Class ComplexBuilder

Create a ComplexBuilder instance

Parameters:

• metal (str) - The atomic symbol of the central atom
• geometry (str) - VESPR geometry of the complex. Should be a module constant: OCTAHEDRAL, TETRAHEDRAL, SQUARE_PLANAR
• isomer (str or None) - For octahedral complexes, can be module constants FACIAL, MERIDIONAL, or NO_ISOMER. For square planar complexes, can be module constants CIS, TRANS or NO_ISOMER. It is ignored for tetrahedral. None may be used instead of NO_ISOMER.
• homoleptic (bool) - If True, the complex is homoleptic and only one ligand should be supplied. If False, the complex is heteroleptic and every ligand must be supplied. Homoleptic = all ligands are identical, heteroleptic = ligands may or may not be identical.
• dentation (int) - Module-level constant describing the dentation type of the ligand - either MONODENTATE or BIDENTATE. Only used to determine the coordination slot order (the order coordination sites are filled) for isomers.

Overrides: object.__init__

Reset the slot order back to ideal slot order

Parameters:

• dentation (int) - Module-level constant describing the dentation type of the ligand - either MONODENTATE or BIDENTATE

Set the order that coordination sites should be used. This should be a list of indexes into the slot_order property. Ligands will be attached at these coordination sites in the order they are added.

Parameters:

• slot_order (list of int) - List of indexes that specifies the order of coordination sites to use.

Raises:

• IndexError - If the list is not the correct length (6 for octahedral, 4 for tetrahedral/square_planar). An example for square_planar might be [0, 2, 1, 3].
• ValueError - If the list contains duplicated indexes or indexes outside the allow range of 0 to len(list)-1

Get the current number of coordination sites required for all copies of all ligands set so far.

Returns: int

The total number of sites required for all currently set ligands. Accounts for the number of copies requested and mono/bi-dentation of each ligand.

Add a monodentate ligand for the complex.

Parameters:

• struct (schrodinger.structure.Structure) - The structure of the ligand
• site (tuple) - An (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.
• slot (int) - The coordination slot this ligand will occupy. The coordination slot is the index into the GEOMETRY_LOCATIONS array that specifies the xyz coordinates for this ligand coordination.
• copies (int) - The number of copies of this ligand. It is a ValueError to specify slot & copies > 1.

Add a bidentate ligand for the complex.

Parameters:

• struct (schrodinger.structure.Structure) - The structure of the ligand
• 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.
• copies (int) - The number of copies of this ligand. It is a ValueError to specify slot & copies > 1.

Create the complex based on the defined ligands

Parameters:

• force (bool) - If true, create a complex even if all slots are not filled. If False (default), raise IndexError if all slots are not filled.

Raises:

• IndexError - If not all sites are filled and force is not True
• IndexError - Too many ligands specified for available sites