public void addSecondaryStructure(sbyte type, char startChainID, int startSeqcode, char endChainID, int endSeqcode)
{
for (int i = polymerCount; --i >= 0;)
{
Polymer polymer = polymers[i];
polymer.addSecondaryStructure(type, startChainID, startSeqcode, endChainID, endSeqcode);
}
}
public void addPolymer(Polymer polymer)
{
if (polymerCount == polymers.Length)
{
polymers = (Polymer[])Util.doubleLength(polymers);
}
polymers[polymerCount++] = polymer;
}
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 void calcHydrogenBonds(BitArray bsA, BitArray bsB)
{
for (int i = model.PolymerCount; --i >= 0;)
{
Polymer otherPolymer = model.getPolymer(i);
if (otherPolymer == this)
{
// don't look at self
continue;
}
if (otherPolymer == null || !(otherPolymer is NucleicPolymer))
{
continue;
}
lookForHbonds((NucleicPolymer)otherPolymer, bsA, bsB);
}
}
public Org.Jmol.Viewer.Polymer TranslateCDKPolymer(Org.OpenScience.CDK.Polymer polymer)
{
// translate all monomers
ICollection monomers = polymer.MonomerNames;
Group[] groups = new Group[monomers.Count];
IEnumerator iter = monomers.GetEnumerator();
int idx = 0;
while (iter.MoveNext())
{
groups[idx++] = TranslateCDKMonomer((Org.OpenScience.CDK.Interfaces.IMonomer)iter.Current);
}
Org.Jmol.Viewer.Polymer lPolymer = Org.Jmol.Viewer.Polymer.allocatePolymer(groups, 0);
return(lPolymer);
}
public Mpspolymer(Polymer polymer, int madOn, int madHelixSheet, int madTurnRandom, int madDnaRna)
{
this.polymer = polymer;
this.madOn = (short)madOn;
this.madHelixSheet = (short)madHelixSheet;
this.madTurnRandom = (short)madTurnRandom;
this.madDnaRna = (short)madDnaRna;
// FIXME
// I don't think that polymer can ever be null for this thing
// so stop checking for null and see if it explodes
monomerCount = polymer == null?0:polymer.monomerCount;
if (monomerCount > 0)
{
colixes = new short[monomerCount];
mads = new short[monomerCount + 1];
monomers = polymer.monomers;
leadMidpoints = polymer.LeadMidpoints;
wingVectors = polymer.WingVectors;
}
}
public void addPolymer(Polymer polymer)
{
if (polymerCount == polymers.Length)
polymers = (Polymer[]) Util.doubleLength(polymers);
polymers[polymerCount++] = polymer;
}
public Cchain(Polymer polymer)
: base(polymer, -2, 3000, 500, 1000)
{
}
public Mpspolymer(Polymer polymer, int madOn, int madHelixSheet, int madTurnRandom, int madDnaRna)
{
this.polymer = polymer;
this.madOn = (short) madOn;
this.madHelixSheet = (short) madHelixSheet;
this.madTurnRandom = (short) madTurnRandom;
this.madDnaRna = (short) madDnaRna;
// FIXME
// I don't think that polymer can ever be null for this thing
// so stop checking for null and see if it explodes
monomerCount = polymer == null?0:polymer.monomerCount;
if (monomerCount > 0)
{
colixes = new short[monomerCount];
mads = new short[monomerCount + 1];
monomers = polymer.monomers;
leadMidpoints = polymer.LeadMidpoints;
wingVectors = polymer.WingVectors;
}
}
public abstract Mpspolymer allocateMpspolymer(Polymer polymer);
public override Mps.Mpspolymer allocateMpspolymer(Polymer polymer)
{
return(new Cchain(/*this, */ polymer));
}
public override Mps.Mpspolymer allocateMpspolymer(Polymer polymer)
{
return new Schain(this, polymer);
}
public Schain(Ribbons enclosingInstance, Polymer polymer)
: base(polymer, -2, 3000, 800, 5000)
{ }
public abstract Mpspolymer allocateMpspolymer(Polymer polymer);
public override Mps.Mpspolymer allocateMpspolymer(Polymer polymer)
{
return new Cchain(/*this, */polymer);
}
public Schain(Ribbons enclosingInstance, Polymer polymer)
: base(polymer, -2, 3000, 800, 5000)
{
}
public override Mps.Mpspolymer allocateMpspolymer(Polymer polymer)
{
return(new Schain(this, polymer));
}
public Cchain(Polymer polymer)
:base(polymer, - 2, 3000, 500, 1000)
{ }
