Package org.biojava.nbio.structure
Interface Bond
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- All Superinterfaces:
Serializable
- All Known Implementing Classes:
BondImpl
public interface Bond extends Serializable
A simple bond -- it stores information about two atoms as well as information about its bond order.- Author:
- Jules Jacobsen
, Ulysse Carion
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description Atom
getAtomA()
Gets atom 'A' of this bond.Atom
getAtomB()
Gets atom 'B' of this bond.int
getBondOrder()
Gets the bond order of this bond.double
getLength()
Gets the distance between the two atoms of this bond.Atom
getOther(Atom exclude)
A utility method to get the other atom in a bond, given one of its atoms.
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Method Detail
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getAtomA
Atom getAtomA()
Gets atom 'A' of this bond. There is no meaning to which atom is 'A' and which is 'B'; the atoms are labeled 'A' or 'B' based on the order in which they are passed to this class's constructor.- Returns:
- one of the two atoms in this bond
- See Also:
getAtomB()
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getAtomB
Atom getAtomB()
Gets atom 'B' of this bond. There is no meaning to which atom is 'A' and which is 'B'; the atoms are labeled 'A' or 'B' based on the order in which they are passed to this class's constructor.- Returns:
- one of the two atoms in this bond
- See Also:
getAtomA()
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getOther
Atom getOther(Atom exclude)
A utility method to get the other atom in a bond, given one of its atoms. If the atom passed is one of the atoms in this bond, then this method is essentially equivalent to sayingatom == bond.getAtomA() ? bond.getAtomB() : bond.getAtomA()
.Note: Comparison of atoms in this method is done with
==
, notequals
.- Parameters:
exclude
- the atom of the bond to not return- Returns:
- the atom in this bond that was not passed as an argument
- Throws:
IllegalArgumentException
- if the passed atom is not in this bond
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getBondOrder
int getBondOrder()
Gets the bond order of this bond. A return value of '1' corresponds to a single bond, '2' to a double bond, etc.- Returns:
- this bond's bond order
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getLength
double getLength()
Gets the distance between the two atoms of this bond.This distance is calculated by
Calc.getDistance(Atom, Atom)
, but this method will suppress the empty threat of aStructureException
that method makes.- Returns:
- the distance between the two atoms of this bond.
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