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

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Class ReactantMolecule

object --+
         |
        ReactantMolecule

Manage a reactant molecule in the reactants structure object.

Instance Methods

[hide private]

__init__(self, molecule)
Create an instance.

setReactiveInds(self, reactive_inds_orig)
Set the two lists of reactive indicies attributes using the provided list of original reactive indicies

dict

combineMapWith(self, other_molecule)
Return the new to orig atom reordering map for this molecule extended by that of the other molecule by offsetting the keys of the map of the other molecule.

addTempHydrogens(self)
Add a temporary hydrogen to the reactive atom of this molecule to act as a bond handle for performing the reaction.

delTempHydrogens(self)
Delete all traces of the previously added temporary hydrogen.

Products

reactWith(self, other_molecule, reverse=False)
React this molecule with the provided other molecule according to their reactive indicies and return the product object.

Products

dissociate(self, dissociation_bond_length)
Dissociate this molecule according to its reactive indicies.

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

Class Variables

[hide private]

BOND_SUM_THRESH = 0.1

COLINEAR_THRESH = 0.01

ZERO_VEC = array([ 0., 0., 0.])

HYDROGEN_SYM = 'H'

HYDROGEN_BOND_ORDER = 1

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, molecule)
(Constructor)

Create an instance.

Parameters:

molecule (schrodinger.structure._Molecule) - reactant molecule to be extracted from the reactants structure

Overrides: object.__init__

setReactiveInds(self, reactive_inds_orig)

Set the two lists of reactive indicies attributes using the provided list of original reactive indicies

Parameters:

reactive_inds_orig (list) - original reactive indicies for this reactant molecule

combineMapWith(self, other_molecule)

Return the new to orig atom reordering map for this molecule extended by that of the other molecule by offsetting the keys of the map of the other molecule.

Parameters:

other_molecule (schrodinger.structure._Molecule) - molecule whose new to orig atom reordering map will be combined with that of the current molecule

Returns: dict

final_map, the combined new to original atom reordering maps of this molecule and the other molecule

addTempHydrogens(self)

Add a temporary hydrogen to the reactive atom of this molecule to act as a bond handle for performing the reaction. All traces of this temporary hydrogen will be removed from this instance once the reactions are complete. Note that the family of functions that handles the temporary hydrogens are put in place so that all reaction channels can be handled just like the bond-bond double displacement type, i.e. the association and single displacement types then become nothing more than double displacement with a fake hydrogen.

reactWith(self, other_molecule, reverse=False)

React this molecule with the provided other molecule according to their reactive indicies and return the product object.

Parameters:

other_molecule (ReactantMolecule) - the input molecule that this molecule will react with
reverse (bool) - specifies to reverse the order of reactive indicies for the other molecule

Returns: Products

dissociate(self, dissociation_bond_length)

Dissociate this molecule according to its reactive indicies.

Parameters:

dissociation_bond_length (float) - final bond length to use for dissociative reaction channels

Returns: Products

Class ReactantMolecule

__init__(self, molecule) (Constructor)

setReactiveInds(self, reactive_inds_orig)

combineMapWith(self, other_molecule)

addTempHydrogens(self)

reactWith(self, other_molecule, reverse=False)

dissociate(self, dissociation_bond_length)

init(self, molecule)
(Constructor)