edu.sdsc.mbt.util
Class BondFactory

java.lang.Object
  edu.sdsc.mbt.util.BondFactory

public class BondFactory

extends java.lang.Object

Constructor Summary

BondFactory()

Method Summary

static double	distance(Atom atomA, Atom atomB) Return the coordinate distance between two Atom objects.
static java.util.Vector	generateBonds(Structure structure) Return a vector of Bond objects extracted from a Structure using 1.8 as the bondLimit distance.
static java.util.Vector	generateBonds(Structure structure, double bondLimit) Return a vector of Bond objects extracted from a Structure using the specified bondLimit distance.
static java.util.Vector	generateCovalentBonds(java.util.Vector atoms) Given a vector of Atom objects, return a Vector of Bond objects.
static java.util.Vector	generateCovalentBonds(java.util.Vector atoms, double cutOffDistance, boolean useCovalentRestrictions) Given a vector of Atom objects, return a Vector of Bond objects.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BondFactory

public BondFactory()

Method Detail

generateBonds

public static java.util.Vector generateBonds(Structure structure)

Return a vector of Bond objects extracted from a Structure using 1.8 as the bondLimit distance.

generateBonds

public static java.util.Vector generateBonds(Structure structure,
                                             double bondLimit)

Return a vector of Bond objects extracted from a Structure using the specified bondLimit distance. The algorithm uses fixed-size cells to "bucket" the atom neighbors.

generateCovalentBonds

public static java.util.Vector generateCovalentBonds(java.util.Vector atoms,
                                                     double cutOffDistance,
                                                     boolean useCovalentRestrictions)

Given a vector of Atom objects, return a Vector of Bond objects. The cutOffDistance parameter specifies the maximum cartesian distance allowed to form a bond. The algorithm uses an octree to find atom neighbors.

generateCovalentBonds

public static java.util.Vector generateCovalentBonds(java.util.Vector atoms)

Given a vector of Atom objects, return a Vector of Bond objects. A default bond cut-off distance of 1.9 is used. The algorithm uses an octree to find atom neighbors.

distance

public static double distance(Atom atomA,
                              Atom atomB)

Return the coordinate distance between two Atom objects.