Class MolDistHistViz

    • Field Detail

      • DESCRIBE_MAPPED

        public static final int DESCRIBE_MAPPED
        Only mapped atoms are described.
        See Also:
        Constant Field Values
      • CAPACITY_INEVITABLE_PPPOINTS

        public static final int CAPACITY_INEVITABLE_PPPOINTS
        See Also:
        Constant Field Values
      • TAG_VIZ_INFO_ENCODED

        public static final java.lang.String TAG_VIZ_INFO_ENCODED
        See Also:
        Constant Field Values
      • COLORS

        public static final transient java.lang.String[] COLORS
        Colors for visualization of the Flexophore mapping.
    • Constructor Detail

      • MolDistHistViz

        public MolDistHistViz()
      • MolDistHistViz

        public MolDistHistViz​(int nNodes)
      • MolDistHistViz

        public MolDistHistViz​(int nNodes,
                              Molecule3D molecule3D)
      • MolDistHistViz

        public MolDistHistViz​(MolDistHist mdh)
    • Method Detail

      • createIndexTables

        public static void createIndexTables()
      • addInevitablePharmacophorePoint

        public void addInevitablePharmacophorePoint​(int indexPPNode)
      • removeInevitablePharmacophorePoint

        public void removeInevitablePharmacophorePoint​(int indexPPNode)
      • setModeFlexophore

        public void setModeFlexophore​(byte modeFlexophore)
      • setMarkAll

        public void setMarkAll​(boolean mark)
      • setMark

        public void setMark​(int index,
                            boolean mark)
      • isMarked

        public boolean isMarked​(int index)
      • addNode

        public int addNode​(PPNodeViz node)
        Parameters:
        node -
        Returns:
        index of the node.
      • check

        public boolean check()
      • copy

        public void copy​(MolDistHistViz copy)
        Parameters:
        copy - This is written into copy.
      • recalculateCoordPPPoints

        public void recalculateCoordPPPoints()
        Recalculates the coordinates off the pharmacophore nodes. Has to be called after changing the coordinates for the Molecule3D.
      • resetInevitablePharmacophorePoints

        public void resetInevitablePharmacophorePoints()
      • resetInfoColor

        public void resetInfoColor()
      • createNodeIndex

        public void createNodeIndex()
        This index is used to track the fate of the nodes MvK 17.07.2007
      • getBondAtom

        public int getBondAtom​(int index,
                               int bond)
        Parameters:
        index - 0 or 1
        bond - index of the bond array
        Returns:
        the atom index
      • getConnAtom

        public int getConnAtom​(int at,
                               int index)
      • getConnBond

        public int getConnBond​(int at,
                               int index)
      • getIndexFromCoord

        public int getIndexFromCoord​(double x,
                                     double y,
                                     double z)
      • getInfo

        public int getInfo​(int index)
      • getNodes

        public java.util.List<PPNodeViz> getNodes()
        Returns:
        shallow copy.
      • set

        public void set​(java.util.List<PPNodeViz> liPPNodeViz)
      • set

        public void set​(Molecule3D ff)
        Parameters:
        ff - has to be the molecule the descriptor was derived from.
      • setMappingIndex

        public void setMappingIndex​(int index,
                                    int info)
      • setSimilarityMappingNodes

        public void setSimilarityMappingNodes​(int index,
                                              float similarityMappingNodes)
      • getName

        public java.lang.String getName()
      • setName

        public void setName​(java.lang.String name)
      • isOnlyCarbon

        public boolean isOnlyCarbon​(int index)
      • canonize

        public void canonize()
      • swapNodes

        public void swapNodes​(int n1,
                              int n2)
      • getNumCExclusiveNodes

        public int getNumCExclusiveNodes()
      • getNumHeteroNodes

        public int getNumHeteroNodes()
      • getInevitablePharmacophorePoints

        public java.util.List<java.lang.Integer> getInevitablePharmacophorePoints()
      • getHashSetIndexInevitablePPPoints

        protected java.util.HashSet<java.lang.Integer> getHashSetIndexInevitablePPPoints()
      • isAliphatic

        public boolean isAliphatic​(int indexNode)
      • isAcceptor

        public boolean isAcceptor​(int indexNode)
      • isDonor

        public boolean isDonor​(int indexNode)
      • isAromatic

        public boolean isAromatic​(int indexNode)
      • isChargePos

        public boolean isChargePos​(int indexNode)
      • isChargeNeg

        public boolean isChargeNeg​(int indexNode)
      • realize

        public void realize()
        Canonizes the MolDistHistViz Must be called after changes in the nodes or distance histograms.
      • blurrSingleBinHistograms

        public void blurrSingleBinHistograms()
      • calculate

        public void calculate()
      • finalizeMolecule

        protected static Molecule3D finalizeMolecule​(Molecule3D mol)
        Remove all atoms without connections.
        Parameters:
        mol -
        Returns:
      • getMolDistHist

        public MolDistHist getMolDistHist()
        Returns:
        deep object.
      • getMaximumDistanceInPPPoint

        public double getMaximumDistanceInPPPoint​(int indexNode)
      • getMolecule

        public Molecule3D getMolecule()
        The atoms of the ff molecule contain the corresponding PPNode indices in the first field of the PPP vector.
        Returns:
      • getMoleculeRemovedUnrelatedAtoms

        public Molecule3D getMoleculeRemovedUnrelatedAtoms()
      • hashCode

        public int hashCode()
        Overrides:
        hashCode in class java.lang.Object
      • toStringInevitable

        public java.lang.String toStringInevitable()
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object
        Returns:
        A canonized representation of the object.
      • toStringPPNodes

        public java.lang.String toStringPPNodes()
        Only nodes without coordinates
        Returns:
      • toStringShort

        public java.lang.String toStringShort()
      • equals

        public boolean equals​(java.lang.Object o)
        Overrides:
        equals in class java.lang.Object
      • setDistanceTables

        public void setDistanceTables​(java.util.List<double[][]> liDistanceTable)
        The distance tables which were generated from the conformations.
        Parameters:
        liDistanceTable -
      • getDistanceTables

        public java.util.List<float[][]> getDistanceTables()
      • formatDescription

        protected static java.lang.String formatDescription​(java.lang.String s)
      • merge

        public static void merge​(MolDistHistViz mdhviz,
                                 MolDistHist mdh)
        Deprecated.
        Merges the histograms from mdh into mdhviz.
        Parameters:
        mdhviz - has new histograms afterwards.
        mdh - stays unchanged.
      • summarizeAlkaneCluster

        public static MolDistHistViz summarizeAlkaneCluster​(MolDistHistViz mdh,
                                                            int maxDistance)
        Summarizes alkane cluster. The central node may not be a alkane cluster. The interaction types of the cluster members are added to the interaction types of the center node.
        Parameters:
        mdh -
        maxDistance -
        Returns: