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

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Class CheckInput

object --+
         |
        CheckInput

Manage checking user input.

Instance Methods

[hide private]

checkFileExists(self, infile, logger=None)
Check if the provided input file exists.

checkInputFile(self, infile, logger=None)
Check user input file.

checkReactants(self, reactants, logger=None)
Check the provided reactants structure.

int or 'all', list, list, set

checkRandomChannelsInput(self, reactants, num_random_channels, random_types, random_seed, allow_adsorption_onto, logger=None)
Check parameters for generating random channels.

list, set

checkAndProcessAllowAdsorptionOnto(self, astructure, allow_adsorption_onto, logger=None)
Check and process the allow adsorption onto option.

checkChannelDefs(self, channeldefs, logger=None)
Check properties of the supplied channel definitions.

bool

checkIfNotAdsorbable(self, astructure, atom_index, matches)
Check if the provided atom can function as an adsorption site, i.e.

list of boolean

checkIfNotSimpleBond(self, astructure, atom_one, atom_two, no_reactive_h)
Check if the provided two atoms do not form a simple bond, i.e.

list

checkChannelUniqueness(self, astructure, bond1idx1, bond1idx2, bond2idx1, bond2idx2)
For the provided structure use SMILES analysis to determine if the defined single or double displacement reaction channels, i.e.

list

checkChannelDefsVsReactants(self, channeldefs, reactants, matches, no_reactive_h, unique, logger=None)
Check user defined channels against user defined reactants.

float

checkDissociationBondLength(self, dissociation_bond_length, logger=None)
Check the specified dissociation bond length.

int or 'all'

checkNumRandomChannels(self, num_random_channels, logger=None)
Check the specified number of random channels.

list of strs

checkRandomTypes(self, random_types, logger=None)
Check the specified types of random channels.

checkRandomSeed(self, random_seed, logger=None)
Check the specified random seed.

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

Class Variables

[hide private]

TITLE_KEY = 's_m_title'

ENTRY_NAME_KEY = 's_m_entry_name'

REACTANT_NAME_BASE = 'reactant'

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

checkFileExists(self, infile, logger=None)

Check if the provided input file exists.

Parameters:

infile (str) - the input file
logger (logging.getLogger) - output logger

checkInputFile(self, infile, logger=None)

Check user input file.

Parameters:

infile (str) - the input file
logger (logging.getLogger) - output logger

checkReactants(self, reactants, logger=None)

Check the provided reactants structure.

Parameters:

reactants (schrodinger.structure.Structure) - the reactants from which channels will be enumerated
logger (logging.getLogger) - output logger

checkRandomChannelsInput(self, reactants, num_random_channels, random_types, random_seed, allow_adsorption_onto, logger=None)

Check parameters for generating random channels.

Parameters:

reactants (schrodinger.structure.Structure) - the reactants from which channels will be enumerated
num_random_channels (int or 'all') - the number of random channels to generate or 'all'
random_types (list) - list of strings specifying which types of channels should be sampled when generating the random reaction channels
random_seed (None or int) - the seed for the random number generator
allow_adsorption_onto (list) - SMARTS patterns of arbitrary adsorption sites to support
logger (logging.getLogger) - output logger

Returns: int or 'all', list, list, set

num_random_channels, random_types, allow_adsorption_onto as defined above, and matches is a set of atom indicies matching the SMARTS present in allow_adsorption_onto

checkAndProcessAllowAdsorptionOnto(self, astructure, allow_adsorption_onto, logger=None)

Check and process the allow adsorption onto option.

Parameters:

astructure (schrodinger.structure.Structure) - the structure
allow_adsorption_onto (list) - SMARTS patterns of arbitrary adsorption sites to support
logger (logging.getLogger) - output logger

Returns: list, set

allow_adsorption_onto and matches, final list of SMARTS patterns on which to allow adsorption and a set of atom indicies matching the SMARTS present in allow_adsorption_onto

checkChannelDefs(self, channeldefs, logger=None)

Check properties of the supplied channel definitions.

Parameters:

channeldefs (ChannelDefinitions) - list of ChannelDefinitions
logger (logging.getLogger) - output logger

checkIfNotAdsorbable(self, astructure, atom_index, matches)

Check if the provided atom can function as an adsorption site, i.e. check if the atom has any open bonding sites or if the atom belongs to the list of arbitary adsorption sites to allow.

Parameters:

astructure (schrodinger.structure.Structure) - the structure that contains the atom whose candidacy for adsorption will be checked
atom_index (int) - the index of the atom to check
matches (set) - a set of atom indicies matching the SMARTS present in the list of allowed adsorption sites

Returns: bool

False if atom can function as an adsorption site, True otherwise

checkIfNotSimpleBond(self, astructure, atom_one, atom_two, no_reactive_h)

Check if the provided two atoms do not form a simple bond, i.e. a single bond that is not in a ring and possibly does not involve a hydrogen atom.

Parameters:

astructure (schrodinger.structure.Structure) - the structure on which the simple bond will be checked
atom_one (int) - the first atom in the potential bond
atom_two (int) - the second atom in the potential bond
no_reactive_h (bool) - specify that R-H bonds be considered inert

Returns: list of boolean

Contains the bool values of whether (1) the two atoms are not bound, (2) the bond they form is not a single bond, (3) the bond they form is in a ring, and (4) if -no_reactive_h has been specified that the bond involves a hydrogen atom. If any of these is True then the bond is not a simple bond.

checkChannelUniqueness(self, astructure, bond1idx1, bond1idx2, bond2idx1, bond2idx2)

For the provided structure use SMILES analysis to determine if the defined single or double displacement reaction channels, i.e. A + B-C --> A-B + C (1st type) or A-C + B (2nd type) or A-B + C-D --> A-C + B-D (1st type) or A-D + B-C (2nd type), respectively, lead to unique products.

Parameters:

astructure (schrodinger.structure.Structure) - the structure for which the channels will be checked for uniqueness
bond1idx1 (int) - the first atom index of the bond in the first molecule
bond1idx2 (int or None) - the second atom index of the bond in the first molecule or None if this is a single displacement channel and there is no bond
bond2idx1 (int) - the first atom index of the bond in the second molecule
bond2idx2 (int or None) - the second atom index of the bond in the second molecule or None if this is a single displacement channel and there is no bond

Returns: list

two booleans, (1) True if the 1st type should be computed, False otherwise and (2) True if the 2nd type should be computed, False otherwise

checkChannelDefsVsReactants(self, channeldefs, reactants, matches, no_reactive_h, unique, logger=None)

Check user defined channels against user defined reactants.

Parameters:

channeldefs (list) - list of ChannelDefinitions
reactants (schrodinger.structure.Structure) - the reactants from which channels will be enumerated
matches (set) - a set of atom indicies matching the SMARTS present in the list of allowed adsorption sites
no_reactive_h (bool) - specify that R-H bonds be considered inert
unique (bool) - provide only unique products
logger (logging.getLogger) - output logger

Returns: list

final_channeldefs, list of good ChannelDefinitions

checkDissociationBondLength(self, dissociation_bond_length, logger=None)

Check the specified dissociation bond length.

Parameters:

dissociation_bond_length (float) - final bond length to use for dissociative reaction channels
logger (logging.getLogger) - output logger

Returns: float

dissociation_bond_length, final bond length to use for dissociative reaction channels

checkNumRandomChannels(self, num_random_channels, logger=None)

Check the specified number of random channels.

Parameters:

num_random_channels (int or 'all') - the desired number of random channels to generate or 'all'
logger (logging.getLogger) - output logger

Returns: int or 'all'

num_random_channels, the desired number of random channels to generate or 'all'

checkRandomTypes(self, random_types, logger=None)

Check the specified types of random channels.

Parameters:

random_types (list of strs) - the desired types of random channels to generate
logger (logging.getLogger) - output logger

Returns: list of strs

random_types, the desired types of random channels to generate

checkRandomSeed(self, random_seed, logger=None)

Check the specified random seed.

Parameters:

random_seed (None or int) - the seed for the random number generator
logger (logging.Logger) - output logger