`ovo.core.database.models_rfdiffusion`¶

Module Contents¶

Classes¶

`RFdiffusionParams`
`ProteinMPNNParams`
`RefoldingParams`
`RFdiffusionWorkflow`	Dataclass for RFdiffusion workflow.
`RFdiffusionScaffoldDesignWorkflow`
`RFdiffusionBinderDesignWorkflow`

Data¶

`MODEL_WEIGHTS_SCAFFOLD`
`MODEL_WEIGHTS_BINDER`

API¶

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

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

class ovo.core.database.models_rfdiffusion.RFdiffusionParams¶

Bases: ovo.core.database.models.WorkflowParams

input_pdb_paths: list[str]¶: ‘field(…)’

contigs: list[str]¶: ‘field(…)’

hotspots: str | None¶: None

model_weights: str | None¶: None

timesteps: int¶: 50

partial_diffusion: bool¶: False

num_designs: int¶: 10

cyclic_offset: bool¶: False

batch_size: int¶: 100

contigmap_length: int | str | None¶: None

inpaint_seq: str | None¶: None

backbone_filters: str | None¶: None

run_parameters: str = <Multiline-String>¶

property input_pdb¶

property contig¶

validate()¶

class ovo.core.database.models_rfdiffusion.ProteinMPNNParams¶

Bases: ovo.core.database.models.WorkflowParams

num_sequences: int¶: 5

fastrelax_cycles: int¶: 0

omit_aa: str¶: ‘CX’

sampling_temp: float | None¶: ‘field(…)’

bias_aa: str = <Multiline-String>¶

run_parameters: str = <Multiline-String>¶

validate()¶

class ovo.core.database.models_rfdiffusion.RefoldingParams¶

Bases: ovo.core.database.models.WorkflowParams

primary_test: str¶: None

esmfold_fp16: bool¶: False

validate()¶

class ovo.core.database.models_rfdiffusion.RFdiffusionWorkflow¶

Bases: ovo.core.database.models.DesignWorkflow, ovo.core.database.models_refolding.RefoldingSupportedDesignWorkflow

Dataclass for RFdiffusion workflow.

rfdiffusion_params: ovo.core.database.models_rfdiffusion.RFdiffusionParams | None¶: ‘field(…)’

protein_mpnn_params: ovo.core.database.models_rfdiffusion.ProteinMPNNParams | None¶: ‘field(…)’

refolding_params: ovo.core.database.models_rfdiffusion.RefoldingParams | None¶: ‘field(…)’

input_name: str | None¶: None

preview_job_id: str | None¶: None

selected_segments: list[str]¶: None

design_ids: list[str]¶: ‘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

get_input_pdb_path(contig_index=None)¶

get_contig(contig_index=0)¶

set_contig(contig: str)¶

get_hotspots()¶

get_cyclic_offset()¶

get_selected_segments(inpainting=False)¶

set_selected_segments(selection: list[str], inpainting=False)¶

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

get_pipeline_name() → str¶

prepare_params(workdir: str) → dict¶

process_results(job: DesignJob, callback: Callable = None) → list[ovo.core.database.models.Base]¶: Process results of a successful workflow - download files from workdir, create Design and DescriptorValue objects

classmethod get_download_fields()¶

get_refolding_design_paths(design_ids: list[str]) → list[str]¶

class ovo.core.database.models_rfdiffusion.RFdiffusionScaffoldDesignWorkflow¶

Bases: ovo.core.database.models_rfdiffusion.RFdiffusionWorkflow

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

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

classmethod visualize_single_design_sequences(design_id: str)¶

get_refolding_design_type() → str¶

get_refolding_native_pdb_path(contig_index: int) → str¶

class ovo.core.database.models_rfdiffusion.RFdiffusionBinderDesignWorkflow¶

Bases: ovo.core.database.models_rfdiffusion.RFdiffusionWorkflow

binder_length: str | None¶: None

chains: dict | None¶: None

start_res_trimmed_chain: int | None¶: None

end_res_trimmed_chain: int | None¶: None

target_chain: str | None¶: None

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

get_target_chain()¶

get_target_trim_boundary()¶

get_selected_segments(contig_index=0, partial_diffusion=False)¶

set_selected_segments(segments: list[str], contig_index=0, partial_diffusion=False)¶

get_target_contig(contig_index=0)¶

get_binder_contig(contig_index=0)¶

set_binder_contig(binder_contig: str, contig_index: int = 0)¶

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

get_refolding_design_type() → str¶

get_refolding_native_pdb_path(contig_index: int) → Optional[str]¶

ovo.core.database.models_rfdiffusion¶

Module Contents¶

Classes¶

Data¶

API¶

`ovo.core.database.models_rfdiffusion`¶