API Reference

Protein

Library Screen

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Stop a running protein library screen

client.Protein.LibraryScreen.Stop(ctx, id) (*ProteinLibraryScreenStopResponse, error)

POST/compute/v1/protein/library-screen/{id}/stop

Stop an in-progress protein library screen early

ParametersExpand Collapse

id string

ReturnsExpand Collapse

type ProteinLibraryScreenStopResponse struct{…}

A protein library screening pipeline run

ID string

Unique ProteinLibraryScreen identifier

CompletedAt Time

formatdate-time

CreatedAt Time

formatdate-time

DataDeletedAt Time

When the input, output, and result data was permanently deleted. Null if data has not been deleted.

formatdate-time

DeprecatedEngine Boltzprot

Use pipeline instead.

Deprecated. Use pipeline instead.

DeprecatedEngineVersion String1_0

Use pipeline_version instead.

Deprecated. Use pipeline_version instead.

Error ProteinLibraryScreenStopResponseError

Code string

Machine-readable error code

Message string

Human-readable error message

Details anyOptional

Additional field-level error details keyed by input path, when available.

Input ProteinLibraryScreenStopResponseInput

Pipeline input (null if data deleted)

Proteins ProteinLibraryScreenStopResponseInputProteins

URL string

URL to download the file

formaturi

URLExpiresAt Time

When the presigned URL expires

formatdate-time

Target ProteinLibraryScreenStopResponseInputTargetUnion

Target specification (structure template or template-free)

One of the following:

type ProteinLibraryScreenStopResponseInputTargetStructureTemplateTargetResponse struct{…}

Target defined by an uploaded 3D structure (CIF or PDB file). Only chains included in chain_selection are used.

ChainSelection map[string, ProteinLibraryScreenStopResponseInputTargetStructureTemplateTargetResponseChainSelectionUnion]

Chains selected from the uploaded structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep, which are epitope residues, which are non-binding residues, and which are flexible.

One of the following:

type ProteinLibraryScreenStopResponseInputTargetStructureTemplateTargetResponseChainSelectionStructureTemplateTargetPolymerChainSpec struct{…}

Per-chain specification for a polymer (protein/RNA/DNA) chain in a structure template target.

ChainType Polymer

CropResidues ProteinLibraryScreenStopResponseInputTargetStructureTemplateTargetResponseChainSelectionStructureTemplateTargetPolymerChainSpecCropResiduesUnion

0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are excluded from the pipeline run.

One of the following:

type ProteinLibraryScreenStopResponseInputTargetStructureTemplateTargetResponseChainSelectionStructureTemplateTargetPolymerChainSpecCropResiduesArray []int64

0-indexed residue indices to keep

type All string

EpitopeResidues []int64Optional

0-indexed residue indices where binder contact is desired (the epitope). All indices must be present in crop_residues and must not overlap non_binding_residues.

FlexibleResidues []int64Optional

0-indexed residue indices allowed to move during design (e.g. flexible loop regions). All indices must be present in crop_residues.

NonBindingResidues []int64Optional

0-indexed residue indices where binder contact should be discouraged. All indices must be present in crop_residues and must not overlap epitope_residues.

type ProteinLibraryScreenStopResponseInputTargetStructureTemplateTargetResponseChainSelectionStructureTemplateTargetLigandChainSpec struct{…}

Per-chain specification for a ligand chain in a structure template target. The full ligand is always included.

ChainType Ligand

Structure ProteinLibraryScreenStopResponseInputTargetStructureTemplateTargetResponseStructure

URL string

URL to download the file

formaturi

URLExpiresAt Time

When the presigned URL expires

formatdate-time

Type StructureTemplate

type ProteinLibraryScreenStopResponseInputTargetNoTemplateTargetResponse struct{…}

Target defined by sequences only, without a 3D structure template

Entities []ProteinLibraryScreenStopResponseInputTargetNoTemplateTargetResponseEntityUnion

Entities (proteins, RNA, DNA, ligands) defining the target complex.

One of the following:

type ProteinLibraryScreenStopResponseInputTargetNoTemplateTargetResponseEntityProteinEntityResponse struct{…}

ChainIDs []string

Chain IDs for this entity

Type Protein

Value string

Amino acid sequence (one-letter codes)

Cyclic boolOptional

Whether the sequence is cyclic

Modifications []ProteinLibraryScreenStopResponseInputTargetNoTemplateTargetResponseEntityProteinEntityResponseModificationOptional

CCD post-translational modifications. Optional; defaults to an empty list when omitted. SMILES modifications are not supported.

ResidueIndex int64

0-based index of the residue to modify

minimum0

Type Ccd

Modification format. Only CCD polymer modifications are supported.

Value string

CCD code from RCSB PDB (e.g. ‘MSE’ for selenomethionine, ‘SEP’ for phosphoserine)

type ProteinLibraryScreenStopResponseInputTargetNoTemplateTargetResponseEntityRnaEntityResponse struct{…}

ChainIDs []string

Chain IDs for this entity

Type Rna

Value string

RNA nucleotide sequence (A, C, G, U, N)

Cyclic boolOptional

Whether the sequence is cyclic

Modifications []ProteinLibraryScreenStopResponseInputTargetNoTemplateTargetResponseEntityRnaEntityResponseModificationOptional

CCD chemical modifications. Optional; defaults to an empty list when omitted. SMILES modifications are not supported.

ResidueIndex int64

0-based index of the residue to modify

minimum0

Type Ccd

Modification format. Only CCD polymer modifications are supported.

Value string

CCD code from RCSB PDB (e.g. ‘MSE’ for selenomethionine, ‘SEP’ for phosphoserine)

type ProteinLibraryScreenStopResponseInputTargetNoTemplateTargetResponseEntityDnaEntityResponse struct{…}

ChainIDs []string

Chain IDs for this entity

Type Dna

Value string

DNA nucleotide sequence (A, C, G, T, N)

Cyclic boolOptional

Whether the sequence is cyclic

Modifications []ProteinLibraryScreenStopResponseInputTargetNoTemplateTargetResponseEntityDnaEntityResponseModificationOptional

CCD chemical modifications. Optional; defaults to an empty list when omitted. SMILES modifications are not supported.

ResidueIndex int64

0-based index of the residue to modify

minimum0

Type Ccd

Modification format. Only CCD polymer modifications are supported.

Value string

CCD code from RCSB PDB (e.g. ‘MSE’ for selenomethionine, ‘SEP’ for phosphoserine)

type ProteinLibraryScreenStopResponseInputTargetNoTemplateTargetResponseEntityLigandCcdEntityResponse struct{…}

ChainIDs []string

Chain IDs for this ligand

Type LigandCcd

Value string

CCD code (e.g., ATP, ADP)

type ProteinLibraryScreenStopResponseInputTargetNoTemplateTargetResponseEntityLigandSmilesEntityResponse struct{…}

ChainIDs []string

Chain IDs for this ligand

Type LigandSmiles

Value string

SMILES string representing the ligand

Type NoTemplate

Bonds []ProteinLibraryScreenStopResponseInputTargetNoTemplateTargetResponseBondOptional

Covalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.

Atom1 ProteinLibraryScreenStopResponseInputTargetNoTemplateTargetResponseBondAtom1Union

Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.

One of the following:

type ProteinLibraryScreenStopResponseInputTargetNoTemplateTargetResponseBondAtom1LigandAtomResponse struct{…}

Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.

AtomName string

Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead.

ChainID string

Chain ID containing the atom

Type LigandAtom

type ProteinLibraryScreenStopResponseInputTargetNoTemplateTargetResponseBondAtom1PolymerAtomResponse struct{…}

AtomName string

Standardized atom name (verifiable in CIF file on RCSB)

ChainID string

Chain ID containing the atom

ResidueIndex int64

0-based residue index

minimum0

Type PolymerAtom

Atom2 ProteinLibraryScreenStopResponseInputTargetNoTemplateTargetResponseBondAtom2Union

Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.

One of the following:

type ProteinLibraryScreenStopResponseInputTargetNoTemplateTargetResponseBondAtom2LigandAtomResponse struct{…}

Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.

AtomName string

Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead.

ChainID string

Chain ID containing the atom

Type LigandAtom

type ProteinLibraryScreenStopResponseInputTargetNoTemplateTargetResponseBondAtom2PolymerAtomResponse struct{…}

AtomName string

Standardized atom name (verifiable in CIF file on RCSB)

ChainID string

Chain ID containing the atom

ResidueIndex int64

0-based residue index

minimum0

Type PolymerAtom

Constraints []ProteinLibraryScreenStopResponseInputTargetNoTemplateTargetResponseConstraintUnionOptional

Structural constraints (pocket and contact). Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.

One of the following:

type ProteinLibraryScreenStopResponseInputTargetNoTemplateTargetResponseConstraintPocketConstraintResponse struct{…}

Constrains the binder to interact with specific pocket residues on the target.

BinderChainID string

Chain ID of the binder molecule

ContactResidues map[string, []int64]

Binding pocket residues keyed by chain ID. Each key is a chain ID (e.g. “A”) and the value is an array of 0-indexed residue indices that define the pocket on that chain.

MaxDistanceAngstrom float64

Maximum allowed distance in Angstroms between binder and pocket residues. Typical range: 4-8 A.

Type Pocket

Force boolOptional

Whether to force the constraint

type ProteinLibraryScreenStopResponseInputTargetNoTemplateTargetResponseConstraintContactConstraintResponse struct{…}

Contact constraint between two tokens. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.

MaxDistanceAngstrom float64

Maximum distance in Angstroms

Token1 ProteinLibraryScreenStopResponseInputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1Union

Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.

One of the following:

type ProteinLibraryScreenStopResponseInputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1PolymerContactTokenResponse struct{…}

ChainID string

Chain ID

ResidueIndex int64

0-based residue index

minimum0

Type PolymerContact

type ProteinLibraryScreenStopResponseInputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1LigandContactTokenResponse struct{…}

Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.

AtomName string

Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead.

ChainID string

Chain ID

Type LigandContact

Token2 ProteinLibraryScreenStopResponseInputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2Union

Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.

One of the following:

type ProteinLibraryScreenStopResponseInputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2PolymerContactTokenResponse struct{…}

ChainID string

Chain ID

ResidueIndex int64

0-based residue index

minimum0

Type PolymerContact

type ProteinLibraryScreenStopResponseInputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2LigandContactTokenResponse struct{…}

Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.

AtomName string

Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead.

ChainID string

Chain ID

Type LigandContact

Type Contact

Force boolOptional

Whether to force the constraint

EpitopeLigandChains []stringOptional

Chain IDs of ligand entities that are part of the binding epitope. Ligands are marked as epitope in full (no residue-level selection).

EpitopeResidues map[string, []int64]Optional

Polymer chain residues where binder contact is desired (the epitope). Each key is a chain ID of a polymer entity, each value is an array of 0-indexed residue indices. Residues must not overlap non_binding_residues on the same chain.

NonBindingResidues map[string, []int64]Optional

Polymer chain residues where binder contact should be discouraged. Each key is a chain ID of a polymer entity, each value is an array of 0-indexed residue indices. Residues must not overlap epitope_residues on the same chain.

Livemode bool

Whether this resource was created with a live API key.

Pipeline Boltzprot

Pipeline used for protein library screen

PipelineVersion String1_0

Pipeline version used for protein library screen

Progress ProteinLibraryScreenStopResponseProgress

NumProteinsFailed int64

Number of accepted proteins that reached terminal failure during screening.

minimum0

NumProteinsScreened int64

Number of accepted proteins that produced usable screening results.

minimum0

TotalProteinsToScreen int64

Total number of proteins accepted into the screening run.

minimum1

LatestResultID stringOptional

ID of the latest result

StartedAt Time

formatdate-time

Status ProteinLibraryScreenStopResponseStatus

One of the following:

const ProteinLibraryScreenStopResponseStatusPending ProteinLibraryScreenStopResponseStatus = "pending"

const ProteinLibraryScreenStopResponseStatusRunning ProteinLibraryScreenStopResponseStatus = "running"

const ProteinLibraryScreenStopResponseStatusSucceeded ProteinLibraryScreenStopResponseStatus = "succeeded"

const ProteinLibraryScreenStopResponseStatusFailed ProteinLibraryScreenStopResponseStatus = "failed"

const ProteinLibraryScreenStopResponseStatusStopped ProteinLibraryScreenStopResponseStatus = "stopped"

StoppedAt Time

formatdate-time

WorkspaceID string

Workspace ID

IdempotencyKey stringOptional

Client-provided idempotency key

Stop a running protein library screen

Go

HTTP

TypeScript

Python

Go

CLI Tool

package main

import (
  "context"
  "fmt"

  "github.com/boltz-bio/boltz-api-go"
  "github.com/boltz-bio/boltz-api-go/option"
)

func main() {
  client := boltzapi.NewClient(
    option.WithAPIKey("My API Key"),
  )
  response, err := client.Protein.LibraryScreen.Stop(context.TODO(), "id")
  if err != nil {
    panic(err.Error())
  }
  fmt.Printf("%+v\n", response.ID)
}

200 example

{
  "id": "id",
  "completed_at": "2019-12-27T18:11:19.117Z",
  "created_at": "2019-12-27T18:11:19.117Z",
  "data_deleted_at": "2019-12-27T18:11:19.117Z",
  "engine": "boltzprot",
  "engine_version": "1.0",
  "error": {
    "code": "code",
    "message": "message",
    "details": {}
  },
  "input": {
    "proteins": {
      "url": "https://example.com",
      "url_expires_at": "2019-12-27T18:11:19.117Z"
    },
    "target": {
      "chain_selection": {
        "A": {
          "chain_type": "polymer",
          "crop_residues": [
            0,
            1,
            2,
            3,
            4,
            5,
            6,
            7,
            8,
            9,
            10,
            11,
            12
          ],
          "epitope_residues": [
            10,
            11,
            12
          ],
          "flexible_residues": [
            5,
            6,
            7
          ],
          "non_binding_residues": [
            0,
            1,
            2
          ]
        }
      },
      "structure": {
        "url": "https://example.com",
        "url_expires_at": "2019-12-27T18:11:19.117Z"
      },
      "type": "structure_template"
    }
  },
  "livemode": true,
  "pipeline": "boltzprot",
  "pipeline_version": "1.0",
  "progress": {
    "num_proteins_failed": 0,
    "num_proteins_screened": 0,
    "total_proteins_to_screen": 1,
    "latest_result_id": "latest_result_id"
  },
  "started_at": "2019-12-27T18:11:19.117Z",
  "status": "pending",
  "stopped_at": "2019-12-27T18:11:19.117Z",
  "workspace_id": "workspace_id",
  "idempotency_key": "idempotency_key"
}

Returns Examples

200 example

{
  "id": "id",
  "completed_at": "2019-12-27T18:11:19.117Z",
  "created_at": "2019-12-27T18:11:19.117Z",
  "data_deleted_at": "2019-12-27T18:11:19.117Z",
  "engine": "boltzprot",
  "engine_version": "1.0",
  "error": {
    "code": "code",
    "message": "message",
    "details": {}
  },
  "input": {
    "proteins": {
      "url": "https://example.com",
      "url_expires_at": "2019-12-27T18:11:19.117Z"
    },
    "target": {
      "chain_selection": {
        "A": {
          "chain_type": "polymer",
          "crop_residues": [
            0,
            1,
            2,
            3,
            4,
            5,
            6,
            7,
            8,
            9,
            10,
            11,
            12
          ],
          "epitope_residues": [
            10,
            11,
            12
          ],
          "flexible_residues": [
            5,
            6,
            7
          ],
          "non_binding_residues": [
            0,
            1,
            2
          ]
        }
      },
      "structure": {
        "url": "https://example.com",
        "url_expires_at": "2019-12-27T18:11:19.117Z"
      },
      "type": "structure_template"
    }
  },
  "livemode": true,
  "pipeline": "boltzprot",
  "pipeline_version": "1.0",
  "progress": {
    "num_proteins_failed": 0,
    "num_proteins_screened": 0,
    "total_proteins_to_screen": 1,
    "latest_result_id": "latest_result_id"
  },
  "started_at": "2019-12-27T18:11:19.117Z",
  "status": "pending",
  "stopped_at": "2019-12-27T18:11:19.117Z",
  "workspace_id": "workspace_id",
  "idempotency_key": "idempotency_key"
}