rmgpy.molecule.Bond

class rmgpy.molecule.Bond(atom1, atom2, order=1)

A chemical bond. The attributes are:

Attribute Type Description
order float The bond type
atom1 Atom An Atom object connecting to the bond
atom2 Atom An Atom object connecting to the bond
applyAction(self, action)

Update the bond as a result of applying action, a tuple containing the name of the reaction recipe action along with any required parameters. The available actions can be found here.

copy(self) → Edge

Generate a deep copy of the current bond. Modifying the attributes of the copy will not affect the original.

decrementOrder(self)

Update the bond as a result of applying a CHANGE_BOND action to decrease the order by one.

equivalent(self, Edge other) → bool

Return True if other is indistinguishable from this bond, or False otherwise. other can be either a Bond or a GroupBond object.

getOrderNum(self) → float

returns the bond order as a number

getOrderStr(self) → str

returns a string representing the bond order

getOtherVertex(self, Vertex vertex) → Vertex

Given a vertex that makes up part of the edge, return the other vertex. Raise a ValueError if the given vertex is not part of the edge.

incrementOrder(self)

Update the bond as a result of applying a CHANGE_BOND action to increase the order by one.

isBenzene(self) → bool

Return True if the bond represents a benzene bond or False if not.

isDouble(self) → bool

Return True if the bond represents a double bond or False if not.

isHydrogenBond(self)

Return True if the bond represents a hydrogen bond or False if not.

isOrder(self, float otherOrder) → bool

Return True if the bond is of order otherOrder or False if not. This compares floats that takes into account floating point error

NOTE: we can replace the absolute value relation with math.isclose when we swtich to python 3.5+

isSingle(self) → bool

Return True if the bond represents a single bond or False if not.

isSpecificCaseOf(self, Edge other) → bool

Return True if self is a specific case of other, or False otherwise. other can be either a Bond or a GroupBond object.

isTriple(self) → bool

Return True if the bond represents a triple bond or False if not.

order

order – ‘float’

setOrderNum(self, float newOrder)

change the bond order with a number

setOrderStr(self, str newOrder)

set the bond order using a valid bond-order character

vertex1

vertex1 – rmgpy.molecule.graph.Vertex

vertex2

vertex2 – rmgpy.molecule.graph.Vertex

Bond types

The bond type simply indicates the order of a chemical bond. We define the following bond types:

Bond type Description
S a single bond
D a double bond
T a triple bond
B a benzene bond