schrodinger.application.matsci.buildcomplex.Ligand

init(self, struct, sites=None, slots=None)
(Constructor)

Create a Ligand object

Parameters:

struct (schrodinger.structure.Structure) - The ligand structure
sites (list of tuple) - Each item of the list is a (X, Y) tuple. X is the index of the atom that will attach to the central metal atom in the complex, and Y is the index of the atom that should be removed to make the attachment. The X-Metal bond will be made along the X-Y bond vector. If Y is 0, the bond will be assumed to be a dative bond, and the X-Metal bond will be formed along an angle that is chosen to minimize sterics.
slots (list of int) - The coordination slots this ligand will occupy. The coordination slot is the index into the GEOMETRY_LOCATIONS array that specifies the xyz coordinates for this ligand coordination. If not supplied, the slots will be supplied based on the isomer of the complex.

Overrides: object.__init__

_findDativeSite(self, site)

Normally, we'd put the X-Metal bond on the same vector as the X-Y bond vector, where Y is the atom that is being removed. However, for a dative X-Metal bond, there is no atom to remove and therefore, there is no predefined bond vector for the X-Metal bond. Find the best vector and place an atom there for removal later.

Parameters:

site (tuple) - (X, Y) tuple indicating the index of atom X, which will be bonded to the metal atom. Y is ignored.

Returns: tuple

(X, Y) tuple, where Y is a new atom added on the vector that the X-Metal bond should be made.

Class Ligand

__init__(self, struct, sites=None, slots=None) (Constructor)

_findDativeSite(self, site)

init(self, struct, sites=None, slots=None)
(Constructor)