Inheritance diagram for qmworks.plams.core.basemol.Bond:

Collaboration diagram for qmworks.plams.core.basemol.Bond:

Public Member Functions
def	__init__ (self, atom1, atom2, order=1, mol=None, other)

def	__str__ (self)

def	__iter__ (self)

def	is_aromatic (self)

def	length (self, unit='angstrom')

def	other_end (self, atom)

def	resize (self, atom, length, unit='angstrom')

Public Attributes
	atom1

	atom2

	order

	mol

	properties

Static Public Attributes
float	AR = 1.5

Detailed Description

A class representing a bond between two atoms.

An instance of this class has the following attributes:
    *   ``atom1`` and ``atom2`` -- two instances of |Atom| that form this bond
    *   ``order`` -- order of the bond. It is either an integer number or the floating point value stored in ``Bond.AR``, indicating aromatic bond
    *   ``mol`` -- a |Molecule| this bond belongs to
    *   ``properties`` -- a |Settings| instance storing all other  information about this bond (initially it is populated with *\*\*other* keyword arguments passed to the constructor)

.. note::

    Newly created bond is **not** added to ``atom1.bonds`` or ``atom2.bonds``. Storing information about |Bond| in |Atom| is relevant only in the context of the whole |Molecule|, so this information is updated by :meth:`~Molecule.add_bond`.

Member Function Documentation

◆ iter()

def qmworks.plams.core.basemol.Bond.__iter__ ( self )

Iterate over bonded atoms (``atom1`` first, then ``atom2``).

◆ str()

def qmworks.plams.core.basemol.Bond.__str__ ( self )

Return string representation of this bond.

◆ is_aromatic()

def qmworks.plams.core.basemol.Bond.is_aromatic ( self )

Check if this bond is aromatic.

◆ length()

def qmworks.plams.core.basemol.Bond.length	(	self,
		unit = `'angstrom'`
	)

Return bond's length, expressed in *unit*.

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◆ other_end()

def qmworks.plams.core.basemol.Bond.other_end	(	self,
		atom
	)

Return the atom on the other end of this bond with respect to *atom*.

*atom* has to be either ``atom1`` or ``atom2``, otherwise an exception is raised.

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◆ resize()

def qmworks.plams.core.basemol.Bond.resize	(	self,
		atom,
		length,
		unit = `'angstrom'`
	)

Change the length of the bond to *length*.

This method works in the following way: one of two atoms forming this bond is moved along the bond in such a way that new length is *length*, in *unit* (direction of the bond in space does not change). Atom indicated by *atom* has to be one of bond's atoms and it is the atom that is **not** moved.

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The documentation for this class was generated from the following file:

/home/docs/checkouts/readthedocs.org/user_builds/pyfragdocument/checkouts/latest/qmworks/plams/core/basemol.py

Public Member Functions

Public Attributes

Static Public Attributes