Package schrodinger :: Package application :: Package matsci :: Package rxn_channel :: Module rxn_channel :: Class Products

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Class Products

object --+
         |
        Products

Manage the properties of the products that result from applying a reaction channel definition to the reactants.

Instance Methods

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__init__(self, prod_one_st, prod_one_map, prod_one_rev_map, prod_two_st=None, prod_two_map=None, prod_two_rev_map=None)
Create an instance.

deleteTmpHydrogens(self, mol_one, mol_two)
Remove any of the previously added temporary hydrogens from the product structures.

buildReorderList(self, mol_one, mol_two)
Build the atom reorder list needed to make the product structure ordering consistent with that of the original reactants.

combineAndReorder(self)
Assemble the final product structure for this reaction channel by combining the structure objects for each product molecule followed by reordering the product atoms to be consistent with the reactants.

extendWithSpectator(self, spectator_st, map_to_orig)
Extend the product structure object with the spectator structure object and reorder the atoms to be consistent with that of the reactants from which they came.

updateProperties(self, index, channeldef, reverse=False)
Set some properties on this product structure.

handleMetalBonding(self, rxn_def, reverse)
Handle zero-order bonds for metals.

isolateProducts(self, isolate_products, flatdef)
If requested isolate the individual products to their own structure objects.

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Variables

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RXN_REPRESENTATION_KEY = 's_matsci_RXN_representation'

PRODUCT_NAME_BASE = 'product'

Properties

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Inherited from object: __class__

Method Details

[hide private]

init(self, prod_one_st, prod_one_map, prod_one_rev_map, prod_two_st=None, prod_two_map=None, prod_two_rev_map=None)
(Constructor)

Create an instance.

Overrides: object.__init__

deleteTmpHydrogens(self, mol_one, mol_two)

Remove any of the previously added temporary hydrogens from the product structures.

Parameters:

mol_one (schrodinger.structure._Molecule) - the first reactant molecule from which these products came
mol_two (schrodinger.structure._Molecule) - the second reactant molecule from which these products came

buildReorderList(self, mol_one, mol_two)

Build the atom reorder list needed to make the product structure ordering consistent with that of the original reactants.

Parameters:

mol_one (schrodinger.structure._Molecule) - the first reactant molecule from which these products came
mol_two (schrodinger.structure._Molecule) - the second reactant molecule from which these products came

extendWithSpectator(self, spectator_st, map_to_orig)

Extend the product structure object with the spectator structure object and reorder the atoms to be consistent with that of the reactants from which they came.

Parameters:

spectator_st (schrodinger.structure.Structure) - the structure object containing all spectator molecules
map_to_orig (dict) - an atom reordering dictionary where the keys are the reactant atom indicies followed by the spectator atom indicies and the values are their values

updateProperties(self, index, channeldef, reverse=False)

Set some properties on this product structure.

Parameters:

index (int) - index of this set of products
channeldef (ChannelDefinition) - the channel definition from which this product came
reverse (bool) - specifies that the order of the reactive indicies for the second molecule were reversed

handleMetalBonding(self, rxn_def, reverse)

Handle zero-order bonds for metals.

Parameters:

rxn_def (list) - a list of two lists containing the reaction channel definitions in terms of atomic indicies
reverse (bool) - specifies that the order of the reactive indicies for the second molecule were reversed

isolateProducts(self, isolate_products, flatdef)

If requested isolate the individual products to their own structure objects.

Parameters:

isolate_products (bool) - specifies that products should be returned individually rather than as a whole
flatdef (list) - list containing the original reactive atom indicies of the input structure

Class Products

__init__(self, prod_one_st, prod_one_map, prod_one_rev_map, prod_two_st=None, prod_two_map=None, prod_two_rev_map=None) (Constructor)

deleteTmpHydrogens(self, mol_one, mol_two)

buildReorderList(self, mol_one, mol_two)

extendWithSpectator(self, spectator_st, map_to_orig)

updateProperties(self, index, channeldef, reverse=False)

handleMetalBonding(self, rxn_def, reverse)

isolateProducts(self, isolate_products, flatdef)

init(self, prod_one_st, prod_one_map, prod_one_rev_map, prod_two_st=None, prod_two_map=None, prod_two_rev_map=None)
(Constructor)