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

[frames] | no frames]

Module autots_bonding

Methods to handle structure reading and bonding in AutoTS.

Classes

[hide private]

ReactiqStructureReader
Local version of StructureReader which redefines bonding when reading

Functions

[hide private]

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

simplify_structure(st)
Make all bonds single bonds and remove all charges.

remove_formal_charges(st)

active_reactant_atom_pairs(reactant, product)
return active atom pairs in reactant structure as a list of pairs of integers

active_atom_pairs(reactant, product)
Determine active bonds and return them as lists of pairs of atoms

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)

simplify_structure(st)

Make all bonds single bonds and remove all charges. This makes using SMARTS much more effective. We do not do this to zero order bonds, which are left as is.

Parameters:

st (schrodinger.structure.Structure) - a structure

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)

simplify_structure(st)

__doc__

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

doc