schrodinger.application.matsci.rxn_channel.rxn

Class Channels

object --+ | Channels

Manage the enumeration of reaction channels.

Instance Methods

__init__(self, reactants, channeldefs, allow_adsorption_onto=None, dissociation_bond_length=10.0, no_minimization=False, isolate_products=False, no_reactive_h=False, unique=False, mae_out_file=None, logger=None)
Create an instance.

setUpFast3D(self)
Set up the fast 3D object.

checkInputParams(self)
Check all input parameters.

updateChannelDefReprs(self)
Update the representations of the reaction channel definitions.

printChannelDefs(self)
Provide a formatted log of the final reaction channel definitions.

initMaestroWriter(self)
Initialize the Maestro writer for the output *mae file and put the reactants structure in there.

termMaestroWriter(self)
Terminate the Maestro writer for the output *mae file.

processProducts(self, product_sts)
Process the product structures.

enumerateChannels(self)
Main function to enumerate reaction channels.

checkOutputFile(self)
Check the output file.

printRxnReprs(self)
Log a formatted print of all reaction channels in their reaction representation.

printFiltered(self)
Log the structures that were filtered by SMILES.

printNotMinimized(self)
Log the structures that were not minimized.

tearDown(self)
Tear down mmffld and mmlewis.

orchestrate(self)
Orchestrate all of the components of this main class.

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

Class Variables

[hide private]

OPLS_VERSION = 14

OPLS_ENERGY_KEY = 'r_ff_Potential_Energy-OPLS_2005'

OPLS_RMS_KEY = 'r_ff_RMS_Derivative-OPLS_2005'

OPLS_CONVERGED_KEY = 'b_ff_Minimization_Converged-OPLS_2005'

init(self, reactants, channeldefs, allow_adsorption_onto=None, dissociation_bond_length=10.0, no_minimization=False, isolate_products=False, no_reactive_h=False, unique=False, mae_out_file=None, logger=None)
(Constructor)

Create an instance.

Parameters:

reactants (schrodinger.structure.Structure) - the reactants from which channels will be enumerated
channeldefs (ChannelDefinitions) - list of ChannelDefinitions
allow_adsorption_onto (None or list) - SMARTS patterns of arbitrary adsorption sites to support
dissociation_bond_length (float) - final bond length to use for dissociative reaction channels
no_minimization (bool) - specifies that product geometries should not be minimized
isolate_products (bool) - specifies that products should be returned individually rather than as a whole
no_reactive_h (bool) - specify that R-H bonds be considered inert
unique (bool) - provide only unique products, firstly do not calculate redundant products and secondly filter out duplicate final structures using SMILES
mae_out_file (str) - the full path, including filename, that will be used to write the output *mae file that will contain the final set of structures, i.e. reactants plus all sets of products
logger (logging.getLogger) - output logger

Overrides: object.__init__

processProducts(self, product_sts)

Process the product structures.

Parameters:

product_sts (list of schrodinger.structure.Structure) - contains all product structures for a given reaction channel

Class Channels

__init__(self, reactants, channeldefs, allow_adsorption_onto=None, dissociation_bond_length=10.0, no_minimization=False, isolate_products=False, no_reactive_h=False, unique=False, mae_out_file=None, logger=None) (Constructor)

processProducts(self, product_sts)

init(self, reactants, channeldefs, allow_adsorption_onto=None, dissociation_bond_length=10.0, no_minimization=False, isolate_products=False, no_reactive_h=False, unique=False, mae_out_file=None, logger=None)
(Constructor)