`ovo.core.database.models`¶

Module Contents¶

Classes¶

`Base`	subclasses will be converted to dataclasses
`JobMixin`
`MetadataMixin`
`UserSettings`
`Project`
`Round`
`WorkflowParams`
`Threshold`
`WorkflowTypes`
`Workflow`
`DescriptorWorkflow`
`DesignDescriptorWorkflow`	Placeholder DescriptorWorkflow used when the descriptors are generated by a design workflow
`DesignWorkflow`
`UnknownWorkflow`	Unknown workflow type, used when the workflow type is not recognized or not registered
`DesignJob`
`Pool`
`DesignChain`
`DesignSpec`
`Design`
`DescriptorJob`
`DescriptorValue`
`Descriptor`
`NumericDescriptor`
`NumericGlobalDescriptor`	Descriptor storing a number for the whole molecule
`NumericResidueDescriptor`	Descriptor storing a number for each residue in a protein chain
`StringGlobalDescriptor`	Descriptor storing a string label for the whole molecule
`StringResidueDescriptor`	Descriptor storing a string for multiple residues, as a {resid -> string} dictionary, stored in the DB as a JSON-encoded string.
`CategoricalResidueDescriptor`	Descriptor storing a category label for each residue in a protein chain, each category represented by a letter.
`ResidueNumberDescriptor`	Descriptor storing list of residue numbers as a value, for example A123,A124,A202
`FileDescriptor`	Descriptor storing a Storage file path as a value
`StructureFileDescriptor`	Descriptor storing a structure file path as a value (PDB, mmCIF)

Data¶

`MODEL_WEIGHTS_SCAFFOLD`
`MODEL_WEIGHTS_BINDER`
`DesignChainType`
`x`
`__all__`

API¶

class ovo.core.database.models.Base¶

Bases: sqlalchemy.orm.MappedAsDataclass, sqlalchemy.orm.DeclarativeBase

subclasses will be converted to dataclasses

class ovo.core.database.models.JobMixin¶

Bases: sqlalchemy.orm.MappedAsDataclass

scheduler_key: sqlalchemy.orm.Mapped[str]¶: ‘mapped_column(…)’

job_id: sqlalchemy.orm.Mapped[str]¶: ‘mapped_column(…)’

job_started_date_utc: sqlalchemy.orm.Mapped[datetime.datetime]¶: ‘mapped_column(…)’

job_finished_date_utc: sqlalchemy.orm.Mapped[datetime.datetime]¶: ‘mapped_column(…)’

job_result: sqlalchemy.orm.Mapped[bool | None]¶: ‘mapped_column(…)’

warnings: sqlalchemy.orm.Mapped[list[str]]¶: ‘mapped_column(…)’

class ovo.core.database.models.MetadataMixin¶

Bases: sqlalchemy.orm.MappedAsDataclass

author: sqlalchemy.orm.Mapped[str]¶: ‘mapped_column(…)’

created_date_utc: sqlalchemy.orm.Mapped[datetime.datetime]¶: ‘mapped_column(…)’

class ovo.core.database.models.UserSettings¶

Bases: ovo.core.database.models.Base

__tablename__¶: ‘user_setting’

username: sqlalchemy.orm.Mapped[str]¶: ‘mapped_column(…)’

last_project_id: sqlalchemy.orm.Mapped[str]¶: ‘mapped_column(…)’

class ovo.core.database.models.Project¶

Bases: ovo.core.database.models.Base, ovo.core.database.models.MetadataMixin

__tablename__¶: ‘project’

__table_args__¶: ()

id: sqlalchemy.orm.Mapped[str]¶: ‘mapped_column(…)’

name: sqlalchemy.orm.Mapped[str]¶: ‘mapped_column(…)’

public: sqlalchemy.orm.Mapped[bool]¶: ‘mapped_column(…)’

class ovo.core.database.models.Round¶

Bases: ovo.core.database.models.Base, ovo.core.database.models.MetadataMixin

__tablename__¶: ‘round’

id: sqlalchemy.orm.Mapped[str]¶: ‘mapped_column(…)’

project_id: sqlalchemy.orm.Mapped[str]¶: ‘mapped_column(…)’

name: sqlalchemy.orm.Mapped[str]¶: ‘mapped_column(…)’

description: sqlalchemy.orm.Mapped[str]¶: ‘mapped_column(…)’

ovo.core.database.models.MODEL_WEIGHTS_SCAFFOLD¶: [‘Base’, ‘ActiveSite’]

ovo.core.database.models.MODEL_WEIGHTS_BINDER¶: [‘Complex_base’, ‘Complex_beta’]

class ovo.core.database.models.WorkflowParams¶

validate()¶

classmethod from_dict(data)¶

to_dict(human_readable=False)¶

class ovo.core.database.models.Threshold¶

min_value: float | None¶: None

max_value: float | None¶: None

enabled: bool¶: True

copy(**kwargs) → ovo.core.database.models.Threshold¶

__eq__(other)¶

format(descriptor_name: str = '') → str | None¶

get_bounds(descriptor: ovo.core.database.models.NumericDescriptor, descriptor_values: pandas.Series) → tuple[float | int, float | int] | None¶

Get min, max bounds for the threshold for a specific set of designs, based on the descriptor values

Can be used to plot the threshold on a histogram or scatter plot.

Parameters:

descriptor – Descriptor object, used to get the min and max values if not set in the threshold
descriptor_values – Series of descriptor values for the designs, used to determine the bounds

Returns:

tuple of (min, max) bounds for the threshold, or None if no bounds are set

class ovo.core.database.models.WorkflowTypes¶

_registry¶: None

classmethod register(workflow_name)¶: Decorator to register a workflow class with a given name

classmethod exists(workflow_name)¶: Check if a workflow type with the given name exists

classmethod get(workflow_name)¶: Get workflow class by name

classmethod get_subclass_names(workflow_name) → list[str]¶: Get list of registered workflow names that are subclasses of the given workflow name (including itself)

class ovo.core.database.models.Workflow¶

name: str¶: ‘field(…)’

is_instance(cls)¶

Safe isinstance that avoids error on objects loaded from Streamlit session state after live reload

This solves the problem that sometimes is_instance returns false in our app even though the object actually is of that class.

See documentation: https://docs.streamlit.io/develop/concepts/design/custom-classes And issue: https://github.com/streamlit/streamlit/issues/8180

classmethod is_subclass(other_cls)¶: Safe issubclass that avoids error on objects loaded from Streamlit session state after live reload

classmethod from_dict(data)¶: Convert dict to Workflow object - NOTE: This method currently cannot be extended, the base class method will always be called! See db.encoder module

get_param_fields(human_readable=False) → dict[str, ovo.core.database.models.WorkflowParams]¶

Get all …_param fields, verify they are instances of WorkflowParams

with human_readble=False, returns dict: field_name -> params instance with human_readble=True, returns dict: Tool name -> params instance

get_param_dict() → dict¶: Get all values of all param fields, as flat dictionary

get_table_row(**kwargs) → pandas.Series¶: Get all values of all param fields, skip fields with metadata.show_to_user=False, return pd.Series

validate()¶

get_time_estimate(scheduler: ovo.core.scheduler.base_scheduler.Scheduler) → str¶

abstractmethod get_pipeline_name() → str¶

abstractmethod prepare_params(workdir: str) → dict¶: Submit the workflow to the scheduler and return the job id

abstractmethod process_results(job: Union[ovo.core.database.models.DesignJob, ovo.core.database.models.DescriptorJob], callback: Callable = None) → list[ovo.core.database.models.Base]¶: Process results of a successful workflow - download files from workdir, create and return objects to be saved such as Designs and DescriptorValues

classmethod get_download_fields()¶

class ovo.core.database.models.DescriptorWorkflow¶

Bases: ovo.core.database.models.Workflow, abc.ABC

chains: List[str]¶: ‘field(…)’

design_ids: List[str]¶: ‘field(…)’

validate()¶

class ovo.core.database.models.DesignDescriptorWorkflow¶

Bases: ovo.core.database.models.DescriptorWorkflow

Placeholder DescriptorWorkflow used when the descriptors are generated by a design workflow

design_job_id: str¶: ‘field(…)’

class ovo.core.database.models.DesignWorkflow¶

Bases: ovo.core.database.models.Workflow

acceptance_thresholds: dict[str, ovo.core.database.models.Threshold]¶: ‘field(…)’

get_table_row(**kwargs) → pandas.Series¶: Get all values of all param fields, skip fields with metadata.show_to_user=False, return pd.Series

validate()¶

abstractmethod classmethod visualize_multiple_designs_structures(design_ids: list[str])¶: Visualize multiple design structures in Streamlit

classmethod visualize_single_design_structures(design_id: str)¶: Visualize single design structures in Streamlit

classmethod visualize_single_design_sequences(design_id: str)¶

class ovo.core.database.models.UnknownWorkflow(data: dict, error: str)¶

Bases: ovo.core.database.models.DesignWorkflow, ovo.core.database.models.DescriptorWorkflow

Unknown workflow type, used when the workflow type is not recognized or not registered

This can happen when a plugin is uninstalled.

Initialization

__do_not_serialize__¶: True

data: dict¶: None

error: str¶: None

class ovo.core.database.models.DesignJob¶

Bases: ovo.core.database.models.Base, ovo.core.database.models.MetadataMixin, ovo.core.database.models.JobMixin

__tablename__¶: ‘design_job’

id: sqlalchemy.orm.Mapped[str]¶: ‘mapped_column(…)’

workflow: sqlalchemy.orm.Mapped[ovo.core.database.models.DesignWorkflow]¶: ‘mapped_column(…)’

class ovo.core.database.models.Pool¶

Bases: ovo.core.database.models.Base, ovo.core.database.models.MetadataMixin

__tablename__¶: ‘pool’

__table_args__¶: ()

id: sqlalchemy.orm.Mapped[str]¶: ‘mapped_column(…)’

round_id: sqlalchemy.orm.Mapped[str]¶: ‘mapped_column(…)’

design_job_id: sqlalchemy.orm.Mapped[str]¶: ‘mapped_column(…)’

name: sqlalchemy.orm.Mapped[str]¶: ‘mapped_column(…)’

description: sqlalchemy.orm.Mapped[str]¶: ‘mapped_column(…)’

processed: sqlalchemy.orm.Mapped[bool]¶: ‘mapped_column(…)’

classmethod generate_id()¶

ovo.core.database.models.DesignChainType¶: None

ovo.core.database.models.x¶: None

class ovo.core.database.models.DesignChain¶

type: ovo.core.database.models.DesignChainType¶: None

chain_ids: list[str]¶: None

sequence: str¶: None

smiles: str¶: None

ccd: str¶: None

contig: str¶: None

cyclic: bool¶: False

class ovo.core.database.models.DesignSpec¶

chains: list[ovo.core.database.models.DesignChain]¶: None

get_chain(chain_id: str)¶

classmethod from_pdb_str(pdb_data: str, chains: list[str], cyclic=False)¶

classmethod from_dict(data)¶

class ovo.core.database.models.Design¶

Bases: ovo.core.database.models.Base

__tablename__¶: ‘design’

id: sqlalchemy.orm.Mapped[str]¶: ‘mapped_column(…)’

pool_id: sqlalchemy.orm.Mapped[str]¶: ‘mapped_column(…)’

structure_path: sqlalchemy.orm.Mapped[str]¶: ‘mapped_column(…)’

structure_descriptor_key: sqlalchemy.orm.Mapped[str]¶: ‘mapped_column(…)’

accepted: sqlalchemy.orm.Mapped[bool]¶: ‘mapped_column(…)’

spec: sqlalchemy.orm.Mapped[ovo.core.database.models.DesignSpec]¶: ‘mapped_column(…)’

contig_index: sqlalchemy.orm.Mapped[int]¶: ‘mapped_column(…)’

__post_init__()¶

classmethod design_id_to_pool_id(design_id: str) → str¶: Get Pool ID from Design ID (ovo_xyz_1234 -> xyz)

classmethod from_pdb_file(storage, filename: str, pdb_str: str, chains: list[str], project_id: str, pool_id: str, id: str = None, **kwargs)¶

class ovo.core.database.models.DescriptorJob¶

Bases: ovo.core.database.models.Base, ovo.core.database.models.MetadataMixin, ovo.core.database.models.JobMixin

__tablename__¶: ‘descriptor_job’

id: sqlalchemy.orm.Mapped[str]¶: ‘mapped_column(…)’

round_id: sqlalchemy.orm.Mapped[str]¶: ‘mapped_column(…)’

processed: sqlalchemy.orm.Mapped[bool]¶: ‘mapped_column(…)’

workflow: sqlalchemy.orm.Mapped[ovo.core.database.models.DescriptorWorkflow]¶: ‘mapped_column(…)’

classmethod generate_id(tries=100)¶: Generate unique UID shortened for memory efficiency in descriptor_value table

class ovo.core.database.models.DescriptorValue¶

Bases: ovo.core.database.models.Base

__tablename__¶: ‘descriptor_value’

design_id: sqlalchemy.orm.Mapped[str]¶: ‘mapped_column(…)’

descriptor_key: sqlalchemy.orm.Mapped[str]¶: ‘mapped_column(…)’

descriptor_job_id: sqlalchemy.orm.Mapped[str]¶: ‘mapped_column(…)’

chains: sqlalchemy.orm.Mapped[str]¶: ‘mapped_column(…)’

value: sqlalchemy.orm.Mapped[str]¶: ‘mapped_column(…)’

class ovo.core.database.models.Descriptor¶

Bases: abc.ABC

name: str¶: None

description: str¶: None

tool: str¶: None

key: str¶: None

serialize(value)¶: Serialize a value into a number or string so that it can be stored in the DB

deserialize(value)¶: De-serialize a value stored in the DB into a meaningful object in python

class ovo.core.database.models.NumericDescriptor¶

Bases: ovo.core.database.models.Descriptor, abc.ABC

comparison: str¶: None

min_value: float¶: None

max_value: float¶: None

warning_value: float¶: None

error_value: float¶: None

unit: str¶: None

color_scale: str¶: None

get_plot_range(values: pandas.Series, padding=0.05) → tuple[float, float] | None¶: Return range for the plot based on min_value, max_value with additional padding

format(value)¶

class ovo.core.database.models.NumericGlobalDescriptor¶

Bases: ovo.core.database.models.NumericDescriptor

Descriptor storing a number for the whole molecule

class ovo.core.database.models.NumericResidueDescriptor¶

Bases: ovo.core.database.models.NumericDescriptor

Descriptor storing a number for each residue in a protein chain

class ovo.core.database.models.StringGlobalDescriptor¶

Bases: ovo.core.database.models.Descriptor

Descriptor storing a string label for the whole molecule

class ovo.core.database.models.StringResidueDescriptor¶

Bases: ovo.core.database.models.Descriptor

Descriptor storing a string for multiple residues, as a {resid -> string} dictionary, stored in the DB as a JSON-encoded string.

serialize(value)¶: Serialize a value into a number or string so that it can be stored in the DB

deserialize(value)¶: De-serialize a value stored in the DB into a meaningful object in python

class ovo.core.database.models.CategoricalResidueDescriptor¶

Bases: ovo.core.database.models.Descriptor

Descriptor storing a category label for each residue in a protein chain, each category represented by a letter.

Annotation for the whole chain is saved as a single string, each category represented by a letter (key in category_labels), for example “EEEHHH—HHH” for DSSP secondary structure annotation.

category_labels: dict[str]¶: ‘field(…)’

class ovo.core.database.models.ResidueNumberDescriptor¶

Bases: ovo.core.database.models.Descriptor

Descriptor storing list of residue numbers as a value, for example A123,A124,A202

class ovo.core.database.models.FileDescriptor¶

Bases: ovo.core.database.models.Descriptor

Descriptor storing a Storage file path as a value

class ovo.core.database.models.StructureFileDescriptor¶

Bases: ovo.core.database.models.FileDescriptor

Descriptor storing a structure file path as a value (PDB, mmCIF)

structure_type: Literal[backbone_design, sequence_design, prediction, experimentally_resolved]¶: None

b_factor_value: Literal[plddt, fractional_plddt]¶: None

ovo.core.database.models.__all__¶: [‘Base’, ‘JobMixin’, ‘MetadataMixin’, ‘UserSettings’, ‘Project’, ‘Round’, ‘WorkflowParams’, ‘Thresho…

ovo.core.database.models¶

Module Contents¶

Classes¶

Data¶

API¶

`ovo.core.database.models`¶