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.

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.PENTAGONAL_BIPYRAMIDAL = 'Pentagonal bipyramidal'¶: VESPR geometry with 7 coordination sites around a central atom

schrodinger.application.matsci.buildcomplex.SQUARE_ANTIPRISMATIC = 'Square antiprismatic'¶: VESPR geometry with 8 coordination sites around a central atom

schrodinger.application.matsci.buildcomplex.TRICAPPED_TRIGONAL_PRISMATIC = 'Tricapped trigonal prismatic'¶: VESPR geometry with 9 coordination sites around a central atom

schrodinger.application.matsci.buildcomplex.SQUARE_PYRAMIDAL = 'Square pyramidal'¶: VESPR geometry with 5 coordination sites around a central atom

schrodinger.application.matsci.buildcomplex.SUPPORTED_GEOMETRIES = ['Octahedral', 'Trigonal bipyramidal', 'Square planar', 'Tetrahedral', 'Trigonal planar', 'Linear', 'Pentagonal bipyramidal', 'Square antiprismatic', 'Tricapped trigonal prismatic', 'Square pyramidal']¶: VESPR geometries that can be built by this module

schrodinger.application.matsci.buildcomplex.CMDLINE_TO_GEOMETRY = {'linear': 'Linear', 'octahedral': 'Octahedral', 'pentagonal_bipyramidal': 'Pentagonal bipyramidal', 'square_antiprismatic': 'Square antiprismatic', 'square_planar': 'Square planar', 'square_pyramidal': 'Square pyramidal', 'tetrahedral': 'Tetrahedral', 'tricapped_trigonal_prismatic': 'Tricapped trigonal prismatic', 'trigonal_bipyramidal': 'Trigonal bipyramidal', 'trigonal_planar': 'Trigonal planar'}¶: mapping from cmd-line name to full name of geometry

schrodinger.application.matsci.buildcomplex.GEOMETRY_TO_CMDLINE = {'Linear': 'linear', 'Octahedral': 'octahedral', 'Pentagonal bipyramidal': 'pentagonal_bipyramidal', 'Square antiprismatic': 'square_antiprismatic', 'Square planar': 'square_planar', 'Square pyramidal': 'square_pyramidal', 'Tetrahedral': 'tetrahedral', 'Tricapped trigonal prismatic': 'tricapped_trigonal_prismatic', 'Trigonal bipyramidal': 'trigonal_bipyramidal', 'Trigonal planar': 'trigonal_planar'}¶: mapping from full name of geometry to cmd-line name

schrodinger.application.matsci.buildcomplex.CMDLINE_GEOMETRIES = ['octahedral', 'trigonal_bipyramidal', 'square_planar', 'tetrahedral', 'trigonal_planar', 'linear', 'pentagonal_bipyramidal', 'square_antiprismatic', 'tricapped_trigonal_prismatic', 'square_pyramidal']¶: list of cmd-line names for geometries

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.PENTAGONAL_BIPYRAMIDAL_LOCATIONS = [(0.0, 0.0, 2.0), (2.0, 0.0, 0.0), (0.6180339887498949, 1.902113032590307, 0.0), (-1.6180339887498947, 1.1755705045849465, 0.0), (-1.6180339887498947, -1.1755705045849465, 0.0), (0.6180339887498949, -1.902113032590307, 0.0), (0.0, 0.0, -2.0)]¶: XYZ coordinates of the pentagonal bipyramidal sites

schrodinger.application.matsci.buildcomplex.SQUARE_ANTIPRISMATIC_LOCATIONS = [(1.696096192312852, 0.0, 1.0598385284664098), (1.2496025204274779, 1.2496025204274779, -0.9364758843038024), (0.0, 1.696096192312852, 1.0598385284664098), (-1.2496025204274779, 1.2496025204274779, -0.9364758843038024), (-1.696096192312852, 0.0, 1.0598385284664098), (-1.2496025204274779, -1.2496025204274779, -0.9364758843038024), (0.0, -1.696096192312852, 1.0598385284664098), (1.2496025204274779, -1.2496025204274779, -0.9364758843038024)]¶: XYZ coordinates of the square antiprismatic sites

schrodinger.application.matsci.buildcomplex.TRICAPPED_TRIGONAL_PRISMATIC_LOCATIONS = [(1.4142135623730951, 0.0, -1.414213562373095), (0.0, 1.4142135623730951, -1.414213562373095), (-1.4142135623730951, 0.0, -1.414213562373095), (0.0, -1.4142135623730951, -1.414213562373095), (1.4142135623730951, -1.0, 0.9999999999999998), (1.4142135623730951, 1.0, 0.9999999999999998), (-1.4142135623730951, 1.0, 0.9999999999999998), (-1.4142135623730951, -1.0, 0.9999999999999998), (0.0, 0.0, 2.0)]¶: XYZ coordinates of the tricapped trigonal prismatic sites

schrodinger.application.matsci.buildcomplex.SQUARE_PYRAMIDAL_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), (0.0, 0.0, 2.0)]¶: XYZ coordinates of the square pyramidal sites

class schrodinger.application.matsci.buildcomplex.LigandInfo(family, abbreviation, charge, name, coordination, formula)¶

Bases: tuple

__contains__(key, /)¶: Return key in self.

__len__()¶: Return len(self).

abbreviation¶: Alias for field number 1

charge¶: Alias for field number 2

coordination¶: Alias for field number 4

count(value, /)¶: Return number of occurrences of value.

family¶: Alias for field number 0

formula¶: Alias for field number 5

index(value, start=0, stop=9223372036854775807, /)¶

Return first index of value.

Raises ValueError if the value is not present.

name¶: Alias for field number 3

class schrodinger.application.matsci.buildcomplex.MinimizeInfo(pos_frozen_idxs)¶

Bases: tuple

__contains__(key, /)¶: Return key in self.

__len__()¶: Return len(self).

count(value, /)¶: Return number of occurrences of value.

index(value, start=0, stop=9223372036854775807, /)¶

Return first index of value.

Raises ValueError if the value is not present.

pos_frozen_idxs¶: Alias for field number 0

schrodinger.application.matsci.buildcomplex.get_ligands_info()¶

Get ligands info from csv file

Returns: Dict with key as smiles string of ligand and values as LIGANDINFO
Return type: Dict

schrodinger.application.matsci.buildcomplex.get_ligand_name(struct)¶

Get abbreviated name of structures from the ligand list

Parameters: struct (schrodinger.structure.Structure) – structure of which abbreviated name to get
Returns: Get ligand name based on abbreviated name or full name or chemical formula
Return type: str

schrodinger.application.matsci.buildcomplex.find_lone_hydrogen(struct, heavy_index)¶

Find the lone hydrogen attached to an atom

Parameters

struct (schrodinger.structure.Structure) – The structure in which the atoms are present
heavy_index (int) – The index of the heavy atom to search for a single hydrogen

Return type

int or None

Returns

The index of the lone attached hydrogen atom or None if 0 or more than 1 hydrogen is attached to the heavy atom

schrodinger.application.matsci.buildcomplex.get_sentinel_sites(sentinel)¶

Find the complex sites on the sentinel ligand using the Template Rx markers

Parameters: sentinel (schrodinger.structure.Structure) – The sentinel ligand - this should come from a Template created with the Complex builder or this panel, and have markers indicating the complex sites.
Return type: list
Returns: A list of tuples. Each tuple is (X, Y), where X is the ligand atom index of the coordinating atom and Y is the ligand atom index of the atom to remove upon coordination. Y=0 if no atom is to be removed. One tuple for each coordination site is given.

schrodinger.application.matsci.buildcomplex.get_pretty_geom_str(geom)¶

Return geometry string in pretty format.

Parameters: geom (str) – a geometry from SUPPORTED_GEOMETRIES in cli format
Return type: str
Returns: a geometry from SUPPORTED_GEOMETRIES in pretty format

schrodinger.application.matsci.buildcomplex.get_cli_geom_str(geom)¶

Return geometry string in cli format.

Parameters: geom (str) – a geometry from SUPPORTED_GEOMETRIES in pretty format
Return type: str
Returns: a geometry from SUPPORTED_GEOMETRIES in cli format

schrodinger.application.matsci.buildcomplex.minimize_complexes(structs, forcefield=14, **kwargs)¶

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

Additional keyword arguments are passed to the Minimizer class constructor

Parameters

structs (list or dict of schrodinger.structure.Structure) – The structures to minimize, use a dict if any structures have structure specific minimize settings, for example frozen atoms, etc., in this case values should be either None (structure has no specific settings) or MinimizeInfo
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.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, monoxide=3)¶

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
monoxide (str) – Whether carbon monoxide-like molecules should be represented by a dative bond to metal and a triple CO bond (TRIPLE_CO_BOND) or by a double bond to the metal and a double CO bond (DOUBLE_CO_BOND). Use TRIPLE_CO_BOND for standard complex building applications and DOUBLE_CO_BOND for SMILES-based ML applications.

schrodinger.application.matsci.buildcomplex.fix_all_metal_bond_orders(struct, monoxide=3)¶

Set the order of bonds containing metals to zero.

Parameters

struct (schrodinger.structure.Structure) – input structure containing metal bonds
monoxide (str) – Whether carbon monoxide-like molecules should be represented by a dative bond to metal and a triple CO bond (TRIPLE_CO_BOND) or by a double bond to the metal and a double CO bond (DOUBLE_CO_BOND). Use TRIPLE_CO_BOND for standard complex building applications and DOUBLE_CO_BOND for SMILES-based ML applications.

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.

schrodinger.application.matsci.buildcomplex.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

schrodinger.application.matsci.buildcomplex.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 atoms
Return 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.

schrodinger.application.matsci.buildcomplex.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

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 atoms
Return type: set
Returns: Each item of the set is the atom index of a marker for an eta-coordination site

schrodinger.application.matsci.buildcomplex.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

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

schrodinger.application.matsci.buildcomplex.lock_marker_atom_in_place(mizer, struct, index)¶

Lock an atom in place before minimization. Freezes the current bond, angle and torsion of the given atom. If the atom is not bonded to anything, no restraints are added. If multiple bonds, angles or torsions are available to lock, only one of each is chosen.

Parameters

mizer (structutils.minimize.Minimizer) – The minimizer
struct (structure.Structure) – The structure to be minimized
index (int) – The index of the atom to lock in place

exception schrodinger.application.matsci.buildcomplex.EtaFFAssignmentError¶

Bases: Exception

Raised when a FF assignment error occurs

__init__(*args, **kwargs)¶

args¶

with_traceback()¶: Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

class schrodinger.application.matsci.buildcomplex.ConvertBondsToDative(struct, atoms=None)¶

Bases: object

Context manager to temporarily convert bonds with order > 0 to dative bonds.

__init__(struct, atoms=None)¶

Create a ConvertBondsToDative context manager

Parameters

struct (structure.Structure) – The structure containing the bonds
atoms (iterable) – The collection of atoms whose bonds should be converted. If not given, all atoms will be used

class schrodinger.application.matsci.buildcomplex.ConvertZOBToSingle(struct)¶

Bases: object

Context manager to temporarily convert zero-order bonds (true ZOBS or dative) to single bonds. Upon exit all former zero-order bonds will be dative. This is intentional.

__init__(struct)¶

Create a ConvertZOBToSingle context manager

Parameters: struct (structure.Structure) – The structure with bonds to convert

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

Eta sites are marked by two dummy atoms X and Y. X is located at the centroid of all eta atoms in the plane of the eta atoms. Y is located at roughly the site of the metal atom.

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

exception schrodinger.application.matsci.buildcomplex.NoMetalError¶

Bases: Exception

Emitted when a metal is not found when one is expected

__init__(*args, **kwargs)¶

args¶

with_traceback()¶: Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

class schrodinger.application.matsci.buildcomplex.EtaFindingMixin¶

Bases: object

A mixin with a method for finding eta ligands in a metal complex

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

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

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

METAL_BINDER_PROP = 'i_matsci_binding_metal'¶

__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.

findBindingAtoms()¶: Make a list of all atoms that bind to metal atoms

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.

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

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

createLigandStructures()¶: Create individual structures for each ligand. A ligand is defined as a molecule that remains intact after deleting the central metal atom.

static markRAtomValues(struct)¶

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

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.

exception schrodinger.application.matsci.buildcomplex.DuplicateCheckError¶

Bases: Exception

Raised internally when checking complexes for duplicates

__init__(*args, **kwargs)¶

args¶

with_traceback()¶: Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

schrodinger.application.matsci.buildcomplex.are_duplicates(ref, comp, tolerance=1.0, check_optical=True)¶

Check if both compounds are duplicate structures. Uses canonical SMILES to detect structures with the same chemical bonding, then Works via actual XYZ coordinates to determine if the structures are duplicates. This is 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
Note: Bonding around the metal atoms is canonicalized during the: comparison to ensure that metal single/dative/ZOB bonding is consistent between the two structures. This done on copies so that the passed-in structures are not modified.

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

Raises

ValueError – If there are fewer than 3 usable atoms for the superposiiton

class schrodinger.application.matsci.buildcomplex.ComplexConformerRmsd(reference_structure, test_structure=None, asl_expr='NOT atom.element H', in_place=True)¶

Bases: schrodinger.structutils.rmsd.ConformerRmsd

__init__(reference_structure, test_structure=None, asl_expr='NOT atom.element H', in_place=True)¶

Parameters

reference_structure (structure.Structure) – Template structure
test_structure (structure.Structure) – The mobile structure.
asl_expr (string) – Atom Language Expression to identify the the atoms used to calculate the RMSD and base the superimpose alignment.
in_place (Boolean) – If True, calculate the RMSD without moving the test_structure. Otherwise, perform the optimal alignment then calculate the RMSD.

calculate()¶

Returns: Root-mean-squared difference of atom coordinates.
Type: float
Raise: ValueError if working versions of the reference and test structures don’t have the same shape (non-confs).

The order of operations:

prepare working copies of the reference and test structures.
** copy the structures. ** encode the original atom indexes as atom properties. ** extract substructure of the atoms matching the ASL. ** reduce to heavy atom graph (instance option, non-default). ** normalize numbering scheme (instance option, default).
determine molecular symmetry mapping (optional, default).
create a numpy coordinate array for the working structures.
numpy linear algebra SVD to superimpose (instance option).
** transform test_structure
numpy array used to calculate RMSD, and max_dist.
decode original indexes to identify atoms involve in max dist.

evaluateAsl(st)¶

Return the atoms of the input structure that match <asl_expr>.

Parameters: st (structure.Structure) – Structure to evaluate
Returns: Atoms matching the ASL
Return type: list of ints

:raise RuntimeError if ASL matching failed.

getRmsdDataname()¶

Returns: m2io property dataname string. The property name indicates the reference structure, the title, the ASL used to identify comparison atoms and if the structure is in-place or mobile.
Return type: string

orig_index_prop = 'i_confrmsd_original_index'¶

renumberBySymmetry()¶: Renumber the atoms in _working_test_st based off the reference structure ussing mmsym.

writeCommand(file_name='rmsd.cmd')¶

Writes a Maestro command file and structures with the pair wise atom mapping in command file mode. The Maestro file has the same basename as the command file. Clobbers existing files.

Parameters: file_name (string) – Path to the maestro command file with the atom pairings.
Raise: ValueError if file_name does not have ‘.cmd’ extension.

writeStructures(file_name='rmsd.mae', mode='w')¶

Writes the reference and test structures to file.

Parameters

file_name (string) – Path of the structure file to write.
mode (string) – ‘w’ => write, clobber as needed ‘a’ => append

renumberWorkingStructures()¶: Renumber the working structure so that it has atoms in the same order as the reference structure