public virtual void render2StrandSegment(int monomerCount, Monomer monomer, short colix, short[] mads, Point3i[] ribbonTopScreens, Point3i[] ribbonBottomScreens, int i)
{
int iLast = monomerCount;
int iPrev = i - 1;
if (iPrev < 0)
{
iPrev = 0;
}
int iNext = i + 1;
if (iNext > iLast)
{
iNext = iLast;
}
int iNext2 = i + 2;
if (iNext2 > iLast)
{
iNext2 = iLast;
}
//colix = Graphics3D.inheritColix(colix, monomer.LeadAtom.colixAtom);
g3d.drawHermite(true, ribbonBorder, colix, isNucleic?4:7, ribbonTopScreens[iPrev], ribbonTopScreens[i], ribbonTopScreens[iNext], ribbonTopScreens[iNext2], ribbonBottomScreens[iPrev], ribbonBottomScreens[i], ribbonBottomScreens[iNext], ribbonBottomScreens[iNext2]);
}
public virtual void render2StrandSegment(int monomerCount, Monomer group, short colix, short[] mads, int i)
{
int iLast = monomerCount;
int iPrev = i - 1;
if (iPrev < 0)
{
iPrev = 0;
}
int iNext = i + 1;
if (iNext > iLast)
{
iNext = iLast;
}
int iNext2 = i + 2;
if (iNext2 > iLast)
{
iNext2 = iLast;
}
//change false -> true to fill in mesh
g3d.drawHermite(true, ribbonBorder, colix, isNucleicPolymer ? 4 : 7, ribbonTopScreens[iPrev], ribbonTopScreens[i], ribbonTopScreens[iNext], ribbonTopScreens[iNext2], ribbonBottomScreens[iPrev], ribbonBottomScreens[i], ribbonBottomScreens[iNext], ribbonBottomScreens[iNext2]);
//g3d.drawHermite(true, ribbonBorder, colix, isNucleicPolymer?4:7, ribbonTopScreens[iPrev], ribbonTopScreens[i], ribbonTopScreens[iNext], ribbonTopScreens[iNext2], ribbonBottomScreens[iPrev], ribbonBottomScreens[i], ribbonBottomScreens[iNext], ribbonBottomScreens[iNext2]);
}
public virtual void render2StrandArrowhead(int monomerCount, Monomer group, short colix, short[] mads, int i)
{
int iLast = monomerCount;
int iPrev = i - 1;
if (iPrev < 0)
{
iPrev = 0;
}
int iNext = i + 1;
if (iNext > iLast)
{
iNext = iLast;
}
int iNext2 = i + 2;
if (iNext2 > iLast)
{
iNext2 = iLast;
}
calc1Screen(leadMidpoints[i], wingVectors[i], mads[i], .7f / 1000, screenArrowTop);
calc1Screen(leadMidpoints[iPrev], wingVectors[iPrev], mads[iPrev], 1.0f / 1000, screenArrowTopPrev);
calc1Screen(leadMidpoints[i], wingVectors[i], mads[i], (-.7f) / 1000, screenArrowBot);
calc1Screen(leadMidpoints[i], wingVectors[i], mads[i], (-1.0f) / 1000, screenArrowBotPrev);
//if (ribbonBorder)
//g3d.fillCylinder(colix, colix, Graphics3D.ENDCAPS_SPHERICAL, 3, screenArrowTop.x, screenArrowTop.y, screenArrowTop.z, screenArrowBot.x, screenArrowBot.y, screenArrowBot.z);
g3d.drawHermite(true, ribbonBorder, colix, isNucleicPolymer?4:7, screenArrowTopPrev, screenArrowTop, leadMidpointScreens[iNext], leadMidpointScreens[iNext2], screenArrowBotPrev, screenArrowBot, leadMidpointScreens[iNext], leadMidpointScreens[iNext2]);
}
public void renderRopeSegment(short colix, short[] mads, int i, int monomerCount, Monomer[] monomers, Point3i[] leadMidpointScreens, bool[] isSpecials)
{
int iPrev1 = i - 1;
if (iPrev1 < 0)
iPrev1 = 0;
int iNext1 = i + 1;
if (iNext1 > monomerCount)
iNext1 = monomerCount;
int iNext2 = i + 2;
if (iNext2 > monomerCount)
iNext2 = monomerCount;
int madThis, madBeg, madEnd;
madThis = madBeg = madEnd = mads[i];
if (isSpecials != null)
{
if (!isSpecials[iPrev1])
madBeg = (mads[iPrev1] + madThis) / 2;
if (!isSpecials[iNext1])
madEnd = (mads[iNext1] + madThis) / 2;
}
int diameterBeg = leadMidpointScreens[i].z;//viewer.scaleToScreen(leadMidpointScreens[i].z, madBeg);
int diameterEnd = leadMidpointScreens[iNext1].z;//viewer.scaleToScreen(leadMidpointScreens[iNext1].z, madEnd);
int diameterMid = monomers[i].LeadAtom.ScreenZ;//viewer.scaleToScreen(monomers[i].LeadAtom.ScreenZ, madThis);
g3d.fillHermite(colix, monomers[i].Nucleic?4:7, diameterBeg, diameterMid, diameterEnd, leadMidpointScreens[iPrev1], leadMidpointScreens[i], leadMidpointScreens[iNext1], leadMidpointScreens[iNext2]);
}
public static Monomer[] getNucleicMonomers(Group[] groups, int firstGroupIndex)
{
NucleicMonomer previous = null;
int count = 0;
for (int i = firstGroupIndex; i < groups.Length; ++i, ++count)
{
Group group = groups[i];
if (!(group is NucleicMonomer))
{
break;
}
NucleicMonomer current = (NucleicMonomer)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] = (NucleicMonomer)groups[firstGroupIndex + j];
}
return(monomers);
}
////////////////////////////////////////////////////////////////
// some utilities
public bool[] calcIsSpecials(int monomerCount, Monomer[] monomers)
{
bool[] isSpecials = new bool[monomerCount + 1];// null;// viewer.allocTempBooleans(monomerCount + 1);
for (int i = monomerCount; --i >= 0; )
isSpecials[i] = monomers[i].HelixOrSheet;
isSpecials[monomerCount] = isSpecials[monomerCount - 1];
return isSpecials;
}
public override bool isConnectedAfter(Monomer possiblyPreviousMonomer)
{
if (possiblyPreviousMonomer == null)
return true;
if (!(possiblyPreviousMonomer is PhosphorusMonomer))
return false;
// 1PN8 73:d and 74:d are 7.001 angstroms apart
float distance = LeadAtomPoint.distance(possiblyPreviousMonomer.LeadAtomPoint);
return distance <= 7.1f;
}
public virtual void render1Chain(int monomerCount, Monomer[] monomers, Point3f[] centers, Vector3f[] vectors, short[] mads, short[] colixes)
{
Point3i[] ribbonTopScreens;
Point3i[] ribbonBottomScreens;
ribbonTopScreens = calcScreens(centers, vectors, mads, isNucleic?1f:0.5f);
ribbonBottomScreens = calcScreens(centers, vectors, mads, isNucleic?0f:- 0.5f);
render2Strand(monomerCount, monomers, mads, colixes, ribbonTopScreens, ribbonBottomScreens);
//viewer.freeTempScreens(ribbonTopScreens);
//viewer.freeTempScreens(ribbonBottomScreens);
}
public virtual int getIndex(Monomer monomer)
{
int i;
for (i = monomerCount; --i >= 0;)
{
if (monomers[i] == monomer)
{
break;
}
}
return(i);
}
public virtual int getIndex(Monomer monomer)
{
Monomer[] monomers = apolymer.monomers;
int i;
for (i = monomerCount; --i >= 0;)
{
if (monomers[monomerIndex + i] == monomer)
{
break;
}
}
return(i);
}
////////////////////////////////////////////////////////////////
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 render1Chain()
{
isSpecials = calcIsSpecials(monomerCount, monomers);
leadMidpointScreens = calcScreenLeadMidpoints(monomerCount, leadMidpoints);
ribbonTopScreens = calcScreens(leadMidpoints, wingVectors, mads, isNucleicPolymer?1f / 1000:0.5f / 1000);
ribbonBottomScreens = calcScreens(leadMidpoints, wingVectors, mads, isNucleicPolymer?0f:(-0.5f) / 1000);
bool lastWasSpecial = false;
for (int i = monomerCount; --i >= 0;)
{
if (mads[i] > 0)
{
Monomer group = monomers[i];
short colix = 0;// Graphics3D.inheritColix(colixes[i], group.LeadAtom.colixAtom);
bool isSpecial = isSpecials[i];
if (isSpecial)
{
if (lastWasSpecial)
{
render2StrandSegment(monomerCount, group, colix, mads, i);
}
else
{
render2StrandArrowhead(monomerCount, group, colix, mads, i);
}
}
else
{
renderRopeSegment(colix, mads, i, monomerCount, monomers, leadMidpointScreens, isSpecials);
//if (isNucleicPolymer)
// renderNucleicBaseStep((NucleicMonomer) group, colix, mads[i], leadMidpointScreens[i + 1]);
}
lastWasSpecial = isSpecial;
}
else
{
// miguel 2004 12 13
// bug [ 1014874 ] Beta pleated sheet arrowheads
// if a segment is not being rendered then we need to
// reset our flag so that the arrowhead will be drawn
// for the next segment
lastWasSpecial = false;
}
}
//viewer.freeTempScreens(ribbonTopScreens);
//viewer.freeTempScreens(ribbonBottomScreens);
//viewer.freeTempScreens(leadMidpointScreens);
//viewer.freeTempBooleans(isSpecials);
}
private void BuildPolymers()
{
for (int i = 0; i < groupCount; ++i)
{
Group group = groups[i];
if (group is Monomer)
{
Monomer monomer = (Monomer)group;
if (monomer.polymer == null)
{
Polymer.allocatePolymer(groups, i);
}
}
}
}
public override bool isConnectedAfter(Monomer possiblyPreviousMonomer)
{
if (possiblyPreviousMonomer == null)
{
return(true);
}
if (!(possiblyPreviousMonomer is AlphaMonomer))
{
return(false);
}
float distance = LeadAtomPoint.distance(possiblyPreviousMonomer.LeadAtomPoint);
// jan reichert in email to miguel on 10 May 2004 said 4.2 looked good
return(distance <= 4.2f);
}
public override bool isConnectedAfter(Monomer possiblyPreviousMonomer)
{
if (possiblyPreviousMonomer == null)
{
return(true);
}
if (!(possiblyPreviousMonomer is PhosphorusMonomer))
{
return(false);
}
// 1PN8 73:d and 74:d are 7.001 angstroms apart
float distance = LeadAtomPoint.distance(possiblyPreviousMonomer.LeadAtomPoint);
return(distance <= 7.1f);
}
public virtual int getSelectedMonomerIndex(Monomer monomer)
{
int selectedMonomerIndex = 0;
for (int i = 0; i < monomerCount; ++i)
{
if (bsSelectedMonomers.Get(i))
{
if (monomers[i] == monomer)
{
return(selectedMonomerIndex);
}
++selectedMonomerIndex;
}
}
return(-1);
}
////////////////////////////////////////////////////////////////
public override bool isConnectedAfter(Monomer possiblyPreviousMonomer)
{
if (possiblyPreviousMonomer == null)
{
return(true);
}
Atom myPhosphorusAtom = PhosphorusAtom;
if (myPhosphorusAtom == null)
{
return(false);
}
if (!(possiblyPreviousMonomer is NucleicMonomer))
{
return(false);
}
NucleicMonomer other = (NucleicMonomer)possiblyPreviousMonomer;
return(other.O3PrimeAtom.isBonded(myPhosphorusAtom));
}
public virtual int getIndex(Monomer monomer)
{
Monomer[] monomers = apolymer.monomers;
int i;
for (i = monomerCount; --i >= 0; )
if (monomers[monomerIndex + i] == monomer)
break;
return i;
}
public virtual void render2Strand(int monomerCount, Monomer[] monomers, short[] mads, short[] colixes, Point3i[] ribbonTopScreens, Point3i[] ribbonBottomScreens)
{
for (int i = monomerCount; --i >= 0; )
if (mads[i] > 0)
render2StrandSegment(monomerCount, monomers[i], colixes[i], mads, ribbonTopScreens, ribbonBottomScreens, i);
}
public virtual int getIndex(Monomer monomer)
{
int i;
for (i = monomerCount; --i >= 0; )
if (monomers[i] == monomer)
break;
return i;
}
public virtual void render2StrandSegment(int monomerCount, Monomer monomer, short colix, short[] mads, Point3i[] ribbonTopScreens, Point3i[] ribbonBottomScreens, int i)
{
int iLast = monomerCount;
int iPrev = i - 1;
if (iPrev < 0)
iPrev = 0;
int iNext = i + 1;
if (iNext > iLast)
iNext = iLast;
int iNext2 = i + 2;
if (iNext2 > iLast)
iNext2 = iLast;
//colix = Graphics3D.inheritColix(colix, monomer.LeadAtom.colixAtom);
g3d.drawHermite(true, ribbonBorder, colix, isNucleic?4:7, ribbonTopScreens[iPrev], ribbonTopScreens[i], ribbonTopScreens[iNext], ribbonTopScreens[iNext2], ribbonBottomScreens[iPrev], ribbonBottomScreens[i], ribbonBottomScreens[iNext], ribbonBottomScreens[iNext2]);
}
public AminoPolymer(Monomer[] monomers)
: base(monomers)
{ }
public abstract bool isConnectedAfter(Monomer possiblyPreviousMonomer);
////////////////////////////////////////////////////////////////
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 int getSelectedMonomerIndex(Monomer monomer)
{
int selectedMonomerIndex = 0;
for (int i = 0; i < monomerCount; ++i)
{
if (bsSelectedMonomers.Get(i))
{
if (monomers[i] == monomer)
return selectedMonomerIndex;
++selectedMonomerIndex;
}
}
return - 1;
}
public NucleicPolymer(Monomer[] monomers)
: base(monomers)
{ }
public static Monomer[] getNucleicMonomers(Group[] groups, int firstGroupIndex)
{
NucleicMonomer previous = null;
int count = 0;
for (int i = firstGroupIndex; i < groups.Length; ++i, ++count)
{
Group group = groups[i];
if (!(group is NucleicMonomer))
break;
NucleicMonomer current = (NucleicMonomer) 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] = (NucleicMonomer) groups[firstGroupIndex + j];
return monomers;
}
public abstract bool isConnectedAfter(Monomer possiblyPreviousMonomer);
public virtual void render2StrandSegment(int monomerCount, Monomer group, short colix, short[] mads, int i)
{
int iLast = monomerCount;
int iPrev = i - 1;
if (iPrev < 0)
iPrev = 0;
int iNext = i + 1;
if (iNext > iLast)
iNext = iLast;
int iNext2 = i + 2;
if (iNext2 > iLast)
iNext2 = iLast;
//change false -> true to fill in mesh
g3d.drawHermite(true, ribbonBorder, colix, isNucleicPolymer ? 4 : 7, ribbonTopScreens[iPrev], ribbonTopScreens[i], ribbonTopScreens[iNext], ribbonTopScreens[iNext2], ribbonBottomScreens[iPrev], ribbonBottomScreens[i], ribbonBottomScreens[iNext], ribbonBottomScreens[iNext2]);
//g3d.drawHermite(true, ribbonBorder, colix, isNucleicPolymer?4:7, ribbonTopScreens[iPrev], ribbonTopScreens[i], ribbonTopScreens[iNext], ribbonTopScreens[iNext2], ribbonBottomScreens[iPrev], ribbonBottomScreens[i], ribbonBottomScreens[iNext], ribbonBottomScreens[iNext2]);
}
public virtual void render2StrandArrowhead(int monomerCount, Monomer group, short colix, short[] mads, int i)
{
int iLast = monomerCount;
int iPrev = i - 1;
if (iPrev < 0)
iPrev = 0;
int iNext = i + 1;
if (iNext > iLast)
iNext = iLast;
int iNext2 = i + 2;
if (iNext2 > iLast)
iNext2 = iLast;
calc1Screen(leadMidpoints[i], wingVectors[i], mads[i], .7f / 1000, screenArrowTop);
calc1Screen(leadMidpoints[iPrev], wingVectors[iPrev], mads[iPrev], 1.0f / 1000, screenArrowTopPrev);
calc1Screen(leadMidpoints[i], wingVectors[i], mads[i], (- .7f) / 1000, screenArrowBot);
calc1Screen(leadMidpoints[i], wingVectors[i], mads[i], (- 1.0f) / 1000, screenArrowBotPrev);
//if (ribbonBorder)
//g3d.fillCylinder(colix, colix, Graphics3D.ENDCAPS_SPHERICAL, 3, screenArrowTop.x, screenArrowTop.y, screenArrowTop.z, screenArrowBot.x, screenArrowBot.y, screenArrowBot.z);
g3d.drawHermite(true, ribbonBorder, colix, isNucleicPolymer?4:7, screenArrowTopPrev, screenArrowTop, leadMidpointScreens[iNext], leadMidpointScreens[iNext2], screenArrowBotPrev, screenArrowBot, leadMidpointScreens[iNext], leadMidpointScreens[iNext2]);
}
////////////////////////////////////////////////////////////////
public override bool isConnectedAfter(Monomer possiblyPreviousMonomer)
{
if (possiblyPreviousMonomer == null)
return true;
Atom myPhosphorusAtom = PhosphorusAtom;
if (myPhosphorusAtom == null)
return false;
if (!(possiblyPreviousMonomer is NucleicMonomer))
return false;
NucleicMonomer other = (NucleicMonomer) possiblyPreviousMonomer;
return other.O3PrimeAtom.isBonded(myPhosphorusAtom);
}
public Polymer(Monomer[] monomers)
{
this.monomers = monomers;
this.monomerCount = monomers.Length;
for (int i = monomerCount; --i >= 0; )
monomers[i].Polymer = this;
model = monomers[0].chain.model;
model.addPolymer(this);
}
public AlphaPolymer(Monomer[] monomers)
: base(monomers)
{ }
public override bool isConnectedAfter(Monomer possiblyPreviousMonomer)
{
if (possiblyPreviousMonomer == null)
return true;
if (!(possiblyPreviousMonomer is AlphaMonomer))
return false;
float distance = LeadAtomPoint.distance(possiblyPreviousMonomer.LeadAtomPoint);
// jan reichert in email to miguel on 10 May 2004 said 4.2 looked good
return distance <= 4.2f;
}