Class AlignmentMolecule

    • Field Detail

      • nodes

        public chemaxon.marvin.alignment.NodeSum nodes
      • molID

        protected int molID
    • Method Detail

      • setMolID

        public void setMolID​(int molID)
      • getNodes

        public chemaxon.marvin.alignment.NodeSum getNodes()
      • initVariables

        public void initVariables​(boolean enableTranslateAndRotate)
        Parameters:
        enableTranslateAndRotate -
      • getColors

        public chemaxon.marvin.alignment.NodeColor getColors()
      • getVisualizable

        public chemaxon.marvin.alignment.Visualizable getVisualizable()
      • getRotBondCount

        public int getRotBondCount()
      • toData

        @Deprecated
        public byte[] toData()
        Deprecated.
      • distanceRangeStore

        public chemaxon.marvin.alignment.DistanceRangeStore distanceRangeStore()
      • getVolume

        public double getVolume()
        Returns:
        the volume of the molecule in A^3
      • getAtomCount

        public int getAtomCount()
      • crdSafeRefresh

        public void crdSafeRefresh()
      • crdMolRefresh

        public void crdMolRefresh()
      • getMolID

        public int getMolID()
      • getNodeCount

        public int getNodeCount()
      • getMolCrd

        public double[][] getMolCrd()
      • getMoleculeOrig

        public Molecule getMoleculeOrig()
        Gets back a clone of the unmodified input structure.
        Returns:
        clone of the unmodified input structure
      • setAssigned

        public void setAssigned​(int i,
                                boolean b)
      • clearAssigned

        public void clearAssigned()
      • isEnableTranslateAndRotate

        public boolean isEnableTranslateAndRotate()
      • setEnableTranslateAndRotate

        public void setEnableTranslateAndRotate​(boolean enableTranslateAndRotate)
                                         throws chemaxon.marvin.alignment.AlignmentException
        Throws:
        chemaxon.marvin.alignment.AlignmentException
      • showSelectedNodes

        public Molecule showSelectedNodes()