molecules-public

List Molecules

List molecules in your organization. Set scope=org to search your organization.

Each molecule includes its chains, scores, metadata, and files inline. Search by name or sequence, or filter by group, owner, jobId, jobName, property, or score.

Results are returned in pages. Use nextCursor to retrieve more results.

get/api/molecules

Request

  • Base URL: https://app.tamarind.bio
  • URL: https://app.tamarind.bio/api/molecules
  • Auth: API key in header x-api-key

Query parameters

groupstring nullable

Limit results to one group by ID (retrieve ID using /api/molecules/groups).

jobIdstring nullable

Limit results to one job's input and output molecules by ID. For batches, use the batch's ID to retrieve molecules for all jobs within the batch.

jobNamestring nullable

List input and output molecules by job or batch name.

ownerstring nullable

Only groups whose owner equals this value, as the owners list returns it.

nodeRunIdstring nullable

Limit results to one pipeline step's output molecules by node run ID (retrieve ID using /pipelines/runs/{run_id}).

typeMoleculeType[] nullable

Filter by molecule type, such as protein, small_molecule, or nucleic_acid.

searchstring nullable

Enter a search term to find molecule names, user-uploaded property names, or tool score names. To search chains instead, set mode=sequence and enter a sequence or exact SMILES. Use at least 3 characters for sequence searches or when searching without a group.

modestring

Choose what search matches: sequence searches amino acid chains by exact or subsequence match, while sequenceMatch=exact_smiles matches a small molecule's stored SMILES exactly. default/name match molecule, property, and score names.

sequenceMatchstring

Only available with mode=sequence: subsequence matches part of an amino-acid chain; exact matches a whole amino-acid chain; exact_smiles matches a whole small-molecule chain exactly, including case.

moleculesPerGroupinteger nullable

Maximum molecules per group across the whole result set. Requires sortBy=groupName; unavailable with mode=sequence.

examplesPerGroupinteger nullable

Deprecated: the old name for moleculesPerGroup.

sequencestring nullable

Match molecules containing this amino-acid subsequence in any chain (case-insensitive, at least 3 characters).

filterstring[] nullable

String in format field:operator:value. "field" can be user-uploaded properties or tool scores (in format tool-id.score). Supported operators: gt, gte, lt, lte, eq, neq, iequals, includes, in (any of a |-separated set of at most 64 members, e.g. stage:in:lead|backup), exists (written field:exists, no value). Append :jobId to a tool score (not with in or exists) to filter only from tool scores from a particular job. Repeat filter to combine conditions; a molecule must match all of them. See /tools endpoint for list of output scores for each tool.

tagsstring[] nullable

Limit results to molecules carrying this tag. Repeat it to require several tags.

scopestring

mine (the default) shows molecules in groups you created; org shows everything across your organization.

sortBystring

Sort by id, added, type, groupName, a property, or a score such as alphafold.ptm. Scores use the tool's "best run." groupName keeps each group together; use moleculesPerGroup to limit its results.

dirstring

asc: ascending order. desc: descending order.

limitinteger

Maximum number of items to return in one page.

cursorstring nullable

Omit for your first request. To get the next page, copy the nextCursor value from the response into this parameter and send another request with the same filters. Repeat until nextCursor is null, even if a page is empty.

Response

Successful Response

nextCursorstring nullable required
modestring nullable required
scanProgressnumber nullable required
sliceMatchedinteger nullable
sliceDeliveredinteger nullable
waitingboolean nullable
retryAfterMsinteger nullable

Changes

No recorded changes to this operation across all 1 revision of this API.