`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`
`ArtifactTypes`
`Artifact`
`UnknownArtifact`	Unknown artifact type, used when the artifact type is not recognized or not registered
`ProjectArtifact`
`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=None)¶: 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_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¶: Get name (for example ovo.rfdiffusion-end-to-end) or github URL of pipeline to be submitted for this workflow

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)¶

get_relevant_descriptor_keys() → list[str]¶

Get list of descriptor keys that are of interest for this workflow

Used to determine which descriptors to show in the Explorer table

By default, we return all descriptors included in the accepted_thresholds field for this workflow (even disabled ones)

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(…)’

project_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.ArtifactTypes¶

_registry¶: None

classmethod register()¶: Decorator to register an Artifact class

classmethod exists(artifact_type)¶: Check if an artifact of the given type exists

classmethod get(artifact_type)¶: Get artifact class by type string

class ovo.core.database.models.Artifact¶

Bases: abc.ABC

artifact_type: str¶: ‘field(…)’

classmethod from_dict(data: dict) → ovo.core.database.models.Artifact¶

abstractmethod get_storage_paths() → list[str]¶

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

Bases: ovo.core.database.models.Artifact

Unknown artifact type, used when the artifact 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

get_storage_paths() → list[str]¶

class ovo.core.database.models.ProjectArtifact¶

Bases: ovo.core.database.models.Base

__tablename__¶: ‘project_artifact’

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

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

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

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

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

artifact: sqlalchemy.orm.Mapped[ovo.core.database.models.Artifact]¶: ‘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`¶