--- title: "How to Export Monomers" slug: "how-to-export-monomers" status: "new" updated: 2026-11-03T16:07:41Z published: 2026-11-03T16:07:41Z canonical: "docs.discngine.com/how-to-export-monomers" --- > ## Documentation Index > Fetch the complete documentation index at: https://docs.discngine.com/llms.txt > Use this file to discover all available pages before exploring further. # How to Export Monomers This guide shows how to download monomers from the catalogue as an SD file, a CSV or Excel file, a SMILES file or JSON, choosing whether each record carries the stored structure with its attachment points or the complete molecule with its cap groups applied. The worked example is `D-Phe_4F`, 4-fluoro-D-phenylalanine from the public library, exported with its cap groups applied so that another tool receives the free amino acid rather than a residue with placeholders. **Prerequisites**: access to Biotoolkit Monomers. Any role can export; the file holds only the monomers you can see. ## Step 1: Choose the monomers On the **Monomers** page, tick the box at the start of each row to export. The ticks survive paging, filtering and searching, and the **Export** button of the title bar counts them. The box in the column heading ticks every monomer of the report as it is filtered, on every page, not only the rows shown (up to 5000); a second click unticks them all. It shows a dash while only some are ticked. ![The Monomers page with the Public scope, searched for Phe_4: D-Phe_4F, D-Phe_4ureido and Phe_4Br ticked, the heading box showing a dash, and the Export (3) button in the title bar](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Documentation/biotoolkit-monomer-service-export-ticked(1).png?sv=2026-02-06&spr=https&st=2026-11-11T08%3A17%3A22Z&se=2026-11-11T09%3A17%3A22Z&sr=c&sp=r&sig=kfGKTSSs%2F2T4mSNvwJGb%2Bn7iEnuZQHpcRoVAll0alzY%3D) To export a whole list instead, filter the report as usual (the chips above it, the search, the column filters) and leave the boxes empty: the dialog offers the report as it is. ## Step 2: Open the export dialog Click **Export**. The **Export monomers** dialog asks four things: | Choice | Options | Notes | | --- | --- | --- | | **What to export** | **Ticked monomers** or **Whole report** | The counts are the ticked rows and the rows the report shows with its current filters. With no tick, only the whole report is offered. | | **Format** | **SD file**, **CSV**, **Excel**, **SMILES**, **JSON** | SD file is the one most tools read whole; the others are described below. | | **CSV delimiter** | **Comma** or **Semicolon** | CSV only. The import page reads a comma; a French Excel opens a semicolon file directly. | | **Main structure** | **R-group placeholders** or **Cap groups applied** | See step 3. | ![The Export monomers dialog: Ticked monomers 3 chosen against Whole report 11, the SD file format, and Cap groups applied as the main structure](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Documentation/biotoolkit-monomer-service-export-dialog(1).png?sv=2026-02-06&spr=https&st=2026-11-11T08%3A17%3A22Z&se=2026-11-11T09%3A17%3A22Z&sr=c&sp=r&sig=kfGKTSSs%2F2T4mSNvwJGb%2Bn7iEnuZQHpcRoVAll0alzY%3D) ## Step 3: Pick the main structure An SD record, a CSV cell or a SMILES line holds one structure. You choose which form it is: - **R-group placeholders**: the structure as stored, each attachment point written as `[*:1]`, `[*:2]`… (or an `R#` atom in the molfile). This is what the import reads back, so a file exported this way re-imports as it is. - **Cap groups applied**: each attachment point replaced by the structure of its cap group, for example H on R1 and OH on R2 of `D-Phe_4F`, which gives the free amino acid. The molecule is complete and parses in RDKit or ChemDraw with no R-group atom left. The other form is never lost: it travels in the same record as a CXSMILES property, `CAPPED_CXSMILES` or `RGROUP_CXSMILES`. Enhanced stereochemistry survives in both: a racemic or unknown centre keeps its group in the CXSMILES, and the molfile is written in the V3000 format when a stereo group needs it. ## Step 4: Export Click **Export**. The browser downloads one file, named `monomers-<form>-<date>.<extension>`, and the dialog says how many monomers it holds. ![The dialog after the export: "3 monomers exported to monomers-capped-20261029-141109.sdf"](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Documentation/biotoolkit-monomer-service-export-result(1).png?sv=2026-02-06&spr=https&st=2026-11-11T08%3A17%3A22Z&se=2026-11-11T09%3A17%3A22Z&sr=c&sp=r&sig=kfGKTSSs%2F2T4mSNvwJGb%2Bn7iEnuZQHpcRoVAll0alzY%3D) When something could not be exported the dialog lists it, one line per monomer: - a monomer whose structure **cannot be capped** (an attachment point without a cap group, or the reverse) is in the file in its stored form, placeholders kept, with the reason in its `EXPORT_WARNING` field; - a monomer whose **cap group has no structure** (a descriptive cap such as `X`) is not in the file; register a structure for the cap group, or export it with the R-group form only after that; - a monomer **deleted in the meantime** is not in the file. ## What each format contains | Format | Content | Reads back with | | --- | --- | --- | | SD file | One record per monomer: the molfile, then the data fields the import reads (`SYMBOL`, `NAME`, `POLYMERTYPE`, `MONOMERTYPE`, `NATURALANALOG`, `AUTHOR`, `ALIASES`, `R1`…`Rn` with the cap group names), the other form's CXSMILES, `MONOMER_ID`, `VERSION_NO`, `EXPORT_WARNING`. | The import page, with **R-group placeholders**. | | CSV, Excel | The columns of the import file, in its order (`SYMBOL`, `NAME`, `SMILES`, `POLYMER_TYPE`, `MONOMER_TYPE`, `NATURAL_ANALOG`, `AUTHOR`, `RGROUPS`, `ALIASES`), then `ISOMER_LABEL`, `RESOLVED_FROM`, the other form's CXSMILES, `MONOMER_ID`, `VERSION_NO`, `EXPORT_WARNING`. | The import page, with **R-group placeholders**. | | SMILES | One line per monomer: the SMILES of the main form, a tab, the symbol (the `.smi` convention). | RDKit, Open Babel, ChemDraw. | | JSON | The monomer objects of the REST API, `smiles` and `molfile` in the main form, the other form as `cappedCxsmiles` or `rgroupCxsmiles`. | `POST /monomer/import` of the service. | The same export is available to scripts through the service's `POST /monomer/export`, described in [REST API](/public/docs/monomer-service-rest-api).