schrodinger.application.matsci.buildcomplex module

This module assists in building organometallic complexes. Given one or more ligands, these ligands will be arranged around a central atom.

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.application.matsci.buildcomplex.MONODENTATE = 'Monodentate'

Name for ligands that have a single coordination site

schrodinger.application.matsci.buildcomplex.BIDENTATE = 'Bidentate'

Name for ligands that have two coordination sites

schrodinger.application.matsci.buildcomplex.OCTAHEDRAL = 'Octahedral'

VESPR geometry with 6 coordination sites around a central atom

schrodinger.application.matsci.buildcomplex.TRIGONAL_BIPYRAMIDAL = 'Trigonal bipyramidal'

VESPR geometry with 5 coordination sites around a central atom

schrodinger.application.matsci.buildcomplex.TETRAHEDRAL = 'Tetrahedral'

VESPR geometry with 4 coordination sites around a central atom

schrodinger.application.matsci.buildcomplex.SQUARE_PLANAR = 'Square planar'

VESPR geometry with 4 coordination sites around a central atom

schrodinger.application.matsci.buildcomplex.TRIGONAL_PLANAR = 'Trigonal planar'

VESPR geometry with 3 coordination sites around a central atom

schrodinger.application.matsci.buildcomplex.LINEAR = 'Linear'

VESPR geometry with 2 coordination sites around a central atom

schrodinger.application.matsci.buildcomplex.SUPPORTED_GEOMETRIES = ['Octahedral', 'Trigonal bipyramidal', 'Tetrahedral', 'Square planar', 'Trigonal planar', 'Linear']

VESPR geometries that can be build by this module

schrodinger.application.matsci.buildcomplex.FACIAL = 'facial'

Octahedral complex with identical atoms on the face of the octahedron

schrodinger.application.matsci.buildcomplex.MERIDIONAL = 'meridional'

Octahedral complex with identical atoms on the meridion of the octahedron

schrodinger.application.matsci.buildcomplex.NO_ISOMER = 'none'

No specific isomer

schrodinger.application.matsci.buildcomplex.CIS = 'cis'

Square planar complex with identical atoms in adjacent sites

schrodinger.application.matsci.buildcomplex.TRANS = 'trans'

Square planar complex with identical atoms in opposite sites

schrodinger.application.matsci.buildcomplex.OCTAHEDRAL_LOCATIONS = [(2.0, 0.0, 0.0), (0.0, 2.0, 0.0), (0.0, 0.0, 2.0), (0.0, -2.0, 0.0), (-2.0, 0.0, 0.0), (0.0, 0.0, -2.0)]

XYZ coordinates of the octahedral coordination sites

schrodinger.application.matsci.buildcomplex.TRIGONAL_BIPYRAMIDAL_LOCATIONS = [(0.0, 2.0, 0.0), (0.0, -2.0, 0.0), (2.0, 0.0, 0.0), (-1.0, 0.0, 1.73205), (-1.0, 0.0, -1.73205)]

XYZ coordinates of the trigonal pyramid coordination sites

schrodinger.application.matsci.buildcomplex.SQUARE_PLANAR_LOCATIONS = [(2.0, 0.0, 0.0), (0.0, 2.0, 0.0), (0.0, -2.0, 0.0), (-2.0, 0.0, 0.0)]

XYZ coordinates of the square planar coordination sites

schrodinger.application.matsci.buildcomplex.TETRAHEDRAL_LOCATIONS = [(0.0, 2.0, 0.0), (1.88562, -0.66667, 0.0), (-0.94281, -0.66667, -1.63299), (-0.94281, -0.66667, 1.63299)]

XYZ coordinates of the tetrahedral coordination sites

schrodinger.application.matsci.buildcomplex.TRIGONAL_PLANAR_LOCATIONS = [(2.0, 0.0, 0.0), (-1.0, 1.73205, 0.0), (-1.0, -1.73205, 0.0)]

XYZ coordinates of the trigonal planar coordination sites

schrodinger.application.matsci.buildcomplex.LINEAR_LOCATIONS = [(2.0, 0.0, 0.0), (-2.0, 0.0, 0.0)]

XYZ coordinates of the linear coordination sites

schrodinger.application.matsci.buildcomplex.minimize_complex(struct, forcefield=14, **kwargs)

Minimize the given structure using the new MMFFLD method of determining parameters for metal complexes.

Additional keyword arguments are passed to the Minimizer class constructor

Parameters:
  • struct (schrodinger.structure.Structure) – The structure to minimize
  • ffld_version (integer) – The force field to use. Should be a module constant from the minimize module.
Raises:
  • ValueError – Typically means atom typing error or valence violations
  • mm.MmException – Due to overlapping atoms
schrodinger.application.matsci.buildcomplex.fix_metal_bond_orders(struct, index)

Fix all the bonds to atom index to be either single or dative depending on whether the other atom has a full valence without this bond or not. Full valence without this bond = dative bond, otherwise bond order = number of open valences. Formal charges are also set to 0 for the metal atom and bonded neighbors.

Note - no bonds are added or removed by this function, only bond orders are changed.

Parameters:
  • struct (schrodinger.structure.Structure) – The structure to operate on - bonds are modified on this structure directly, not a copy
  • index (int) – The atom index of the metal atom with bonds to adjust
schrodinger.application.matsci.buildcomplex.transmute_atom(atom, element, color=None)

Transmute atom from its current element to a new element. The new name will be element + index (ex. H17), and the new color if not supplied will be the Maestro default (or purple if no Maestro default).

Parameters:
  • atom (schrodinger.structure._StructureAtom) – The atom object to transmute to a new element
  • element (str) – The atomic symbol of the new element
  • color (str) – The new color of the atom in a format accepted by the _StructAtom.color property. The default is to use Maestro’s default color for the new element, or purple if the default color is not defined.
Raises:

ValueError – if element is not a recognized atomic symbol
schrodinger.application.matsci.buildcomplex.find_atoms_to_remove(struct, keep_atom, root_atom)

Return a list of atoms bound to root atom (and recursively all atoms bound to those atoms, ad infinitum). keep_atom and all atoms recursively bound to it will not be added to the list.

If keep_atom and root_atom are part of the same ring system, root_atom will be the only atom returned in the list.

For structure A-B-C-D-E, if keep_atom=B and root_atom=C, the returned list will be [C, D, E].

Parameters:
  • struct (schrodinger.structure.Structure) – The structure to use
  • keep_atom (int) – The index of the atom to keep
  • root_atom (int) – The index of the first atom to remove. All neighbors of this atom that are not keep_atom will be added to the list.
Return type:

list
Returns:

A list of all atoms recursively bound to root atom. keep_atom and all atoms bound to it are excluded from the list.
class schrodinger.application.matsci.buildcomplex.Ligand(struct, sites=None, slots=None)

Bases: object

Stores information about a ligand structure

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

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. If X is negative, the site is an eta-coordination site.
  • 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.
minimizeEtaPosition()

For bidentate eta ligands, orient the eta plane(s) to be face-on to roughly where the metal atom will be

class schrodinger.application.matsci.buildcomplex.ComplexBuilder(metal='Ir', geometry='Octahedral', isomer='facial', homoleptic=True, dentation='Bidentate')

Bases: object

A class used to build an organometallic complex

__init__(metal='Ir', geometry='Octahedral', isomer='facial', homoleptic=True, dentation='Bidentate')

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.
resetSlots(dentation='Bidentate')

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
setSlotOrder(slot_order)

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
getNumUsedCoordSites()

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

Return type:int
Returns: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.
addMonodentateLigand(struct, site, slot=None, copies=1)

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. If X is negative, the site is an eta-coordination site.
  • 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.
addBidentateLigand(struct, sites, slots=None, 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. If X is negative, the site is an eta-coordination site.
  • 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.
clearLigands()

Remove all added ligands

createComplex(force=False)

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