Package schrodinger :: Package application :: Package jaguar :: Module autots_bonding

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Module autots_bonding

Methods to handle structure reading and bonding in AutoTS.

Classes

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ReactiqStructureReader
Local version of StructureReader which redefines bonding when reading

Functions

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clean_st(st, mmjag=True, cov_offset=0.4)
Clean up a st via redefining bonding.

copy_autots_atom_properties(st1, st2)
copy all known atom-level AutoTS-specific properties from st1 to st2.

copy_autots_st_properties(st1, st2)
copy all known structure-level AutoTS-specific properties from st1 to st2.

copy_autots_bond_properties(st1, st2)
copy all known bond-level AutoTS-specific properties.

copy_autots_properties(st1, st2)
copy all known atom-, bond- and st-level AutoTS-specific properties from st1 to st2.

clear_autots_atom_properties(st)
clear all known atom-level AutoTS-specific properties.

clear_autots_st_properties(st, exceptions=('i_m_Molecular_charge', 'i_m_Spin_multiplicity'))
Copy all known structure-level AutoTS-specific properties.

clear_autots_bond_properties(st)
clear all known bond-level AutoTS-specific properties.

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

zero_order_metal_bonds(st)
Set the order of bonds containing metals to zero.

Structure instance

delete_ghosts(st)
Delete ghost/dummy atoms from the structure and return the modified structure.

_replace_ghost_bonding(st, ghosts)
Replace the bonding to ghost atoms for any bond to transition metals (TM).

get_mmlewis_bonding(st)
Get bonding from mmlewis.

_get_mmlewis_bonding(st)
get bonding from mmlewis

Variables

[hide private]

__doc__ = """ Methods to handle structure reading and bonding ...

__package__ = 'schrodinger.application.jaguar'

Function Details

[hide private]

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

Returns:

the cleaned up structure

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.

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.

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.

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)

zero_order_metal_bonds(st)

Set the order of bonds containing metals to zero.

Parameters:

st (Structure instance) - the structure containing metal bonds

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

Returns: Structure instance

the structure without the ghost atoms

_replace_ghost_bonding(st, ghosts)


Replace the bonding to ghost atoms for any bond to transition metals (TM).
The idea is to replace 
                    C
                   /|
                  / |
               M-Gh |
                  \ |
                   \|
                    C

   with

                    C
                   /|
                  / |
                 M  |
                  \ |
                   \|
                    C


   We only add bonds between the metal and the other atoms the ghost is bonded to.
  
   We'll also add bonds if the Ghost is only bonded to two atoms, i.e.
                  A-Gh-A -> A-A
   All added bonds are zero order.

@type st: Structure instance
@param st: structure to modify bonding for
@type ghosts: list of ints
@param ghosts: list of indexes for ghost atoms

get_mmlewis_bonding(st)

Get bonding from mmlewis. Do it molecule by molecule.

Parameters:

st (Structure instance) - the structure to get bond orders for (must be connected)

_get_mmlewis_bonding(st)

get bonding from mmlewis

Parameters:

st (Structure instance) - the structure to get bond orders for (must be connected)

Variables Details

[hide private]

doc

Value:

""" Methods to handle structure reading and bonding in AutoTS. """

Module autots_bonding

clean_st(st, mmjag=True, cov_offset=0.4)

copy_autots_atom_properties(st1, st2)

copy_autots_bond_properties(st1, st2)

copy_autots_properties(st1, st2)

clear_autots_st_properties(st, exceptions=('i_m_Molecular_charge', 'i_m_Spin_multiplicity'))

zero_order_metal_bonds(st)

delete_ghosts(st)

_replace_ghost_bonding(st, ghosts)

get_mmlewis_bonding(st)

_get_mmlewis_bonding(st)

__doc__

clear_autots_st_properties(st, exceptions=`('i_m_Molecular_charge',` `'i_m_Spin_multiplicity')`)

doc