Extract tools

AtomLens validates the source first, confirms counts, and then writes files or tables with progress feedback.

Split multi-structure SDF into multiple files

1. Choose File > Extract > Split multi-structure SDF into multiple files... .
2. Select an SDF file with two or more structures.
3. Confirm the count and choose a destination folder.
4. AtomLens writes one .sdf file per structure.

Extract multi-structure SDF attributes into CSV

1. Choose File > Extract > Extract multi-structure SDF attributes into CSV table... .
2. Select a multi-structure SDF file.
3. Confirm the number of parsable structures and choose the destination .csv file.
4. AtomLens writes one quoted CSV table with all discovered SDF fields.

When a structure has multiple values for one field, AtomLens joins them with | . Invalid records are skipped and reported at the end.

Split multi-reaction SMILES into multiple files

1. Choose File > Extract > Split multi-reaction SMILES into multiple files... .
2. Select a multi-line Reaction SMILES source file.
3. Confirm the number of valid reactions and choose a destination folder.
4. AtomLens writes one .rsmi file per valid reaction.

Split multi-reaction SMILES into RXN files

1. Choose File > Extract > Split multi-reaction SMILES into multiple RXN files... .
2. Select a multi-line Reaction SMILES source file.
3. Confirm the count, choose a destination folder, and start extraction.
4. AtomLens converts each valid reaction entry into an individual .rxn file.

On macOS, Extract writes to the destination you choose. It does not currently write directly into Managed Repository.

Reaction support

AtomLens opens reaction files directly, including .rsmi , .rinchi , .rxn , .rdf , and reaction-bearing .cml .

• Reaction drawings include reactants, agents, products, plus signs, and arrow layout.
• The same pan, zoom, rotate, reset, and snapshot tools work in reaction mode.
• Reaction documents use a split layout with the drawing above and the participant list below.
• If atom-map numbers are available, map-oriented visual controls are enabled automatically.
• Reaction content is also supported in Quick Look and Spotlight metadata.

Advanced notation

AtomLens 2.0 continues to support modern CXSMILES features and related advanced annotations.

• Markush and R-group definitions render as a main scaffold plus a clearly separated legend box.
• Repeat-unit and link-node notation is depicted when present.
• Imported highlights, supported query atoms, query bonds, and related annotations are preserved where possible.
• Not every advanced source feature maps to every export format. For example, Export writes standard SMILES, not CXSMILES text.

Supported input formats

.mol and .sdf input may use V2000 or V3000 syntax, and standard SMILES text files may still contain CXSMILES extensions. The document input sidebar can also convert supported IUPAC names to CML before rendering.

Format	Extensions	UTI
MDL Molfile	.mol	de.losko.atomlens.molfile
MDL SDFile	.sdf , .sd	de.losko.atomlens.sdfile
MDL RGfile	.rgf	de.losko.atomlens.rgfile
SMILES	.smi , .smiles , .ism , .can	de.losko.atomlens.smiles
CXSMILES	.cxsmiles	de.losko.atomlens.cxsmiles
Reaction SMILES	.rsmi	de.losko.atomlens.rsmi
RInChI	.rinchi	de.losko.atomlens.rinchi
InChI	.inchi , .ich	de.losko.atomlens.inchi
Tripos MOL2	.mol2	de.losko.atomlens.mol2
Protein Data Bank	.pdb , .ent	de.losko.atomlens.pdb
XYZ Coordinates	.xyz	de.losko.atomlens.xyz
Chemical Markup Language	.cml	de.losko.atomlens.cml
MDL RXN	.rxn	de.losko.atomlens.rxn
MDL RDF	.rdf	de.losko.atomlens.rdf
Plain text auto-detect	.txt	public.plain-text

Supported export formats

Use File > Export... to export the current molecule or reaction context as chemistry files. Use File > Share for SVG, PNG, or PDF depictions of the current molecule or whole reaction.

Export format	Extensions	Notes
SVG depiction	.svg	Uses the current depiction style.
MDL Molfile (V2000)	.mol	Single structure.
MDL Molfile (V3000)	.mol	Single structure in the newer syntax.
MDL SDFile	.sdf , .sd	Single or multiple structures.
MDL RGfile	.rgf	Condition-dependent export when the current structure can be written with R-group data.
SMILES	.smi , .smiles , .can	Standard flavor.
SMILES (Isomeric)	.ism	Stereochemistry-aware output.
InChI	.inchi , .ich	Generated locally.
Tripos MOL2	.mol2	Text export.
Protein Data Bank	.pdb , .ent	Text export.
XYZ Coordinates	.xyz	Text export.
Chemical Markup Language	.cml	XML export for molecules and reactions.
MDL RXN	.rxn	Whole-reaction export when viewing a reaction document.
MDL RDF	.rdf	Whole-reaction export when viewing a reaction document.
Reaction SMILES	.rsmi	Whole-reaction text export.
RInChI	.rinchi	Whole-reaction identifier export.

Roundtrip support

AtomLens aims to preserve the important chemical meaning of supported source formats when you inspect and export them again.

• MDL V2000/V3000 and SDF retain more coordinates, stereochemistry, Sgroups, highlights, query features, and related annotations than earlier AtomLens versions.
• RGfile support carries R-group oriented structures when the source and export target can represent that information.
• CML support is stronger for both modern molecules and reaction-bearing content.
• CXSMILES parsing and depiction is stronger for Markush, repeat/link-node, highlight, and related layers.