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.

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:

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.

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

The same export is available to scripts through the service's POST /monomer/export, described in REST API.