Interface MacromoleculeSettings

The URL of the JMS monomer service macromolecule convert endpoint (POST).

Converts a HELM string to another structure format using the configured monomer libraries. All input is sent in the JSON request body.

Request body (required):

• heavyAtomCountLimit (integer, 1–500): heavy-atom count eavy atom count limit of the imported structure.
• inputFormat (string): the input format of the macromolecule; supported values: helm, biln, cxonb.
• libraries (array of integers, ≥ 1 item): the list of selected library IDs.
• macromolecule (string, ≥ 1 character): macromolecule in a string format.
• outputFormat (string): converted structure format; supported values: small molecule formats, helm, cxonb.

Example request body:

{
  "heavyAtomCountLimit": 500,
  "inputFormat": "helm",
  "libraries": [0, 1],
  "macromolecule": "PEPTIDE1{A}$$$$V2.0",
  "outputFormat": "cxon"
}
Copy

The URL of the JMS monomer service.

It must point to the monomers endpoint of a specific monomer library and include all of the query parameters required to return the monomers in a format Marvin can consume. The path segment after monomer-libraries is the library id.

Required query parameters:

• type=AMINO_ACID - only amino acid monomers are supported
• monomerStatus=ACTIVE - only active monomers are returned
• outputFormat=cxon - structures are returned in CXON format
• outputRepresentation=SUPERATOM_SGROUP - structures are returned as superatom s-groups

Example: /monomers/rest-v1/monomer-libraries/{libraryId}/monomers?type=AMINO_ACID&monomerStatus=ACTIVE&outputFormat=cxon&outputRepresentation=SUPERATOM_SGROUP