Class BondLengthSet


  • public class BondLengthSet
    extends java.lang.Object
    • Constructor Summary

      Constructors 
      Constructor Description
      BondLengthSet​(StereoMolecule mol)
      Calculates and caches a list of bond length estimates from molecule.
    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      static int getAtomPi​(StereoMolecule mol, int atom)
      Returns an atom's pi electron count for the purpose of classifying a connected bond to determine its length.
      static float getBondCount​(int index)  
      static int getBondID​(StereoMolecule mol, int bond)
      Constructs a bond classification index from a specific bond in a molecule.
      static java.lang.String getBondIDString​(int index)  
      static int getBondIndex​(int bondOrder, boolean isAromatic, boolean isDelocalized, int atomicNo1, int atomicNo2, int atomPi1, int atomPi2)
      Constructs a bond classification ID from individual parameters and returns the ID's index in the sorted list of bond length information.
      static int getBondIndex​(StereoMolecule mol, int bond)
      Constructs a bond classification ID from a specific bond in a molecule and returns the ID's index in the sorted list of bond length information.
      static float getBondLength​(int index)
      Returns an estimate of the bond length based on atom and bond characteristics.
      static float getBondLengthFromCovalentRadii​(StereoMolecule mol, int bond)
      Returns an estimate of the bond length based on atom and bond characteristics.
      static float getBondStdDev​(int index)
      Returns an the standard deviation of bond lengths from bonds with similar characteristics from crystallographic data.
      float getLength​(int bond)  
      float getStdDev​(int bond)  
      static float getStdDevFromCovalentRadii​(StereoMolecule mol, int bond)
      Returns an the standard deviation of bond lengths from bonds with similar characteristics from crystallographic data.
      static boolean isPiConsidered​(int atomicNo)  
      static float lookupBondLength​(StereoMolecule mol, int bond)
      Returns an estimate of the bond length based on atom and bond characteristics.
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • BondLengthSet

        public BondLengthSet​(StereoMolecule mol)
        Calculates and caches a list of bond length estimates from molecule.
        Parameters:
        mol -
    • Method Detail

      • getLength

        public float getLength​(int bond)
      • getStdDev

        public float getStdDev​(int bond)
      • getBondIDString

        public static java.lang.String getBondIDString​(int index)
      • getBondIndex

        public static int getBondIndex​(int bondOrder,
                                       boolean isAromatic,
                                       boolean isDelocalized,
                                       int atomicNo1,
                                       int atomicNo2,
                                       int atomPi1,
                                       int atomPi2)
        Constructs a bond classification ID from individual parameters and returns the ID's index in the sorted list of bond length information. The index can be used to get typical bond length and standard deviation.
        Parameters:
        bondOrder -
        isAromatic -
        isDelocalized -
        atomicNo1 -
        atomicNo2 -
        atomPi1 -
        atomPi2 -
        Returns:
      • getBondIndex

        public static int getBondIndex​(StereoMolecule mol,
                                       int bond)
        Constructs a bond classification ID from a specific bond in a molecule and returns the ID's index in the sorted list of bond length information. The index can be used to get typical bond length and standard deviation.
        Parameters:
        mol -
        bond -
        Returns:
      • getBondID

        public static int getBondID​(StereoMolecule mol,
                                    int bond)
        Constructs a bond classification index from a specific bond in a molecule. The index can be used to get typical bond length and standard deviation.
        Parameters:
        mol -
        bond -
        Returns:
      • isPiConsidered

        public static final boolean isPiConsidered​(int atomicNo)
        Parameters:
        atomicNo -
        Returns:
        whether this atomicNo uses the atom's pi count to further distinguish bond type cases
      • getAtomPi

        public static int getAtomPi​(StereoMolecule mol,
                                    int atom)
        Returns an atom's pi electron count for the purpose of classifying a connected bond to determine its length. The returned value may differ from the formal pi-electron count if the formal count does not represent the real mesomeric situation well.
        Parameters:
        mol -
        atom -
        Returns:
        pi electron count
      • lookupBondLength

        public static float lookupBondLength​(StereoMolecule mol,
                                             int bond)
        Returns an estimate of the bond length based on atom and bond characteristics. The bond is classified based on its characteristics the returned value is the median of equally classified bonds within the COD database. Statistics of purely organic bonds (no metal atoms) are taken from the organic subset of the COD. Requires cHelperRings level of helper arrays.
        Parameters:
        mol -
        bond -
        Returns:
      • getBondLengthFromCovalentRadii

        public static float getBondLengthFromCovalentRadii​(StereoMolecule mol,
                                                           int bond)
        Returns an estimate of the bond length based on atom and bond characteristics. The bond is classified based on its characteristics the returned value is the median of equally classified bonds within the COD or CSD database. Statistics of purely organic bonds (no metal atoms) are taken from the organic subset of the COD/CSD. If there are no similar bond in the crystallographic data sets, the the bond length is estimated from the covalent radii, which if not available may be estimated from the van-der-waals radii.
        Parameters:
        mol -
        bond -
        Returns:
      • getStdDevFromCovalentRadii

        public static float getStdDevFromCovalentRadii​(StereoMolecule mol,
                                                       int bond)
        Returns an the standard deviation of bond lengths from bonds with similar characteristics from crystallographic data. If the estimate is based on covalent radii or van-der-waals radii, the standard deviation reflects that.
        Parameters:
        mol -
        bond -
        Returns:
      • getBondLength

        public static float getBondLength​(int index)
        Returns an estimate of the bond length based on atom and bond characteristics. The bond is classified based on its characteristics the returned value is the median of equally classified bonds within the COD or CSD database. Statistics of purely organic bonds (no metal atoms) are taken from the organic subset of the COD/CSD.
        Parameters:
        index - bond id index obtained with getBondIndex()
        Returns:
      • getBondCount

        public static float getBondCount​(int index)
      • getBondStdDev

        public static float getBondStdDev​(int index)
        Returns an the standard deviation of bond lengths from bonds with similar characteristics from crystallographic data.
        Parameters:
        index - bond id index obtained with getBondIndex()
        Returns: