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.
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schrodinger.application.matsci.buildcomplex.
MONODENTATE
= 'Monodentate'¶ Name for ligands that have a single coordination site
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BIDENTATE
= 'Bidentate'¶ Name for ligands that have two coordination sites
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OCTAHEDRAL
= 'Octahedral'¶ VESPR geometry with 6 coordination sites around a central atom
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TRIGONAL_BIPYRAMIDAL
= 'Trigonal bipyramidal'¶ VESPR geometry with 5 coordination sites around a central atom
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TETRAHEDRAL
= 'Tetrahedral'¶ VESPR geometry with 4 coordination sites around a central atom
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SQUARE_PLANAR
= 'Square planar'¶ VESPR geometry with 4 coordination sites around a central atom
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TRIGONAL_PLANAR
= 'Trigonal planar'¶ VESPR geometry with 3 coordination sites around a central atom
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LINEAR
= 'Linear'¶ VESPR geometry with 2 coordination sites around a central atom
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SUPPORTED_GEOMETRIES
= ['Octahedral', 'Trigonal bipyramidal', 'Tetrahedral', 'Square planar', 'Trigonal planar', 'Linear']¶ VESPR geometries that can be build by this module
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FACIAL
= 'facial'¶ Octahedral complex with identical atoms on the face of the octahedron
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MERIDIONAL
= 'meridional'¶ Octahedral complex with identical atoms on the meridion of the octahedron
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NO_ISOMER
= 'none'¶ No specific isomer
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CIS
= 'cis'¶ Square planar complex with identical atoms in adjacent sites
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schrodinger.application.matsci.buildcomplex.
TRANS
= 'trans'¶ Square planar complex with identical atoms in opposite sites
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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
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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
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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
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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
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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
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LINEAR_LOCATIONS
= [(2.0, 0.0, 0.0), (-2.0, 0.0, 0.0)]¶ XYZ coordinates of the linear coordination sites
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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
- struct (
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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
- struct (
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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
- atom (
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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.
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convert_old_marker_props_to_new
(struct)¶ Some template strutures may still use old-style properties to mark Rx atoms. This function converts those properties to new-style properties and removes the old ones.
Parameters: struct ( schrodinger.structure.Structure
) – The structure with properties to read and modify
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get_marker_atom_indexes_from_structure
(struct)¶ Get the indexes of atoms marked as Rx atoms
Parameters: struct ( schrodinger.structure.Structure
) – The structure with the Rx atomsReturn type: (dict, int) Returns: dict keys are the int value of x in Rx, values are lists of atom indexes set to that Rx value (atom indexes are 1-based). The int return value is the highest value of x in the keys of the dictionary.
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mark_eta_positions
(struct, rx_atoms)¶ Add a structure property that gives the index of each eta-coordination marker
Parameters: - struct (
schrodinger.structure.Structure
) – The structure with the Rx atoms - rx_atoms (dict) – Keys are x value and values are lists of atoms denoted with that Rx marker
- struct (
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schrodinger.application.matsci.buildcomplex.
get_eta_marker_indexes
(struct)¶ Get a set of all atom indexes for eta-coordination markers
Parameters: struct ( schrodinger.structure.Structure
) – The structure with the Rx atomsReturn type: set Returns: Each item of the set is the atom index of a marker for an eta-coordination site
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clear_marker_properties
(struct)¶ Clear any marker properties that exist on the structure
Parameters: struct ( schrodinger.structure.Structure
) – The structure with the marker properties to clear
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schrodinger.application.matsci.buildcomplex.
set_marker_properties
(struct, rx_atoms, clear=True)¶ Set the structure properties that store the atoms
Parameters: - struct (
schrodinger.structure.Structure
) – The structure with the Rx atoms - rx_atoms (dict) – keys are the int value of x in Rx, values are lists of atom indexes set to that Rx value (atom indexes are 1-based)
- clear (bool) – Clear any existing marker properties before setting new ones
- struct (
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class
schrodinger.application.matsci.buildcomplex.
Ligand
(struct, sites=None, slots=None)¶ Bases:
object
Stores information about a ligand structure
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__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.
- struct (
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minimizeEtaPosition
()¶ For bidentate eta ligands, orient the eta plane(s) to be face-on to roughly where the metal atom will be
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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
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__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.
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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
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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
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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.
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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.
- struct (
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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.
- struct (
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clearLigands
()¶ Remove all added ligands
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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
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exception
schrodinger.application.matsci.buildcomplex.
NoMetalError
¶ Bases:
Exception
Emitted when a metal is not found when one is expected
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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args
¶
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with_traceback
()¶ Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.
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class
schrodinger.application.matsci.buildcomplex.
EtaFindingMixin
¶ Bases:
object
A mixin with a method for finding eta ligands in a metal complex
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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findEtaGroups
(dummy_style=True)¶ Find each Eta group
We define an Eta group as 2 or more atoms that are bound together and also bound to a metal atom
Parameters: dummy_style (bool) – Whether to also find eta ligands that are bound by bonding all the ligand atoms to a dummy and then the dummy to the metal. If False, only those ligands that have all eta atoms bound directly to the metal will be found. Note: The function assumes that the self.metals property is set to a list of metal atoms and it creates the self.eta_groups and self_all_eta_atoms properties
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class
schrodinger.application.matsci.buildcomplex.
ComplexSplitter
(struct, asl='metals', metals=None)¶ Bases:
schrodinger.application.matsci.buildcomplex.EtaFindingMixin
Splits a metal complex into a set of ligand structures that bind to the metal
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findEtaGroups
(dummy_style=True)¶ Find each Eta group
We define an Eta group as 2 or more atoms that are bound together and also bound to a metal atom
Parameters: dummy_style (bool) – Whether to also find eta ligands that are bound by bonding all the ligand atoms to a dummy and then the dummy to the metal. If False, only those ligands that have all eta atoms bound directly to the metal will be found. Note: The function assumes that the self.metals property is set to a list of metal atoms and it creates the self.eta_groups and self_all_eta_atoms properties
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METAL_BINDER_PROP
= 'i_matsci_binding_metal'¶
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__init__
(struct, asl='metals', metals=None)¶ Create a ComplexSplitter instance
Parameters: - struct (
schrodinger.structure.Structure
) – The organometallic complex - asl (str) – The ASL for finding metal atoms. Ignored if metals is given
- metals (list of
schrodinger.structure._StructureAtom
) – Each item is a metal atom to search for binding ligands. Overrides the asl argument.
- struct (
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findBindingAtoms
()¶ Make a list of all atoms that bind to metal atoms
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addDummyAtoms
()¶ Add a dummy atom to each binding atom. For eta ligands, a single dummy atom is added at the centroid of the eta atoms. For non-eta ligands, a dummy atom is added along the atom-metal bond vector.
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addEtaDummy
(group)¶ Put a dummy atom at the centroid of the haptic ligand
Parameters: group (list) – A list of atom objects that form the haptic ligand
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addBinderDummy
(atom)¶ Add a dummy atom on the atom-metal bond vector that will indicate the proper bond direction after the metal atom is deleted.
Parameters: atom ( schrodinger.structure._StructureAtom
) – An atom that is bound to the metal
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createLigandStructures
()¶ Create individual structures for each ligand. A ligand is defined as a molecule that remains intact after deleting the central metal atom.
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static
markRAtomValues
(struct)¶
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splitIntoLigands
()¶ Split the metal complex into ligands
Return type: list Returns: A list of schrodinger.structure.Structure
objects, each one represents a unique ligand from the original complex. The ligands will have binding sites to the metal marked with dummy atoms
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static
getUniqueLigands
(ligands, title=None)¶ Remove duplicate ligands
Parameters: ligands (list) – A list of schrodinger.structure.Structure
objects, each one represents a ligand.Return type: list Returns: A list of schrodinger.structure.Structure
objects, taken from the input ligands and with duplicates removed.
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schrodinger.application.matsci.buildcomplex.
are_duplicates
(ref, comp, tolerance=1.0, check_optical=True)¶ Check if both compounds are duplicate structures. Works via actual XYZ coordinates rather than unique SMILES, so slow, but works for metal complexes.
Note: Requires compounds with reasonable (or consistent) 3D coordinates
- Note: Rotomers of haptic ligands about the haptic axis are generally found
- to be different compounds with the default tolerance of 1.0
- Note: Has been tested and seems to work with coordination numbers of 3-6,
- and monodentate, bidentate and haptic ligands
Parameters: - ref (schrodinger.structure.Structure) – The reference complex
- comp (schrodinger.structure.Structure) – The structure to compare to the reference
- tolerance (float) – The maximum displacement of any one atom before the compounds are considered different complexes
- check_optical (bool) – If True, check for optical isomers (and consider them duplicates) by inverting comp about the first atom (assumed to be the metal atom) and performing the same RMSD check against ref. If False, no check is made.
Return type: bool
Returns: True if the compounds are found to be identical, False if not