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 override Mps.Mpspolymer allocateMpspolymer(Polymer polymer) { return new Cchain(/*this, */polymer); }
public override Mps.Mpspolymer allocateMpspolymer(Polymer polymer) { return(new Schain(this, polymer)); }
public Cchain(Polymer polymer) :base(polymer, - 2, 3000, 500, 1000) { }