Examples of atoms()

Examples of org.openscience.cdk.interfaces.IRing.atoms()

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            sharedAtomsCenter, ringCenterVector, bondLength);
      }
    }

    // add the ring to the source container/phantoms
    for (IAtom ringAtom : newRing.atoms()) {
      if (ringAtom != atom) {
        if (phantom)
          this.addPhantomAtom(ringAtom);
        else
          sourceContainer.addAtom(ringAtom);
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Examples of org.openscience.cdk.interfaces.IRing.atoms()

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        this.addPhantomBond(ringBond);
      else
        sourceContainer.addBond(ringBond);
    }
    if (!phantom)
      updateAtoms(sourceContainer, newRing.atoms());
    for (IAtom newatom : newRing.atoms()) {
      if (atom != newatom && getClosestAtom(atom) != null) {
        JChemPaintRendererModel rModel = this.getRenderer().getRenderer2DModel();
        double d = rModel.getHighlightDistance() / rModel.getScale();
        atom.getPoint2d().x += d;
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Examples of org.openscience.cdk.interfaces.IRing.atoms()

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      else
        sourceContainer.addBond(ringBond);
    }
    if (!phantom)
      updateAtoms(sourceContainer, newRing.atoms());
    for (IAtom newatom : newRing.atoms()) {
      if (atom != newatom && getClosestAtom(atom) != null) {
        JChemPaintRendererModel rModel = this.getRenderer().getRenderer2DModel();
        double d = rModel.getHighlightDistance() / rModel.getScale();
        atom.getPoint2d().x += d;
      }
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Examples of org.openscience.cdk.interfaces.IRing.atoms()

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    // atoms
    IRing newRing = createAttachRing(sharedAtoms, size, "C", phantom);
    ringPlacer.placeFusedRing(newRing, sharedAtoms, sharedAtomsCenter,
        ringCenterVector, bondLength);
    // add the new atoms and bonds
    for (IAtom ringAtom : newRing.atoms()) {
      if (ringAtom != firstAtom && ringAtom != secondAtom) {
        if (phantom)
          addPhantomAtom(ringAtom);
        else
          sourceContainer.addAtom(ringAtom);
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Examples of org.openscience.cdk.interfaces.IRing.atoms()

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        else
          sourceContainer.addBond(ringBond);
      }
    }
    if (!phantom)
      updateAtoms(sourceContainer, newRing.atoms());

    JChemPaintRendererModel rModel = this.getRenderer().getRenderer2DModel();
    double d = rModel.getHighlightDistance() / rModel.getScale();
    for (IAtom atom : newRing.atoms()) {
      if (atom != firstAtom && atom != secondAtom
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Examples of org.openscience.cdk.interfaces.IRing.atoms()

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    if (!phantom)
      updateAtoms(sourceContainer, newRing.atoms());

    JChemPaintRendererModel rModel = this.getRenderer().getRenderer2DModel();
    double d = rModel.getHighlightDistance() / rModel.getScale();
    for (IAtom atom : newRing.atoms()) {
      if (atom != firstAtom && atom != secondAtom
          && getClosestAtom(atom) != null) {
        atom.getPoint2d().x += d;
      }
    }
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Examples of org.openscience.cdk.interfaces.IRing.atoms()

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    } else { // assume Order.DOUBLE, so only need to add 2 double bonds
      newRing.getBond(2).setOrder(IBond.Order.DOUBLE);
      newRing.getBond(4).setOrder(IBond.Order.DOUBLE);
    }
    // add the new atoms and bonds
    for (IAtom ringAtom : newRing.atoms()) {
      if (ringAtom != firstAtom && ringAtom != secondAtom) {
        if (phantom)
          this.addPhantomAtom(ringAtom);
        else
          sourceContainer.addAtom(ringAtom);
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Examples of org.openscience.cdk.interfaces.IRing.atoms()

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        else
          sourceContainer.addBond(ringBond);
      }
    }
    if (!phantom)
      updateAtoms(sourceContainer, newRing.atoms());

    JChemPaintRendererModel rModel = this.getRenderer().getRenderer2DModel();
    double d = rModel.getHighlightDistance() / rModel.getScale();
    for (IAtom atom : newRing.atoms()) {
      if (atom != firstAtom && atom != secondAtom
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Examples of org.openscience.cdk.interfaces.IRing.atoms()

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    if (!phantom)
      updateAtoms(sourceContainer, newRing.atoms());

    JChemPaintRendererModel rModel = this.getRenderer().getRenderer2DModel();
    double d = rModel.getHighlightDistance() / rModel.getScale();
    for (IAtom atom : newRing.atoms()) {
      if (atom != firstAtom && atom != secondAtom
          && getClosestAtom(atom) != null) {
        atom.getPoint2d().x += d;
      }
    }
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Examples of org.openscience.cdk.interfaces.IRing.atoms()

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        if (singleSelection == null) {
            //we add the ring
        IRing newRing = this.addRingToEmptyCanvas(worldCoord);
            chemModelRelay.getRenderer().getRenderer2DModel().getMerge().clear();
            //we look if it would merge
            for(IAtom atom : newRing.atoms()){
                IAtom closestAtomInRing = this.chemModelRelay.getClosestAtom(atom);
                if( closestAtomInRing != null) {
                        chemModelRelay.getRenderer().getRenderer2DModel().getMerge().put(atom, closestAtomInRing);
                }
            }
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