Examples of bonds()

Examples of org.openscience.cdk.interfaces.IAtomContainer.bonds()

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      if(selectedAC == null)
          return;
      for(IAtom atom:selectedAC.atoms()) {
          chemModelRelay.removeAtom(atom);
      }
      for(IBond bond:selectedAC.bonds()) {
        chemModelRelay.removeBondAndLoneAtoms( bond );
      }
      setSelection( AbstractSelection.EMPTY_SELECTION );
  }
 
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Examples of org.openscience.cdk.interfaces.IAtomContainer.bonds()

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              for (IAtom mAt : droppedContainer.atoms()) {
                if (!containerWithMerge.contains(mAt)) {
                  containerWithMerge.addAtom(mAt);
                }
              }
              for (IBond mBond : droppedContainer.bonds()) {
                if (!containerWithMerge.contains(mBond)) {
                  containerWithMerge.addBond(mBond);
                }
              }
              chemModelRelay.getChemModel().getMoleculeSet().removeAtomContainer(droppedContainer);
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Examples of org.openscience.cdk.interfaces.IAtomContainer.bonds()

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              for (IAtom mAt : droppedContainer.atoms()) {
                if (containerWithMerge.contains(mAt)) {
                  containerWithMerge.removeAtom(mAt);
                }
              }
              for (IBond mBond : droppedContainer.bonds()) {
                if (containerWithMerge.contains(mBond)) {
                  containerWithMerge.removeBond(mBond);
                }
              }
              //restore removed container atc2
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Examples of org.openscience.cdk.interfaces.IAtomContainer.bonds()

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           atomsToMove = new HashSet<IAtom>();

            for (IAtom atom : selectedAC.atoms()) {
                atomsToMove.add(atom);
            }
            for (IBond bond : selectedAC.bonds()) {
                for (IAtom atom : bond.atoms()){
                    atomsToMove.add(atom);
                    selectedAC.addAtom(atom);
                }
            }
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Examples of org.openscience.cdk.interfaces.IRing.bonds()

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          else
            sourceContainer.addAtom(ringAtom);
        }
      }

      for (IBond ringBond : newRing.bonds()) {
        if (phantom)
          this.addPhantomBond(ringBond);
        else
          sourceContainer.addBond(ringBond);
      }
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Examples of org.openscience.cdk.interfaces.IRing.bonds()

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        else
          sourceContainer.addAtom(ringAtom);
      }
    }

    for (IBond ringBond : newRing.bonds()) {
      if (phantom)
        this.addPhantomBond(ringBond);
      else
        sourceContainer.addBond(ringBond);
    }
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Examples of org.openscience.cdk.interfaces.IRing.bonds()

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          addPhantomAtom(ringAtom);
        else
          sourceContainer.addAtom(ringAtom);
      }
    }
    for (IBond ringBond : newRing.bonds()) {
      if (ringBond != bond) {
        if (phantom)
          addPhantomBond(ringBond);
        else
          sourceContainer.addBond(ringBond);
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Examples of org.openscience.cdk.interfaces.IRing.bonds()

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          this.addPhantomAtom(ringAtom);
        else
          sourceContainer.addAtom(ringAtom);
      }
    }
    for (IBond ringBond : newRing.bonds()) {
      if (ringBond != bond) {
        if (phantom)
          this.addPhantomBond(ringBond);
        else
          sourceContainer.addBond(ringBond);
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Examples of org.openscience.cdk.interfaces.IRing.bonds()

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            ringPlacer.placeRing(ring, worldCoord, bondLength, RingPlacer.jcpAngles);
           
            for(IAtom atom : ring.atoms())
                this.chemModelRelay.addPhantomAtom(atom);
            for(IBond atom : ring.bonds())
                this.chemModelRelay.addPhantomBond(atom);
            //and look if it would merge somewhere
            chemModelRelay.getRenderer().getRenderer2DModel().getMerge().clear();
            for(IAtom atom : ring.atoms()){
                IAtom closestAtomInRing = this.chemModelRelay.getClosestAtom(atom);
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