schrodinger.application.jaguar.autots_bonding module

Methods to handle structure reading and bonding in AutoTS.

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

schrodinger.application.jaguar.autots_bonding.canonicalize_atom_names(st)

Canonicalize the atom names

Parameters:st (Structure) – Structure containing atoms to name
class schrodinger.application.jaguar.autots_bonding.ReactiqStructureReader(*args, reset_bonding=True, **kwargs)

Bases: schrodinger.structure.structure.StructureReader

Local version of StructureReader which redefines bonding when reading

__init__(*args, reset_bonding=True, **kwargs)

The format is determined from the file extension if no format is specified.

Parameters:
  • filename (str or pathlib.Path) – The filename to read.
  • index (int) – The index of the first structure to read.
  • error_handler (int) – The handle of the mmerr object to use for error logging. Defaults to schrodinger.infra.mm.error_handler.
  • format (str) – The format of the file, either ‘pdb’, ‘sd’, ‘mol2’, ‘maestro’ or ‘maestro_text’ (determined from file extension by default).
  • ignore_errors (bool) – If True, bad structures will be skipped instead of raising an exception. Currently only used by the SD reader.
  • input_string (str) – Use of this argument is pending deprecation. Please use the StructureReader.fromString static method instead. If this is specified then the structure will be read from this string and the filename will be ignored. The format must be specified. Currently this is only supported for Maestro and SD format.
clearReadErrors()

Clear any queued read errors.

close()
static fromString(input_string, index=1, error_handler=None, format='maestro', ignore_errors=False)

Create a StructureReader from an input string. Currently this is only supported for Maestro and SD format.

Parameters:
  • input_string (str) – The string representation of the Structure.
  • index (int) – The index of the first structure to read.
  • error_handler (int) – The handle of the mmerr object to use for error logging. Defaults to schrodinger.infra.mm.error_handler.
  • format (str) – The format of the file, either SD (‘sd’) or MAESTRO (‘maestro’). Defaults to MAESTRO.
  • ignore_errors (bool) – If True, bad structures will be skipped instead of raising an exception. Currently only used by the SD reader.
getReadErrors()

Return any queued read errors.

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.

schrodinger.application.jaguar.autots_bonding.copy_autots_st_properties(st1, st2)

copy all known structure-level AutoTS-specific properties from st1 to st2.

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.

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.

schrodinger.application.jaguar.autots_bonding.clear_autots_atom_properties(st)

clear all known atom-level AutoTS-specific properties.

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)

schrodinger.application.jaguar.autots_bonding.clear_autots_bond_properties(st)

clear all known bond-level AutoTS-specific properties.

schrodinger.application.jaguar.autots_bonding.clear_autots_properties(st)

Remove all known atom-, bond- and st-level AutoTS specific properties.

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
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
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).
schrodinger.application.jaguar.autots_bonding.simplify_structure(st)

Make all bonds single bonds and remove all charges.

Parameters:st (schrodinger.structure.Structure) – a structure
schrodinger.application.jaguar.autots_bonding.remove_formal_charges(st)
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

schrodinger.application.jaguar.autots_bonding.active_atom_pairs(reactant, product)

Determine active bonds and return them as lists of pairs of atoms

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.

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”.

__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)
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

adjust(st)

adjust this coordinate for a structure If coordinate is in a ring no adjustment is made

setValue(st)

Set value of coordinate using structure

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
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

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

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.
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
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