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, mmjag=True, cov_offset=0.4)¶ 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 intance) – structure to clean
- mmjag (boolean) – if True use mmjag, else use schrodinger.application.matsci.nano.xtal.connect_atoms
- cov_offset (float) – additional value to add to covalent radii, applicable only if mjag=False
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, **kwargs)¶ Bases:
schrodinger.structure.StructureReader
Local version of StructureReader which redefines bonding when reading
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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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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.
@type constraints: list of Coordinate @param constraints: the constraints @type st: Structure @param st: structure which should satisfy constraints @type tol: float @param tol: tolerance @type enforce: boolean @param enforce: 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.