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
- apply_action(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.
- decrement_order(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, orFalse
otherwise. other can be either aBond
or aGroupBond
object.
- get_bde(self)¶
estimate the bond dissociation energy in J/mol of the bond based on the order of the bond and the atoms involved in the bond
- get_bond_string(self) unicode ¶
Represent the bond object as a string (eg. ‘C#N’). The returned string is independent of the atom ordering, with the atom labels in alphabetical order (i.e. ‘C-H’ is possible but not ‘H-C’) :return: str
- get_order_num(self) float ¶
returns the bond order as a number
- get_order_str(self) unicode ¶
returns a string representing the bond order
- get_other_vertex(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.
- increment_order(self)¶
Update the bond as a result of applying a CHANGE_BOND action to increase the order by one.
- is_benzene(self) bool ¶
Return
True
if the bond represents a benzene bond orFalse
if not.
- is_double(self) bool ¶
Return
True
if the bond represents a double bond orFalse
if not.
- is_hydrogen_bond(self)¶
Return
True
if the bond represents a hydrogen bond orFalse
if not.
- is_order(self, float other_order) bool ¶
Return
True
if the bond is of order other_order orFalse
if not. This compares floats that takes into account floating point errorNOTE: we can replace the absolute value relation with math.isclose when we swtich to python 3.5+
- is_quadruple(self) bool ¶
Return
True
if the bond represents a quadruple bond orFalse
if not.
- is_single(self) bool ¶
Return
True
if the bond represents a single bond orFalse
if not.
- is_specific_case_of(self, Edge other) bool ¶
Return
True
if self is a specific case of other, orFalse
otherwise. other can be either aBond
or aGroupBond
object.
- is_triple(self) bool ¶
Return
True
if the bond represents a triple bond orFalse
if not.
- is_van_der_waals(self) bool ¶
Return
True
if the bond represents a van der Waals bond orFalse
if not.
- order¶
‘float’
- Type:
order
- set_order_num(self, float new_order)¶
change the bond order with a number
- set_order_str(self, unicode new_order)¶
set the bond order using a valid bond-order character
- sorting_key¶
Returns a sorting key for comparing Bond objects. Read-only
- vertex1¶
rmgpy.molecule.graph.Vertex
- Type:
vertex1
- vertex2¶
rmgpy.molecule.graph.Vertex
- Type:
vertex2
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