parmed.topologyobjects.Bond

class parmed.topologyobjects.Bond(atom1, atom2, type=None, order=1.0)

A covalent bond connecting two atoms.

Parameters

atom1Atom

The first atom involved in the bond

atom2Atom

The other atom involved in the bond

typeBondType or None, optional

The bond type that defines the parameters for this bond. Default is None

orderfloat, optional

The bond order of this bond. Bonds are classified as follows:

1.0 – single bond 2.0 – double bond 3.0 – triple bond 1.5 – aromatic bond 1.25 – amide bond

Default is 1.0

Notes

You can test whether an Atom is contained within the bond using the in operator. A MoleculeError is raised if atom1 and atom2 are identical. This bond instance is append`ed to the `bonds list for both atom1 and atom2 and is automatically removed from those lists upon garbage collection

Examples

>>> a1, a2 = Atom(), Atom()
>>> bond = Bond(a1, a2)
>>> a1 in bond and a2 in bond
True

Attributes

order

Bond order.

Methods

delete()	Deletes this bond from the atoms that make it up.
energy()	Measures the current bond energy
measure()	Measures the current bond
uenergy()	Same as energy(), but with units
umeasure()	Same as “measure”, but with units

__init__(atom1, atom2, type=None, order=1.0)

Bond constructor

Methods

__init__(atom1, atom2[, type, order])	Bond constructor
delete()	Deletes this bond from the atoms that make it up.
energy()	Measures the current bond energy
measure()	Measures the current bond
uenergy()	Same as energy(), but with units
umeasure()	Same as “measure”, but with units

Attributes

order

Bond order.