schrodinger.application.jaguar.autots_bonding module¶
Methods to handle structure reading and bonding in AutoTS.
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schrodinger.application.jaguar.autots_bonding.
clean_st
(st, reset_bonding=True)¶ Clean up a st via redefining bonding.
We also delete formal charges because they get in the way of the SMARTS pattern based matching used in many places.
Parameters: - st (schrodinger.structure.Structure instance) – structure to clean
- reset_bonding (boolean) – recompute bonding with mmjag
Rtype st: schrodinger.structure.Structure instance
Returns: the cleaned up structure
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schrodinger.application.jaguar.autots_bonding.
canonicalize_atom_names
(st)¶ Canonicalize the atom names
Parameters: st (Structure) – Structure containing atoms to name
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class
schrodinger.application.jaguar.autots_bonding.
ReactiqStructureReader
(*args, reset_bonding=True, **kwargs)¶ Bases:
schrodinger.structure._io.StructureReader
Local version of StructureReader which redefines bonding when reading
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__init__
(*args, reset_bonding=True, **kwargs)¶ Initializes the reader, automatically determining format from the extension of the specified file.
Parameters: - filename (str or pathlib.Path) – the filename to read.
- index (int) – the index of the first structure to read.
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clearReadErrors
()¶ Clear any queued read errors.
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close
()¶
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static
fromString
(input_string, index=1, format='maestro')¶ Creates a reader iterator from an input string. This is only supported for Maestro and SD formats.
Parameters: - input_string (str) – the string representation of the Structure.
- index (int) – the index of the first structure to read.
- format (str) – the string format, either MAESTRO or SD.
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getReadErrors
()¶ Return any queued read errors.
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static
read
(filename, index=1)¶ Reads the first Structure from the given file.
Parameters: - filename (str or pathlib.Path) – filename to read from
- index (int) – the positional index of the structure to read
Returns: first structure from the given file
Return type:
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schrodinger.application.jaguar.autots_bonding.
copy_autots_atom_properties
(st1, st2)¶ copy all known atom-level AutoTS-specific properties from st1 to st2. Atoms in st1 and st2 must be in the same order.
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schrodinger.application.jaguar.autots_bonding.
copy_autots_st_properties
(st1, st2)¶ copy all known structure-level AutoTS-specific properties from st1 to st2.
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schrodinger.application.jaguar.autots_bonding.
copy_autots_bond_properties
(st1, st2)¶ copy all known bond-level AutoTS-specific properties. Atoms in st1 and st2 must be in the same order but the bonds do not. However, a bond with the same atom indexes and bond order must exist in order to copy the properties.
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schrodinger.application.jaguar.autots_bonding.
copy_autots_properties
(st1, st2)¶ copy all known atom-, bond- and st-level AutoTS-specific properties from st1 to st2. Atoms in st1 and st2 must be in the same order.
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schrodinger.application.jaguar.autots_bonding.
clear_autots_atom_properties
(st)¶ clear all known atom-level AutoTS-specific properties.
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schrodinger.application.jaguar.autots_bonding.
clear_autots_st_properties
(st, exceptions=('i_m_Molecular_charge', 'i_m_Spin_multiplicity'))¶ Copy all known structure-level AutoTS-specific properties. Any properties in exceptions are not cleared (charge and mult by default)
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schrodinger.application.jaguar.autots_bonding.
clear_autots_bond_properties
(st)¶ clear all known bond-level AutoTS-specific properties.
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schrodinger.application.jaguar.autots_bonding.
clear_autots_properties
(st)¶ Remove all known atom-, bond- and st-level AutoTS specific properties.
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schrodinger.application.jaguar.autots_bonding.
zero_order_metal_bonds
(st)¶ Set the order of bonds containing metals to zero.
Parameters: st (Structure instance) – the structure containing metal bonds
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schrodinger.application.jaguar.autots_bonding.
delete_ghosts
(st)¶ Delete ghost/dummy atoms from the structure and return the modified structure.
Ghosts are identified by the attribute _StructureAtom.atomic_number = 0. The original structure is unmodified.
Parameters: st (Structure instance) – the structure with the ghost atoms Return type: Structure instance Returns: the structure without the ghost atoms
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schrodinger.application.jaguar.autots_bonding.
get_mmlewis_bonding
(st, require_charge_conservation=True, debug=False)¶ Get bonding from mmlewis. Do it molecule by molecule.
Parameters: - st (Structure instance) – the structure to get bond orders for (must be connected)
- require_charge_conservation (boolean) – if True we require the sum of formal charges after running through mmlewis to equal the total charge. (defined either by PROPERTY_KEY_CHARGE or by the sum of formal charges).
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schrodinger.application.jaguar.autots_bonding.
simplify_structure
(st)¶ Make all bonds single bonds and remove all charges.
Parameters: st (schrodinger.structure.Structure) – a structure
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schrodinger.application.jaguar.autots_bonding.
remove_formal_charges
(st)¶
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schrodinger.application.jaguar.autots_bonding.
active_reactant_atom_pairs
(reactant, product)¶ return active atom pairs in reactant structure as a list of pairs of integers
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schrodinger.application.jaguar.autots_bonding.
active_atom_pairs
(reactant, product)¶ Determine active bonds and return them as lists of pairs of atoms
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schrodinger.application.jaguar.autots_bonding.
copy_bonding
(st1, st2)¶ Impose the bonding and formal charges of st1 onto st2 The two structures must have the same number of atoms or a ValueError is raised.
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class
schrodinger.application.jaguar.autots_bonding.
Coordinate
(value, *args)¶ Bases:
object
An internal coordinate. The value and indexes are stored as data “value” and “indices”.
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__init__
(value, *args)¶ Create an internal coordinate with a value
Parameters: - value (float) – value of coordinate
- args (tuple) – atom indexes defining constraint
- Example usage
- torsion = Coordinate(91.2, 4, 5, 8, 12) bond = Coordinate(1.2, 12, 14)
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similar_coordinate
(other)¶ A similar coordinate is one that describes the same degree of freedom. For example, the torsion 1 2 3 4 and torsion 1 2 3 6 describe rotation about the same bond.
Parameters: other (Coordinate) – the other coordinate for comparison :return True if the other coordinate is similar, else False
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adjust
(st)¶ adjust this coordinate for a structure If coordinate is in a ring no adjustment is made
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setValue
(st)¶ Set value of coordinate using structure
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schrodinger.application.jaguar.autots_bonding.
examine_constraints
(constraints, st, tol=0.01, enforce=True)¶ Examine the satisfaction of constraints. Returns a list of Coordinate instances representing the error in any constraints which are not satisfied to a specified tolerance.
Parameters: - constraints (list of Coordinate) – the constraints
- st (Structure) – structure which should satisfy constraints
- tol (float) – tolerance
- enforce (boolean) – if True attempt to enforce constraints with Structure.adjust
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schrodinger.application.jaguar.autots_bonding.
get_static_constraints
(constraints)¶ Convert a list of constraints into static constraints. This just means returning a list of constraints with the value set to None
Parameters: constraints (list) – list of Coordinate instances :return : a list of Coordinates
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schrodinger.application.jaguar.autots_bonding.
atoms_in_ring
(st, i, j)¶ Determine if two atoms are in the same ring :type st: Structure :param st: structure :type i: int :param i: atom index :type j: int :param j: atom index
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schrodinger.application.jaguar.autots_bonding.
coord_in_ring
(st, *args)¶ Determine whether or not an internal coordinate is in a ring.
For a bond: returns True if both atoms are in the same ring. For an angle: returns True if all three atoms are in the same ring. For a torsion: returns True if the two central atoms are in the same ring.
Parameters: - st (Structure) – Structure used to test if indexes are in the same ring
- args (tuple/list) – indexes of the coordinate.
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schrodinger.application.jaguar.autots_bonding.
remove_agostic_bonds
(st)¶ Remove zero-order bonds from metals to valence saturated C and H atom.
These agostic interactions are very weak and easily broken and their presence or absence can mess up codes that use connectivity.
Parameters: st (Structure instance) – Structure to remove agostic bonds
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schrodinger.application.jaguar.autots_bonding.
bound_hydrogen
(bond, metal_indices)¶ Returns whether a hydrogen atom bound to a metal is a bound H2 molecule
Parameters: - bond (StructureBond) – the H-metal bond of interest
- metal_indices (set of ints) – set of atom indexes which are metals
Return param: True if H-metal bond is part of bound H2 molecule
Return type: boolean