ATOMLENS 3.1 / IPAD HELPApp Store ↗

Troubleshooting, Privacy, and Licenses

Resolve common issues, understand search and storage boundaries, and review AtomLens privacy and third-party notes.

If a file does not parse as expected

The most common problems are format mismatch, malformed pasted text, or chemistry details that the source format cannot represent cleanly.

Try reopening the original file through Import instead of copying text through another app.
If you pasted text, confirm that the structure block or SMILES string is complete before choosing Apply & Render.
For reaction sources, check whether the file is actually a molecule-only saved output.

Search and storage boundaries

On iPad, AtomLens works within the app sandbox and its Files provider. Managed Repository search and system search integration are therefore narrower than on macOS.

Enable repository sync on each device using the same Apple Account. Keep AtomLens open while a large initial library sync completes and check repository status; search indexes and previews may finish later than content delivery.

Turning iCloud sync off keeps repository-backed Save, Extract, Browse, Files, Quick Look, and search features available through local Managed Repository storage.

Cross-device visibility still depends on iCloud delivery and system wake-up timing, so remote changes are not guaranteed to appear instantly on every surface.

Managed Repository focuses on AtomLens-owned library content.
Core Spotlight entries are donated for saved Managed Repository files, not for every chemistry document on the device.

Export diagnostics for a problem report

Open Settings > About > Export Diagnostics. Choose a destination in Files, then share the saved JSON report when requesting help. Include the approximate incident time, app build, and the action you were performing.

Diagnostics include recent memory and activity measurements, app/device details, and available Apple MetricKit reports. Local history is limited to seven days and a fixed size; molecule contents and document paths are not included. Nothing is sent automatically. A forced termination may leave no final event.

Privacy and third-party software

AtomLens performs PDF text extraction, chemical-name recognition, parsing, depiction, inspection, and chemistry identifier generation on-device. Managed Repository content can sync through your private iCloud container when you enable iCloud sync; otherwise it remains in local app storage.

AtomLens dynamically links LGPL-2.1-or-later CDKSwiftNativePort 1.4.26 for chemistry functionality, uses MIT-licensed OPSINSwift for supported IUPAC-name translation, uses Apache-2.0 SMSDProSwift for graph matching, and includes MIT-licensed IUPAC InChI source vendored through CDKSwiftNativePort.

Document chemistry recognition uses an embedded native port of MIT-licensed ChemDataExtractor2 with an Apache-2.0 SciBERT base model. The fine-tuned weights and tokenizer are redistributed under the project owner's recorded authorization and are never downloaded at runtime.

The exact CDKSwiftNativePort 1.4.26 corresponding source is preserved by the immutable release at https://github.com/SaschaLosko/CDKSwiftNativePort/releases/tag/1.4.26 and its source archive at https://github.com/SaschaLosko/CDKSwiftNativePort/archive/refs/tags/1.4.26.zip.

The complete GNU Lesser General Public License 2.1 text and applicable dependency notices are packaged with AtomLens.

View full LGPL license