genui.generators.extensions.genuidrugex package

Subpackages

Submodules

genui.generators.extensions.genuidrugex.admin module

genui.generators.extensions.genuidrugex.apps module

class genui.generators.extensions.genuidrugex.apps.GenuidrugexConfig(app_name, app_module)[source]

Bases: AppConfig

name = 'genui.generators.extensions.genuidrugex'

genui.generators.extensions.genuidrugex.genuisetup module

genuisetup

Created by: Martin Sicho On: 5/3/20, 6:36 PM

genui.generators.extensions.genuidrugex.genuisetup.setup(*args, **kwargs)[source]

genui.generators.extensions.genuidrugex.models module

class genui.generators.extensions.genuidrugex.models.ClippedScore(id, polymorphic_ctype, name, description, created, updated, project, scoremodifier_ptr, upper, lower, high, low, smooth)[source]

Bases: ScoreModifier

exception DoesNotExist: Bases: DoesNotExist

exception MultipleObjectsReturned: Bases: MultipleObjectsReturned

getInstance()[source]

high: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

low: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

lower: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

polymorphic_primary_key_name = 'id'

polymorphic_super_sub_accessors_replaced = False

scoremodifier_ptr

Accessor to the related object on the forward side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Restaurant.place is a ForwardOneToOneDescriptor instance.

scoremodifier_ptr_id

smooth: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

static test(inputs, **kwargs)[source]

upper: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

class genui.generators.extensions.genuidrugex.models.DrugEx(id, polymorphic_ctype, name, description, created, updated, project, generator_ptr, agent, molset, inputFile)[source]

Bases: Generator

exception DoesNotExist: Bases: DoesNotExist

exception MultipleObjectsReturned: Bases: MultipleObjectsReturned

agent

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

agent_id

generator_ptr

Accessor to the related object on the forward side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Restaurant.place is a ForwardOneToOneDescriptor instance.

generator_ptr_id

get(n_samples)[source]

All generators should override this. This should return a list of SMILES strings of size N.

Returns: list of SMILES strings

inputFile

The descriptor for the file attribute on the model instance. Return a FieldFile when accessed so you can write code like:

>>> from myapp.models import MyModel
>>> instance = MyModel.objects.get(pk=1)
>>> instance.file.size

Assign a file object on assignment so you can do:

>>> with open('/path/to/hello.world') as f:
...     instance.file = File(f)

molset

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

molset_id

polymorphic_primary_key_name = 'id'

polymorphic_super_sub_accessors_replaced = False

tasks

Accessor to the related objects manager on the one-to-many relation created by GenericRelation.

In the example:

class Post(Model):
    comments = GenericRelation(Comment)

post.comments is a ReverseGenericManyToOneDescriptor instance.

class genui.generators.extensions.genuidrugex.models.DrugExAgent(id, polymorphic_ctype, name, description, created, updated, project, builder, model_ptr, environment, explorationNet, exploitationNet)[source]

Bases: Model

exception DoesNotExist: Bases: DoesNotExist

exception MultipleObjectsReturned: Bases: MultipleObjectsReturned

environment

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

environment_id

exploitationNet

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

exploitationNet_id

explorationNet

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

explorationNet_id

getDataSetFromMolset(molset, data_file, rewrite=True, n_proc=4)[source]

getGenerator()[source]

model_ptr

Accessor to the related object on the forward side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Restaurant.place is a ForwardOneToOneDescriptor instance.

model_ptr_id

polymorphic_primary_key_name = 'id'

polymorphic_super_sub_accessors_replaced = False

tasks

Accessor to the related objects manager on the one-to-many relation created by GenericRelation.

In the example:

class Post(Model):
    comments = GenericRelation(Comment)

post.comments is a ReverseGenericManyToOneDescriptor instance.

class genui.generators.extensions.genuidrugex.models.DrugExAgentTraining(id, polymorphic_ctype, algorithm, mode, modelInstance, trainingstrategy_ptr, explorer)[source]

Bases: TrainingStrategy

exception DoesNotExist: Bases: DoesNotExist

class ExplorerClass(value)[source]

Bases: TextChoices

An enumeration.

graph = 'GE'

smiles = 'SE'

smiles_molecules = 'SM'

exception MultipleObjectsReturned: Bases: MultipleObjectsReturned

explorer: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

getExplorerInstance(agent, env, mutate, epsilon, beta, batch_size=32)[source]

get_explorer_display(*, field=<django.db.models.fields.CharField: explorer>)

property modelClass

polymorphic_primary_key_name = 'id'

polymorphic_super_sub_accessors_replaced = False

trainingstrategy_ptr

Accessor to the related object on the forward side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Restaurant.place is a ForwardOneToOneDescriptor instance.

trainingstrategy_ptr_id

class genui.generators.extensions.genuidrugex.models.DrugExAgentValidation(id, polymorphic_ctype, modelInstance, validationstrategy_ptr, validSetSize)[source]

Bases: ValidationStrategy

exception DoesNotExist: Bases: DoesNotExist

exception MultipleObjectsReturned: Bases: MultipleObjectsReturned

polymorphic_primary_key_name = 'id'

polymorphic_super_sub_accessors_replaced = False

validSetSize: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

validationstrategy_ptr

Accessor to the related object on the forward side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Restaurant.place is a ForwardOneToOneDescriptor instance.

validationstrategy_ptr_id

class genui.generators.extensions.genuidrugex.models.DrugExEnvironment(id, polymorphic_ctype, name, description, created, updated, project, rewardScheme)[source]

Bases: DataSet

exception DoesNotExist: Bases: ObjectDoesNotExist

exception MultipleObjectsReturned: Bases: MultipleObjectsReturned

class RewardScheme(value)[source]

Bases: TextChoices

An enumeration.

paretoCrowding = 'PC'

paretoSimilarity = 'PS'

weightedSum = 'WS'

created: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

description: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

drugexEnviron

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

getInstance(use_modifiers=True)[source]

get_next_by_created(*, field=<django.db.models.fields.DateTimeField: created>, is_next=True, **kwargs)

get_next_by_updated(*, field=<django.db.models.fields.DateTimeField: updated>, is_next=True, **kwargs)

get_previous_by_created(*, field=<django.db.models.fields.DateTimeField: created>, is_next=False, **kwargs)

get_previous_by_updated(*, field=<django.db.models.fields.DateTimeField: updated>, is_next=False, **kwargs)

get_rewardScheme_display(*, field=<django.db.models.fields.CharField: rewardScheme>)

id: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

name: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

polymorphic_ctype: The model field that stores the ContentType reference to the actual class.

polymorphic_ctype_id

polymorphic_primary_key_name = 'id'

polymorphic_super_sub_accessors_replaced = False

project

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

project_id

rewardScheme: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

scorers

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

scores

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

updated: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

class genui.generators.extensions.genuidrugex.models.DrugExEnvironmentScores(id, polymorphic_ctype, name, description, created, updated, project, molecules, activityset_ptr, environment, modifiersOn)[source]

Bases: ActivitySet

exception DoesNotExist: Bases: DoesNotExist

exception MultipleObjectsReturned: Bases: MultipleObjectsReturned

activityset_ptr

Accessor to the related object on the forward side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Restaurant.place is a ForwardOneToOneDescriptor instance.

activityset_ptr_id

environment

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

environment_id

modifiersOn: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

polymorphic_primary_key_name = 'id'

polymorphic_super_sub_accessors_replaced = False

tasks

Accessor to the related objects manager on the one-to-many relation created by GenericRelation.

In the example:

class Post(Model):
    comments = GenericRelation(Comment)

post.comments is a ReverseGenericManyToOneDescriptor instance.

class genui.generators.extensions.genuidrugex.models.DrugExNet(id, polymorphic_ctype, name, description, created, updated, project, builder, model_ptr, molset, parent)[source]

Bases: Model

CORPUS_FILE_TRAIN_NOTE = 'drugex_corpus_train'

CORPUS_FILE_VALID_NOTE = 'drugex_corpus_test'

exception DoesNotExist: Bases: DoesNotExist

exception MultipleObjectsReturned: Bases: MultipleObjectsReturned

VOC_FILE_NOTE = 'drugex_voc'

property corpusFileTest

property corpusFileTrain

property corpusTest

property corpusTrain

createCorpusFile(note, name)[source]

drugexExploit

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

drugexExplore

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

drugexnet_set

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

getCorpus(_file)[source]

getDataSetFromMolset(molset, data_file, rewrite=True, n_proc=4)[source]

getDefaultVoc()[source]

getModel()[source]

model_ptr

Accessor to the related object on the forward side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Restaurant.place is a ForwardOneToOneDescriptor instance.

model_ptr_id

molset

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

molset_id

parent

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

parent_id

polymorphic_primary_key_name = 'id'

polymorphic_super_sub_accessors_replaced = False

prepareData(vocabulary=None, n_proc=4, chunk_size=1000)[source]

static standardize(smiles, n_proc=4)[source]

tasks

Accessor to the related objects manager on the one-to-many relation created by GenericRelation.

In the example:

class Post(Model):
    comments = GenericRelation(Comment)

post.comments is a ReverseGenericManyToOneDescriptor instance.

property vocFile

class genui.generators.extensions.genuidrugex.models.DrugExNetTraining(id, polymorphic_ctype, algorithm, mode, modelInstance, trainingstrategy_ptr, modelClass, inputType)[source]

Bases: TrainingStrategy

exception DoesNotExist: Bases: DoesNotExist

class ModelClass(value)[source]

Bases: TextChoices

An enumeration.

graphTrans = 'GT'

smilesRNNSingle = 'SS'

smilesTrans = 'ST'

exception MultipleObjectsReturned: Bases: MultipleObjectsReturned

class StructureInputType(value)[source]

Bases: TextChoices

An enumeration.

frags = 'FS'

molecules = 'MS'

get_inputType_display(*, field=<django.db.models.fields.CharField: inputType>)

get_modelClass_display(*, field=<django.db.models.fields.CharField: modelClass>)

inputType: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

modelClass: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

polymorphic_primary_key_name = 'id'

polymorphic_super_sub_accessors_replaced = False

processMetaData(metadata)[source]

trainingstrategy_ptr

Accessor to the related object on the forward side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Restaurant.place is a ForwardOneToOneDescriptor instance.

trainingstrategy_ptr_id

class genui.generators.extensions.genuidrugex.models.DrugExNetValidation(id, polymorphic_ctype, modelInstance, validationstrategy_ptr, validSetSize)[source]

Bases: ValidationStrategy

exception DoesNotExist: Bases: DoesNotExist

exception MultipleObjectsReturned: Bases: MultipleObjectsReturned

polymorphic_primary_key_name = 'id'

polymorphic_super_sub_accessors_replaced = False

validSetSize: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

validationstrategy_ptr

Accessor to the related object on the forward side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Restaurant.place is a ForwardOneToOneDescriptor instance.

validationstrategy_ptr_id

class genui.generators.extensions.genuidrugex.models.DrugExScorer(id, polymorphic_ctype, name, description, created, updated, project, environment, modifier, method, threshold)[source]

Bases: DataSet

exception DoesNotExist: Bases: ObjectDoesNotExist

exception MultipleObjectsReturned: Bases: MultipleObjectsReturned

created: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

description: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

environment

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

environment_id

getInstance(use_modifiers=True)[source]

getThreshold()[source]

get_next_by_created(*, field=<django.db.models.fields.DateTimeField: created>, is_next=True, **kwargs)

get_next_by_updated(*, field=<django.db.models.fields.DateTimeField: updated>, is_next=True, **kwargs)

get_previous_by_created(*, field=<django.db.models.fields.DateTimeField: created>, is_next=False, **kwargs)

get_previous_by_updated(*, field=<django.db.models.fields.DateTimeField: updated>, is_next=False, **kwargs)

id: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

method

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

method_id

modifier

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

modifier_id

name: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

polymorphic_ctype: The model field that stores the ContentType reference to the actual class.

polymorphic_ctype_id

polymorphic_primary_key_name = 'id'

polymorphic_super_sub_accessors_replaced = False

project

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

project_id

threshold: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

updated: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

class genui.generators.extensions.genuidrugex.models.GenUIModelScorer(id, polymorphic_ctype, name, description, created, updated, project, scoringmethod_ptr, model)[source]

Bases: ScoringMethod

exception DoesNotExist: Bases: DoesNotExist

class ModelScorer(model, modifier=None)[source]

Bases: Scorer

getKey()[source]

getScores(mols, frags=None)[source]

Returns scores for the input molecules.

Args:: mols: molecules to score frags: input fragments
Returns:: scores (list): list of scores for “mols”

exception MultipleObjectsReturned: Bases: MultipleObjectsReturned

getInstance(modifier)[source]

model

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

model_id

polymorphic_primary_key_name = 'id'

polymorphic_super_sub_accessors_replaced = False

scoringmethod_ptr

Accessor to the related object on the forward side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Restaurant.place is a ForwardOneToOneDescriptor instance.

scoringmethod_ptr_id

class genui.generators.extensions.genuidrugex.models.ModelPerformanceDrugEx(id, polymorphic_ctype, metric, value, model, modelperformance_ptr, epoch, step, modelperfomancenn_ptr, isOnValidationSet, note)[source]

Bases: ModelPerfomanceNN

exception DoesNotExist: Bases: DoesNotExist

exception MultipleObjectsReturned: Bases: MultipleObjectsReturned

isOnValidationSet: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

modelperfomancenn_ptr

Accessor to the related object on the forward side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Restaurant.place is a ForwardOneToOneDescriptor instance.

modelperfomancenn_ptr_id

note: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

polymorphic_primary_key_name = 'id'

polymorphic_super_sub_accessors_replaced = False

class genui.generators.extensions.genuidrugex.models.PropertyScorer(id, polymorphic_ctype, name, description, created, updated, project, scoringmethod_ptr, prop)[source]

Bases: ScoringMethod

exception DoesNotExist: Bases: DoesNotExist

exception MultipleObjectsReturned: Bases: MultipleObjectsReturned

getInstance(modifier)[source]

get_prop_display(*, field=<django.db.models.fields.CharField: prop>)

polymorphic_primary_key_name = 'id'

polymorphic_super_sub_accessors_replaced = False

prop: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

scoringmethod_ptr

Accessor to the related object on the forward side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Restaurant.place is a ForwardOneToOneDescriptor instance.

scoringmethod_ptr_id

class genui.generators.extensions.genuidrugex.models.ScoreModifier(id, polymorphic_ctype, name, description, created, updated, project)[source]

Bases: DataSet

exception DoesNotExist: Bases: ObjectDoesNotExist

exception MultipleObjectsReturned: Bases: MultipleObjectsReturned

clippedscore

Accessor to the related object on the reverse side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Place.restaurant is a ReverseOneToOneDescriptor instance.

created: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

description: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

drugexscorer_set

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

getInstance()[source]

get_next_by_created(*, field=<django.db.models.fields.DateTimeField: created>, is_next=True, **kwargs)

get_next_by_updated(*, field=<django.db.models.fields.DateTimeField: updated>, is_next=True, **kwargs)

get_previous_by_created(*, field=<django.db.models.fields.DateTimeField: created>, is_next=False, **kwargs)

get_previous_by_updated(*, field=<django.db.models.fields.DateTimeField: updated>, is_next=False, **kwargs)

id: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

name: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

polymorphic_ctype: The model field that stores the ContentType reference to the actual class.

polymorphic_ctype_id

polymorphic_primary_key_name = 'id'

polymorphic_super_sub_accessors_replaced = False

project

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

project_id

smoothhump

Accessor to the related object on the reverse side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Place.restaurant is a ReverseOneToOneDescriptor instance.

static test(inputs, **kwargs)[source]

updated: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

class genui.generators.extensions.genuidrugex.models.ScoringMethod(id, polymorphic_ctype, name, description, created, updated, project)[source]

Bases: DataSet

exception DoesNotExist: Bases: ObjectDoesNotExist

exception MultipleObjectsReturned: Bases: MultipleObjectsReturned

created: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

description: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

drugexscorer_set

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

genuimodelscorer

Accessor to the related object on the reverse side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Place.restaurant is a ReverseOneToOneDescriptor instance.

getInstance(modifier)[source]

get_next_by_created(*, field=<django.db.models.fields.DateTimeField: created>, is_next=True, **kwargs)

get_next_by_updated(*, field=<django.db.models.fields.DateTimeField: updated>, is_next=True, **kwargs)

get_previous_by_created(*, field=<django.db.models.fields.DateTimeField: created>, is_next=False, **kwargs)

get_previous_by_updated(*, field=<django.db.models.fields.DateTimeField: updated>, is_next=False, **kwargs)

id: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

name: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

polymorphic_ctype: The model field that stores the ContentType reference to the actual class.

polymorphic_ctype_id

polymorphic_primary_key_name = 'id'

polymorphic_super_sub_accessors_replaced = False

project

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

project_id

propertyscorer

Accessor to the related object on the reverse side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Place.restaurant is a ReverseOneToOneDescriptor instance.

updated: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

class genui.generators.extensions.genuidrugex.models.SmoothHump(id, polymorphic_ctype, name, description, created, updated, project, scoremodifier_ptr, upper, lower, sigma)[source]

Bases: ScoreModifier

exception DoesNotExist: Bases: DoesNotExist

exception MultipleObjectsReturned: Bases: MultipleObjectsReturned

getInstance()[source]

lower: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

polymorphic_primary_key_name = 'id'

polymorphic_super_sub_accessors_replaced = False

scoremodifier_ptr

Accessor to the related object on the forward side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Restaurant.place is a ForwardOneToOneDescriptor instance.

scoremodifier_ptr_id

sigma: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

static test(inputs, **kwargs)[source]

upper: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

genui.generators.extensions.genuidrugex.serializers module

serializers

Created by: Martin Sicho On: 5/3/20, 6:43 PM

class genui.generators.extensions.genuidrugex.serializers.ClippedSerializer(*args, **kwargs)[source]

Bases: ModifierSerializer

class Meta[source]

Bases: object

fields = ('id', 'name', 'description', 'created', 'updated', 'project', 'upper', 'lower', 'high', 'low', 'smooth')

model: alias of ClippedScore

read_only_fields = ('id', 'created', 'updated')

class genui.generators.extensions.genuidrugex.serializers.DrugExAgentInitSerializer(*args, **kwargs)[source]

Bases: DrugExAgentSerializer

class Meta[source]

Bases: object

fields = ['id', 'name', 'description', 'created', 'updated', 'project', 'trainingStrategy', 'validationStrategy', 'modelFile', 'build', 'taskID', 'environment', 'explorationNet', 'exploitationNet']

model: alias of DrugExAgent

read_only_fields = ['id', 'created', 'updated', 'modelFile', 'taskID']

create(validated_data, **kwargs)[source]

We have a bit of extra checking around this in order to provide descriptive messages when something goes wrong, but this method is essentially just:

return ExampleModel.objects.create(**validated_data)

If there are many to many fields present on the instance then they cannot be set until the model is instantiated, in which case the implementation is like so:

example_relationship = validated_data.pop(‘example_relationship’) instance = ExampleModel.objects.create(**validated_data) instance.example_relationship = example_relationship return instance

The default implementation also does not handle nested relationships. If you want to support writable nested relationships you’ll need to write an explicit .create() method.

class genui.generators.extensions.genuidrugex.serializers.DrugExAgentSerializer(*args, **kwargs)[source]

Bases: ModelSerializer

class Meta[source]

Bases: object

fields = ['id', 'name', 'description', 'created', 'updated', 'project', 'trainingStrategy', 'validationStrategy', 'modelFile', 'build', 'taskID', 'environment', 'explorationNet', 'exploitationNet']

model: alias of DrugExAgent

read_only_fields = ['id', 'created', 'updated', 'modelFile', 'taskID']

class genui.generators.extensions.genuidrugex.serializers.DrugExAgentTrainingStrategyInitSerializer(*args, **kwargs)[source]

Bases: TrainingStrategyInitSerializer

class Meta[source]

Bases: object

fields = ('algorithm', 'mode', 'parameters', 'explorer')

model: alias of DrugExAgentTraining

class genui.generators.extensions.genuidrugex.serializers.DrugExAgentTrainingStrategySerializer(*args, **kwargs)[source]

Bases: TrainingStrategySerializer

class Meta[source]

Bases: object

fields = ('algorithm', 'mode', 'parameters', 'explorer')

model: alias of DrugExAgentTraining

class genui.generators.extensions.genuidrugex.serializers.DrugExAgentValidationStrategyInitSerializer(*args, **kwargs)[source]

Bases: ValidationStrategyInitSerializer

class Meta[source]

Bases: object

fields = ('metrics', 'validSetSize')

model: alias of DrugExAgentValidation

class genui.generators.extensions.genuidrugex.serializers.DrugExAgentValidationStrategySerializer(*args, **kwargs)[source]

Bases: ValidationStrategySerializer

class Meta[source]

Bases: object

fields = ('metrics', 'validSetSize')

model: alias of DrugExAgentValidation

class genui.generators.extensions.genuidrugex.serializers.DrugExEnvironmentCalculationSerializer(*args, **kwargs)[source]

Bases: Serializer

class Meta[source]

Bases: object

fields = ('molsets', 'useModifiers', 'task')

read_only_fields = ('task',)

class genui.generators.extensions.genuidrugex.serializers.DrugExEnvironmentSerializer(*args, **kwargs)[source]

Bases: HyperlinkedModelSerializer

class Meta[source]

Bases: object

fields = ('id', 'name', 'description', 'created', 'updated', 'project', 'rewardScheme', 'scorers')

model: alias of DrugExEnvironment

read_only_fields = ('id', 'created', 'updated', 'scorers')

class genui.generators.extensions.genuidrugex.serializers.DrugExGeneratorSerializer(*args, **kwargs)[source]

Bases: GeneratorSerializer

class Meta[source]

Bases: object

fields = ('id', 'name', 'description', 'project', 'compounds', 'className', 'extraArgs', 'agent', 'molset')

model: alias of DrugEx

class genui.generators.extensions.genuidrugex.serializers.DrugExNetInitSerializer(*args, **kwargs)[source]

Bases: DrugExNetSerializer

class Meta[source]

Bases: object

fields = ['id', 'name', 'description', 'created', 'updated', 'project', 'trainingStrategy', 'validationStrategy', 'modelFile', 'build', 'taskID', 'molset', 'parent']

model: alias of DrugExNet

read_only_fields = ['id', 'created', 'updated', 'modelFile', 'taskID']

create(validated_data, **kwargs)[source]

We have a bit of extra checking around this in order to provide descriptive messages when something goes wrong, but this method is essentially just:

return ExampleModel.objects.create(**validated_data)

If there are many to many fields present on the instance then they cannot be set until the model is instantiated, in which case the implementation is like so:

example_relationship = validated_data.pop(‘example_relationship’) instance = ExampleModel.objects.create(**validated_data) instance.example_relationship = example_relationship return instance

The default implementation also does not handle nested relationships. If you want to support writable nested relationships you’ll need to write an explicit .create() method.

class genui.generators.extensions.genuidrugex.serializers.DrugExNetSerializer(*args, **kwargs)[source]

Bases: ModelSerializer

class Meta[source]

Bases: object

fields = ['id', 'name', 'description', 'created', 'updated', 'project', 'trainingStrategy', 'validationStrategy', 'modelFile', 'build', 'taskID', 'molset', 'parent']