnitVector.normalize();
widthUnitVector = vectorCOSum;
widthUnitVector.cross(axisUnitVector, heightUnitVector);
}
}
public virtual void bondAminoHydrogen(int indexDonor, Point3f hydrogenPoint, BitArray bsA, BitArray bsB)
{
AminoMonomer source = (AminoMonomer)monomers[indexDonor];
Point3f sourceAlphaPoint = source.LeadAtomPoint;
Point3f sourceNitrogenPoint = source.NitrogenAtomPoint;
int energyMin1 = 0;
int energyMin2 = 0;
int indexMin1 = -1;
int indexMin2 = -1;
for (int i = monomerCount; --i >= 0;)
{
if ((i == indexDonor || (i + 1) == indexDonor) || (i - 1) == indexDonor)
{
continue;
}
AminoMonomer target = (AminoMonomer)monomers[i];
Point3f targetAlphaPoint = target.LeadAtomPoint;
float dist2 = sourceAlphaPoint.distanceSquared(targetAlphaPoint);
if (dist2 > maxHbondAlphaDistance2)
{
continue;
}
int energy = calcHbondEnergy(sourceNitrogenPoint, hydrogenPoint, target);
if (debugHbonds)
{
System.Console.Out.WriteLine("HbondEnergy=" + energy + " dist2=" + dist2 + " max^2=" + maxHbondAlphaDistance2);
}
if (energy < energyMin1)
{
energyMin2 = energyMin1;
indexMin2 = indexMin1;
energyMin1 = energy;
indexMin1 = i;
}
else if (energy < energyMin2)
{
energyMin2 = energy;
indexMin2 = i;
}
}
if (indexMin1 >= 0)
{
mainchainHbondOffsets[indexDonor] = (short)(indexDonor - indexMin1);
min1Indexes[indexDonor] = (short)indexMin1;
min1Energies[indexDonor] = (short)energyMin1;
createResidueHydrogenBond(indexDonor, indexMin1, bsA, bsB);
if (indexMin2 >= 0)
{
createResidueHydrogenBond(indexDonor, indexMin2, bsA, bsB);
min2Indexes[indexDonor] = (short)indexMin2;
min2Energies[indexDonor] = (short)energyMin2;
}
}
}
public virtual void calcPhiPsiAngles(AminoMonomer leadingResidue, AminoMonomer trailingResidue, float[] phi_psi)
{
Point3f nitrogen1 = leadingResidue.NitrogenAtomPoint;
Point3f alphacarbon1 = leadingResidue.LeadAtomPoint;
Point3f carbon1 = leadingResidue.CarbonylCarbonAtomPoint;
Point3f nitrogen2 = trailingResidue.NitrogenAtomPoint;
Point3f alphacarbon2 = trailingResidue.LeadAtomPoint;
Point3f carbon2 = trailingResidue.CarbonylCarbonAtomPoint;
phi_psi[0] = Measurement.computeTorsion(carbon1, nitrogen2, alphacarbon2, carbon2);
phi_psi[1] = Measurement.computeTorsion(nitrogen1, alphacarbon1, carbon1, nitrogen2);
}
////////////////////////////////////////////////////////////////
public override bool isConnectedAfter(Monomer possiblyPreviousMonomer)
{
if (possiblyPreviousMonomer == null)
{
return(true);
}
if (!(possiblyPreviousMonomer is AminoMonomer))
{
return(false);
}
AminoMonomer other = (AminoMonomer)possiblyPreviousMonomer;
return(other.CarbonylCarbonAtom.isBonded(NitrogenAtom));
}
public virtual void createResidueHydrogenBond(int indexAminoGroup, int indexCarbonylGroup, BitArray bsA, BitArray bsB)
{
short order;
int aminoBackboneHbondOffset = indexAminoGroup - indexCarbonylGroup;
if (debugHbonds)
{
System.Console.Out.WriteLine("aminoBackboneHbondOffset=" + aminoBackboneHbondOffset + " amino:" + monomers[indexAminoGroup].SeqcodeString + " carbonyl:" + monomers[indexCarbonylGroup].SeqcodeString);
}
switch (aminoBackboneHbondOffset)
{
case 2:
order = JmolConstants.BOND_H_PLUS_2;
break;
case 3:
order = JmolConstants.BOND_H_PLUS_3;
break;
case 4:
order = JmolConstants.BOND_H_PLUS_4;
break;
case 5:
order = JmolConstants.BOND_H_PLUS_5;
break;
case -3:
order = JmolConstants.BOND_H_MINUS_3;
break;
case -4:
order = JmolConstants.BOND_H_MINUS_4;
break;
default:
order = JmolConstants.BOND_H_REGULAR;
break;
}
if (debugHbonds)
{
Console.Out.WriteLine("createResidueHydrogenBond(" + indexAminoGroup + "," + indexCarbonylGroup);
}
AminoMonomer donor = (AminoMonomer)monomers[indexAminoGroup];
Atom nitrogen = donor.NitrogenAtom;
AminoMonomer recipient = (AminoMonomer)monomers[indexCarbonylGroup];
Atom oxygen = recipient.CarbonylOxygenAtom;
model.mmset.frame.bondAtoms(nitrogen, oxygen, order, bsA, bsB);
}
private void distinguishAndPropogateGroup(int groupIndex, Chain chain, string group3,
int seqcode, int firstAtomIndex, int maxAtomIndex)
{
// System.out.println("distinguish & propogate group:" +
// " group3:" + group3 +
// " seqcode:" + Group.getSeqcodeString(seqcode) +
// " firstAtomIndex:" + firstAtomIndex +
// " maxAtomIndex:" + maxAtomIndex);
int distinguishingBits = 0;
// clear previous specialAtomIndexes
for (int i = JmolConstants.ATOMID_MAX; --i >= 0;)
{
specialAtomIndexes[i] = Int32.MinValue;
}
if (specialAtomIDs != null)
{
for (int i = maxAtomIndex; --i >= firstAtomIndex;)
{
int specialAtomID = specialAtomIDs[i];
if (specialAtomID > 0)
{
if (specialAtomID < JmolConstants.ATOMID_DISTINGUISHING_ATOM_MAX)
{
distinguishingBits |= 1 << specialAtomID;
}
specialAtomIndexes[specialAtomID] = i;
}
}
}
int lastAtomIndex = maxAtomIndex - 1;
if (lastAtomIndex < firstAtomIndex)
{
throw new System.NullReferenceException();
}
Group group = null;
// System.out.println("distinguishingBits=" + distinguishingBits);
if ((distinguishingBits & JmolConstants.ATOMID_PROTEIN_MASK) == JmolConstants.ATOMID_PROTEIN_MASK)
{
// System.out.println("may be an AminoMonomer");
group = AminoMonomer.validateAndAllocate(chain, group3, seqcode, firstAtomIndex, lastAtomIndex, specialAtomIndexes, atoms);
}
else if (distinguishingBits == JmolConstants.ATOMID_ALPHA_ONLY_MASK)
{
// System.out.println("AlphaMonomer.validateAndAllocate");
group = AlphaMonomer.validateAndAllocate(chain, group3, seqcode, firstAtomIndex, lastAtomIndex, specialAtomIndexes, atoms);
}
else if (((distinguishingBits & JmolConstants.ATOMID_NUCLEIC_MASK) == JmolConstants.ATOMID_NUCLEIC_MASK))
{
group = NucleicMonomer.validateAndAllocate(chain, group3, seqcode, firstAtomIndex, lastAtomIndex, specialAtomIndexes, atoms);
}
else if (distinguishingBits == JmolConstants.ATOMID_PHOSPHORUS_ONLY_MASK)
{
// System.out.println("PhosphorusMonomer.validateAndAllocate");
group = PhosphorusMonomer.validateAndAllocate(chain, group3, seqcode, firstAtomIndex, lastAtomIndex, specialAtomIndexes, atoms);
}
if (group == null)
{
group = new Group(chain, group3, seqcode, firstAtomIndex, lastAtomIndex);
}
chain.addGroup(group);
groups[groupIndex] = group;
////////////////////////////////////////////////////////////////
for (int i = maxAtomIndex; --i >= firstAtomIndex;)
{
atoms[i].Group = group;
}
}
public virtual void calcPhiPsiAngles(AminoMonomer leadingResidue, AminoMonomer trailingResidue, float[] phi_psi)
{
Point3f nitrogen1 = leadingResidue.NitrogenAtomPoint;
Point3f alphacarbon1 = leadingResidue.LeadAtomPoint;
Point3f carbon1 = leadingResidue.CarbonylCarbonAtomPoint;
Point3f nitrogen2 = trailingResidue.NitrogenAtomPoint;
Point3f alphacarbon2 = trailingResidue.LeadAtomPoint;
Point3f carbon2 = trailingResidue.CarbonylCarbonAtomPoint;
phi_psi[0] = Measurement.computeTorsion(carbon1, nitrogen2, alphacarbon2, carbon2);
phi_psi[1] = Measurement.computeTorsion(nitrogen1, alphacarbon1, carbon1, nitrogen2);
}
public virtual int calcHbondEnergy(Point3f nitrogenPoint, Point3f hydrogenPoint, AminoMonomer target)
{
Point3f targetOxygenPoint = target.CarbonylOxygenAtomPoint;
float distON2 = targetOxygenPoint.distanceSquared(nitrogenPoint);
if (distON2 < minimumHbondDistance2)
return - 9900;
//why would this not have been in here? RMH 03/8/06
// if (distON2 > hbondMax2)
// return 0;
//nevermind! :)
if (debugHbonds)
System.Console.Out.WriteLine("calchbondenergy: " + hydrogenPoint.x + "," + hydrogenPoint.y + "," + hydrogenPoint.z);
float distOH2 = targetOxygenPoint.distanceSquared(hydrogenPoint);
if (distOH2 < minimumHbondDistance2)
return - 9900;
Point3f targetCarbonPoint = target.CarbonylCarbonAtomPoint;
float distCH2 = targetCarbonPoint.distanceSquared(hydrogenPoint);
if (distCH2 < minimumHbondDistance2)
return - 9900;
float distCN2 = targetCarbonPoint.distanceSquared(nitrogenPoint);
if (distCN2 < minimumHbondDistance2)
return - 9900;
double distOH = System.Math.Sqrt(distOH2);
double distCH = System.Math.Sqrt(distCH2);
double distCN = System.Math.Sqrt(distCN2);
double distON = System.Math.Sqrt(distON2);
//UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1042'"
int energy = (int) ((QConst / distOH - QConst / distCH + QConst / distCN - QConst / distON));
if (debugHbonds)
System.Console.Out.WriteLine(" distOH=" + distOH + " distCH=" + distCH + " distCN=" + distCN + " distON=" + distON + " energy=" + energy);
if (energy < - 9900)
return - 9900;
if (energy > - 500)
return 0;
return energy;
}
public static new Monomer validateAndAllocate(Chain chain, string group3, int seqcode, int firstAtomIndex, int lastAtomIndex, int[] specialAtomIndexes, Atom[] atoms)
{
sbyte[] offsets = scanForOffsets(firstAtomIndex, specialAtomIndexes, interestingAminoAtomIDs);
if (offsets == null)
return null;
if (specialAtomIndexes[JmolConstants.ATOMID_CARBONYL_OXYGEN] < 0)
{
int carbonylOxygenIndex = specialAtomIndexes[JmolConstants.ATOMID_O1];
System.Console.Out.WriteLine("I see someone who does not have a carbonyl oxygen");
if (carbonylOxygenIndex < 0)
return null;
offsets[1] = (sbyte) (carbonylOxygenIndex - firstAtomIndex);
}
if (!isBondedCorrectly(firstAtomIndex, offsets, atoms))
return null;
AminoMonomer aminoMonomer = new AminoMonomer(chain, group3, seqcode, firstAtomIndex, lastAtomIndex, offsets);
return aminoMonomer;
}
/*
* If someone wants to work on this code for secondary structure
* recognition that would be great
*
* miguel 2004 06 16
*/
/*
* New code for assigning secondary structure based on
* phi-psi angles instead of hydrogen bond patterns.
*
* old code is commented below the new.
*
* molvisions 2005 10 12
*
*/
public override void calculateStructures()
{
char[] structureTags = new char[monomerCount];
float[] phi_psi = new float[2];
for (int i = 0; i < monomerCount - 1; ++i)
{
AminoMonomer leadingResidue = (AminoMonomer)monomers[i];
AminoMonomer trailingResidue = (AminoMonomer)monomers[i + 1];
calcPhiPsiAngles(leadingResidue, trailingResidue, phi_psi);
if (isHelix(phi_psi))
{
structureTags[i] = '4';
//structureTags[i+1] = '4';
}
else if (isSheet(phi_psi))
{
structureTags[i] = 's';
//structureTags[i+1] = 's';
}
else if (isTurn(phi_psi))
{
structureTags[i] = 't';
//structureTags[i+1] = 't';
}
else
{
structureTags[i] = '\x0000';
//structureTags[i+1] = '\0';
}
}
// build alpha helix stretches
for (int start = 0; start < monomerCount; ++start)
{
if (structureTags[start] == '4')
{
int end;
for (end = start + 1; end < monomerCount && structureTags[end] == '4'; ++end)
{
}
end--;
if (end >= start + 3)
{
addSecondaryStructure(JmolConstants.PROTEIN_STRUCTURE_HELIX, start, end);
}
start = end;
}
}
// build beta sheet stretches
for (int start = 0; start < monomerCount; ++start)
{
if (structureTags[start] == 's')
{
int end;
for (end = start + 1; end < monomerCount && structureTags[end] == 's'; ++end)
{
}
end--;
if (end >= start + 2)
{
addSecondaryStructure(JmolConstants.PROTEIN_STRUCTURE_SHEET, start, end);
}
start = end;
}
}
// build turns
for (int start = 0; start < monomerCount; ++start)
{
if (structureTags[start] == 't')
{
int end;
for (end = start + 1; end < monomerCount && structureTags[end] == 't'; ++end)
{
}
end--;
if (end >= start + 2)
{
addSecondaryStructure(JmolConstants.PROTEIN_STRUCTURE_TURN, start, end);
}
start = end;
}
}
}
public virtual int calcHbondEnergy(Point3f nitrogenPoint, Point3f hydrogenPoint, AminoMonomer target)
{
Point3f targetOxygenPoint = target.CarbonylOxygenAtomPoint;
float distON2 = targetOxygenPoint.distanceSquared(nitrogenPoint);
if (distON2 < minimumHbondDistance2)
{
return(-9900);
}
//why would this not have been in here? RMH 03/8/06
// if (distON2 > hbondMax2)
// return 0;
//nevermind! :)
if (debugHbonds)
{
System.Console.Out.WriteLine("calchbondenergy: " + hydrogenPoint.x + "," + hydrogenPoint.y + "," + hydrogenPoint.z);
}
float distOH2 = targetOxygenPoint.distanceSquared(hydrogenPoint);
if (distOH2 < minimumHbondDistance2)
{
return(-9900);
}
Point3f targetCarbonPoint = target.CarbonylCarbonAtomPoint;
float distCH2 = targetCarbonPoint.distanceSquared(hydrogenPoint);
if (distCH2 < minimumHbondDistance2)
{
return(-9900);
}
float distCN2 = targetCarbonPoint.distanceSquared(nitrogenPoint);
if (distCN2 < minimumHbondDistance2)
{
return(-9900);
}
double distOH = System.Math.Sqrt(distOH2);
double distCH = System.Math.Sqrt(distCH2);
double distCN = System.Math.Sqrt(distCN2);
double distON = System.Math.Sqrt(distON2);
//UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1042'"
int energy = (int)((QConst / distOH - QConst / distCH + QConst / distCN - QConst / distON));
if (debugHbonds)
{
System.Console.Out.WriteLine(" distOH=" + distOH + " distCH=" + distCH + " distCN=" + distCN + " distON=" + distON + " energy=" + energy);
}
if (energy < -9900)
{
return(-9900);
}
if (energy > -500)
{
return(0);
}
return(energy);
}
