API Reference

Small Molecule

Design

Copy Markdown

Open in Claude

Open in ChatGPT

Open in Cursor

---

Copy Markdown

View as Markdown

Estimate cost for a small molecule design run

client.SmallMolecule.Design.EstimateCost(ctx, body) (*SmallMoleculeDesignEstimateCostResponse, error)

POST/compute/v1/small-molecule/design/estimate-cost

Estimate the billed cost of a small molecule design run without creating any resource or consuming GPU. Includes generation charges implied by the scheduler iteration cap plus structure-scoring charges for each requested molecule.

ParametersExpand Collapse

body SmallMoleculeDesignEstimateCostParams

NumMolecules param.Field[int64]

Number of molecules to generate. Must be between 10 and 1,000,000.

minimum10

maximum1000000

Target param.Field[SmallMoleculeDesignEstimateCostParamsTarget]

Target protein sequences for small molecule design or screening.

Entities []SmallMoleculeDesignEstimateCostParamsTargetEntity

Protein entities defining the target structure. Each entity represents a protein chain.

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 []SmallMoleculeDesignEstimateCostParamsTargetEntityModificationOptional

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)

Bonds []SmallMoleculeDesignEstimateCostParamsTargetBondOptional

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

Atom1 SmallMoleculeDesignEstimateCostParamsTargetBondAtom1Union

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

One of the following:

type SmallMoleculeDesignEstimateCostParamsTargetBondAtom1LigandAtom 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 SmallMoleculeDesignEstimateCostParamsTargetBondAtom1PolymerAtom 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 SmallMoleculeDesignEstimateCostParamsTargetBondAtom2Union

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

One of the following:

type SmallMoleculeDesignEstimateCostParamsTargetBondAtom2LigandAtom 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 SmallMoleculeDesignEstimateCostParamsTargetBondAtom2PolymerAtom 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 []SmallMoleculeDesignEstimateCostParamsTargetConstraintUnionOptional

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

One of the following:

type SmallMoleculeDesignEstimateCostParamsTargetConstraintPocketConstraint 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 SmallMoleculeDesignEstimateCostParamsTargetConstraintContactConstraint 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 SmallMoleculeDesignEstimateCostParamsTargetConstraintContactConstraintToken1Union

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

One of the following:

type SmallMoleculeDesignEstimateCostParamsTargetConstraintContactConstraintToken1PolymerContactToken struct{…}

ChainID string

Chain ID

ResidueIndex int64

0-based residue index

minimum0

Type PolymerContact

type SmallMoleculeDesignEstimateCostParamsTargetConstraintContactConstraintToken1LigandContactToken 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 SmallMoleculeDesignEstimateCostParamsTargetConstraintContactConstraintToken2Union

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

One of the following:

type SmallMoleculeDesignEstimateCostParamsTargetConstraintContactConstraintToken2PolymerContactToken struct{…}

ChainID string

Chain ID

ResidueIndex int64

0-based residue index

minimum0

Type PolymerContact

type SmallMoleculeDesignEstimateCostParamsTargetConstraintContactConstraintToken2LigandContactToken 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

PocketResidues map[string, []int64]Optional

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 binding pocket on that chain. When provided, these residues guide pocket extraction and add a derived pocket constraint during affinity predictions. That derived constraint remains separate from any explicit pocket constraints in target.constraints. When omitted, the model auto-detects the pocket.

ReferenceLigands []stringOptional

Reference ligands as SMILES strings that help the model identify the binding pocket. When omitted, a set of drug-like default ligands is used for pocket detection.

Type stringOptional

Target is defined directly by protein sequences rather than a structure template.

ChemicalSpace param.Field[SmallMoleculeDesignEstimateCostParamsChemicalSpace]Optional

Chemical space to constrain generated molecules. Currently only ‘enamine_real’ (Enamine REAL chemical space) is supported. Additional options may be added in the future.

const SmallMoleculeDesignEstimateCostParamsChemicalSpaceEnamineReal SmallMoleculeDesignEstimateCostParamsChemicalSpace = "enamine_real"

IdempotencyKey param.Field[string]Optional

Client-provided key to prevent duplicate submissions on retries

maxLength255

MoleculeFilters param.Field[SmallMoleculeDesignEstimateCostParamsMoleculeFilters]Optional

Molecule filtering configuration. Controls both Boltz built-in SMARTS filtering and custom filters.

BoltzSmartsCatalogFilterLevel SmallMoleculeDesignEstimateCostParamsMoleculeFiltersBoltzSmartsCatalogFilterLevelOptional

Controls the stringency of Boltz’s built-in SMARTS structural alert filtering, which removes molecules matching known problematic substructures. ‘recommended’ (default): applies a curated set of alerts balancing safety and hit rate. ‘extra’: adds additional alerts beyond the recommended set for stricter filtering. ‘aggressive’: applies the most comprehensive alert set — may reject viable molecules. ‘disabled’: turns off Boltz SMARTS filtering entirely; only custom_filters will be applied.

One of the following:

const SmallMoleculeDesignEstimateCostParamsMoleculeFiltersBoltzSmartsCatalogFilterLevelRecommended SmallMoleculeDesignEstimateCostParamsMoleculeFiltersBoltzSmartsCatalogFilterLevel = "recommended"

const SmallMoleculeDesignEstimateCostParamsMoleculeFiltersBoltzSmartsCatalogFilterLevelExtra SmallMoleculeDesignEstimateCostParamsMoleculeFiltersBoltzSmartsCatalogFilterLevel = "extra"

const SmallMoleculeDesignEstimateCostParamsMoleculeFiltersBoltzSmartsCatalogFilterLevelAggressive SmallMoleculeDesignEstimateCostParamsMoleculeFiltersBoltzSmartsCatalogFilterLevel = "aggressive"

const SmallMoleculeDesignEstimateCostParamsMoleculeFiltersBoltzSmartsCatalogFilterLevelDisabled SmallMoleculeDesignEstimateCostParamsMoleculeFiltersBoltzSmartsCatalogFilterLevel = "disabled"

CustomFilters []SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterUnionOptional

Custom filters to apply. Molecules must pass all filters (AND logic).

One of the following:

type SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterLipinskiFilter struct{…}

Lipinski’s Rule of Five filter. Rejects molecules that violate drug-likeness criteria based on molecular weight, LogP, hydrogen bond donors, and hydrogen bond acceptors.

MaxHba float64

Maximum number of hydrogen bond acceptors. Lipinski threshold: 10

MaxHbd float64

Maximum number of hydrogen bond donors. Lipinski threshold: 5

MaxLogp float64

Maximum LogP. Lipinski threshold: 5

MaxMw float64

Maximum molecular weight (Da). Lipinski threshold: 500

Type LipinskiFilter

AllowSingleViolation boolOptional

If true, one rule violation is allowed (classic Rule of Five). Defaults to false (all rules must pass).

type SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterRdkitDescriptorFilter struct{…}

Filter molecules by RDKit molecular descriptors. Each descriptor is constrained to a min/max range. Only descriptors you provide are checked — omitted descriptors are unconstrained.

Type RdkitDescriptorFilter

FractionCsp3 SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterRdkitDescriptorFilterFractionCsp3Optional

Min/max range constraint for an RDKit molecular descriptor

Max float64Optional

Maximum allowed value (inclusive)

Min float64Optional

Minimum allowed value (inclusive)

MolLogp SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterRdkitDescriptorFilterMolLogpOptional

Min/max range constraint for an RDKit molecular descriptor

Max float64Optional

Maximum allowed value (inclusive)

Min float64Optional

Minimum allowed value (inclusive)

MolWt SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterRdkitDescriptorFilterMolWtOptional

Min/max range constraint for an RDKit molecular descriptor

Max float64Optional

Maximum allowed value (inclusive)

Min float64Optional

Minimum allowed value (inclusive)

NumAromaticRings SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterRdkitDescriptorFilterNumAromaticRingsOptional

Min/max range constraint for an RDKit molecular descriptor

Max float64Optional

Maximum allowed value (inclusive)

Min float64Optional

Minimum allowed value (inclusive)

NumHAcceptors SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterRdkitDescriptorFilterNumHAcceptorsOptional

Min/max range constraint for an RDKit molecular descriptor

Max float64Optional

Maximum allowed value (inclusive)

Min float64Optional

Minimum allowed value (inclusive)

NumHDonors SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterRdkitDescriptorFilterNumHDonorsOptional

Min/max range constraint for an RDKit molecular descriptor

Max float64Optional

Maximum allowed value (inclusive)

Min float64Optional

Minimum allowed value (inclusive)

NumHeteroatoms SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterRdkitDescriptorFilterNumHeteroatomsOptional

Min/max range constraint for an RDKit molecular descriptor

Max float64Optional

Maximum allowed value (inclusive)

Min float64Optional

Minimum allowed value (inclusive)

NumRings SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterRdkitDescriptorFilterNumRingsOptional

Min/max range constraint for an RDKit molecular descriptor

Max float64Optional

Maximum allowed value (inclusive)

Min float64Optional

Minimum allowed value (inclusive)

NumRotatableBonds SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterRdkitDescriptorFilterNumRotatableBondsOptional

Min/max range constraint for an RDKit molecular descriptor

Max float64Optional

Maximum allowed value (inclusive)

Min float64Optional

Minimum allowed value (inclusive)

Tpsa SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterRdkitDescriptorFilterTpsaOptional

Min/max range constraint for an RDKit molecular descriptor

Max float64Optional

Maximum allowed value (inclusive)

Min float64Optional

Minimum allowed value (inclusive)

type SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterSmartsCustomFilter struct{…}

Filter molecules by custom SMARTS patterns. Molecules matching any pattern are rejected.

Patterns []string

SMARTS patterns. Molecules matching any pattern are rejected.

Type SmartsCustomFilter

type SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterSmartsCatalogFilter struct{…}

Filter molecules using a predefined SMARTS catalog of structural alerts.

Catalog string

Predefined SMARTS catalog to apply. PAINS, BRENK, ChEMBL, and NIH catalogs reject known problematic substructures.

One of the following:

const SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterSmartsCatalogFilterCatalogPains SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterSmartsCatalogFilterCatalog = "PAINS"

const SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterSmartsCatalogFilterCatalogPainsA SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterSmartsCatalogFilterCatalog = "PAINS_A"

const SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterSmartsCatalogFilterCatalogPainsB SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterSmartsCatalogFilterCatalog = "PAINS_B"

const SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterSmartsCatalogFilterCatalogPainsC SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterSmartsCatalogFilterCatalog = "PAINS_C"

const SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterSmartsCatalogFilterCatalogBrenk SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterSmartsCatalogFilterCatalog = "BRENK"

const SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterSmartsCatalogFilterCatalogChembl SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterSmartsCatalogFilterCatalog = "CHEMBL"

const SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterSmartsCatalogFilterCatalogChemblBms SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterSmartsCatalogFilterCatalog = "CHEMBL_BMS"

const SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterSmartsCatalogFilterCatalogChemblDundee SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterSmartsCatalogFilterCatalog = "CHEMBL_Dundee"

const SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterSmartsCatalogFilterCatalogChemblGlaxo SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterSmartsCatalogFilterCatalog = "CHEMBL_Glaxo"

const SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterSmartsCatalogFilterCatalogChemblInpharmatica SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterSmartsCatalogFilterCatalog = "CHEMBL_Inpharmatica"

const SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterSmartsCatalogFilterCatalogChemblLint SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterSmartsCatalogFilterCatalog = "CHEMBL_LINT"

const SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterSmartsCatalogFilterCatalogChemblMlsmr SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterSmartsCatalogFilterCatalog = "CHEMBL_MLSMR"

const SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterSmartsCatalogFilterCatalogChemblSureChEmbl SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterSmartsCatalogFilterCatalog = "CHEMBL_SureChEMBL"

const SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterSmartsCatalogFilterCatalogNih SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterSmartsCatalogFilterCatalog = "NIH"

Type SmartsCatalogFilter

type SmallMoleculeDesignEstimateCostParamsMoleculeFiltersCustomFilterSmilesRegexFilter struct{…}

Filter molecules by regex patterns on their SMILES representation.

Patterns []string

Regex patterns applied to SMILES strings. Molecules matching any pattern are rejected.

Type SmilesRegexFilter

WorkspaceID param.Field[string]Optional

Target workspace ID (admin keys only; ignored for workspace keys)

ReturnsExpand Collapse

type SmallMoleculeDesignEstimateCostResponse struct{…}

Estimate response with monetary values encoded as decimal strings to preserve precision.

Breakdown SmallMoleculeDesignEstimateCostResponseBreakdown

Cost breakdown for the billed application.

Application SmallMoleculeDesignEstimateCostResponseBreakdownApplication

One of the following:

const SmallMoleculeDesignEstimateCostResponseBreakdownApplicationStructureAndBinding SmallMoleculeDesignEstimateCostResponseBreakdownApplication = "structure_and_binding"

const SmallMoleculeDesignEstimateCostResponseBreakdownApplicationSmallMoleculeDesign SmallMoleculeDesignEstimateCostResponseBreakdownApplication = "small_molecule_design"

const SmallMoleculeDesignEstimateCostResponseBreakdownApplicationSmallMoleculeLibraryScreen SmallMoleculeDesignEstimateCostResponseBreakdownApplication = "small_molecule_library_screen"

const SmallMoleculeDesignEstimateCostResponseBreakdownApplicationProteinDesign SmallMoleculeDesignEstimateCostResponseBreakdownApplication = "protein_design"

const SmallMoleculeDesignEstimateCostResponseBreakdownApplicationProteinRedesign SmallMoleculeDesignEstimateCostResponseBreakdownApplication = "protein_redesign"

const SmallMoleculeDesignEstimateCostResponseBreakdownApplicationProteinLibraryScreen SmallMoleculeDesignEstimateCostResponseBreakdownApplication = "protein_library_screen"

const SmallMoleculeDesignEstimateCostResponseBreakdownApplicationAdme SmallMoleculeDesignEstimateCostResponseBreakdownApplication = "adme"

CostPerUnitUsd string

Estimated cost per displayed unit as a decimal string, rounded up to 4 decimal places. This may include token-size multipliers or generation overhead; estimated_cost_usd is the authoritative total.

NumUnits int64

Number of billable units in the estimate. The unit depends on the endpoint: samples for structure-and-binding, molecules for ADME, and requested proteins or molecules for design/screen endpoints.

Disclaimer string

EstimatedCostUsd string

Estimated total cost as a decimal string

Estimate cost for a small molecule design run

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.SmallMolecule.Design.EstimateCost(context.TODO(), boltzapi.SmallMoleculeDesignEstimateCostParams{
    NumMolecules: 10,
    Target: boltzapi.SmallMoleculeDesignEstimateCostParamsTarget{
      Entities: []boltzapi.SmallMoleculeDesignEstimateCostParamsTargetEntity{boltzapi.SmallMoleculeDesignEstimateCostParamsTargetEntity{
        ChainIDs: []string{"string"},
        Value: "value",
      }},
    },
  })
  if err != nil {
    panic(err.Error())
  }
  fmt.Printf("%+v\n", response.Breakdown)
}

200 example

{
  "breakdown": {
    "application": "structure_and_binding",
    "cost_per_unit_usd": "0.0500",
    "num_units": 1
  },
  "disclaimer": "This is an estimate only and may differ from your actual charges. Final billing is based on exact token counts computed at run time. For large library screens, the estimate is extrapolated from a sample and may be less accurate for highly variable inputs.",
  "estimated_cost_usd": "0.0500"
}

Returns Examples

200 example

{
  "breakdown": {
    "application": "structure_and_binding",
    "cost_per_unit_usd": "0.0500",
    "num_units": 1
  },
  "disclaimer": "This is an estimate only and may differ from your actual charges. Final billing is based on exact token counts computed at run time. For large library screens, the estimate is extrapolated from a sample and may be less accurate for highly variable inputs.",
  "estimated_cost_usd": "0.0500"
}