parmed.topologyobjects.UreyBradley

class parmed.topologyobjects.UreyBradley(atom1, atom2, type=None)

A Urey-Bradley angle type with a set of parameters. It has the same functional form as a bond, but it is defined between two atoms forming a valence angle separated by two bonds.

Parameters

atom1Atom

The first atom involved in the Urey-Bradley bond

atom2Atom

The other atom involved in the Urey-Bradley bond

typeBondType

The Urey-Bradley bond type that defines the parameters for this bond

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. You can also test that a Bond is contained in this Urey-Bradley valence angle

Examples

>>> a1, a2, a3 = Atom(), Atom(), Atom()
>>> b1 = Bond(a1, a2)
>>> b2 = Bond(a2, a3)
>>> angle = Angle(a1, a2, a3)
>>> urey = UreyBradley(a1, a3)
>>> a1 in urey and a3 in urey
True
>>> b1 in urey and b2 in urey
True

Attributes

order

Bond order.

Methods

delete()	Deletes this Urey-Bradley 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)

Bond constructor

Methods

__init__(atom1, atom2[, type])	Bond constructor
delete()	Deletes this Urey-Bradley 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.