Sugar SMILES Finder

Thu, 08 Oct 2026 00:00:00 +0000

Description

Sugar SMILES Finder is a small Streamlit app for quickly getting machine-readable structures of carbohydrates. Type the name of a sugar (e.g. glucose, sucrose, α-L-fucose). The app searches PubChem and shows the isomeric and connectivity SMILES, InChIKey, molecular formula, molecular weight, IUPAC name, and an interactive 3D structure.

Open the app directly via the site link.

Simple search

Enter a name and press Search. You get the PubChem entry with its SMILES (ready to copy) and the PubChem 3D conformer in an interactive viewer.

Advanced search

Tick the Advanced search box to choose the exact form of the sugar and the conformation of its ring:

Ring puckering: chair (⁴C₁ or ¹C₄), boat or envelope
Anomer: α or β
Configuration: D or L

The anomer and D/L choices are used to build the PubChem query (e.g. glucose + α + D → alpha-D-glucose). Because SMILES does not encode ring conformation, the 3D structures are generated with RDKit. The app embeds a conformer ensemble with ETKDG, optimises it with the MMFF94 force field, and classifies each ring using Cremer–Pople puckering parameters and IUPAC conformation names (e.g. ⁴C₁, B₂,₅, ²E).

Conformers that match the requested pucker are ranked by energy relative to the lowest-energy conformer found. If the requested pucker is not a relaxed minimum (for example, a boat for β-D-glucose), the app enforces it with ring-torsion restraints and reports the resulting strain energy. Each conformer can be viewed in 3D and downloaded as a .mol file.

Source code

The code is available on GitHub.

References

S. Kim et al. PubChem 2023 update. Nucleic Acids Research 51, D1373–D1380 (2023). https://doi.org/10.1093/nar/gkac956
RDKit: Open-source cheminformatics. https://www.rdkit.org
S. Riniker and G. A. Landrum. Better Informed Distance Geometry: Using What We Know To Improve Conformation Generation. J. Chem. Inf. Model. 55, 2562–2574 (2015). https://doi.org/10.1021/acs.jcim.5b00654
T. A. Halgren. Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94. J. Comput. Chem. 17, 490–519 (1996).
D. Cremer and J. A. Pople. General definition of ring puckering coordinates. J. Am. Chem. Soc. 97, 1354–1358 (1975). https://doi.org/10.1021/ja00839a011
IUPAC-IUB Joint Commission on Biochemical Nomenclature. Conformational nomenclature for five- and six-membered ring forms of monosaccharides and their derivatives. Eur. J. Biochem. 111, 295–298 (1980).

SXM Image Analyzer

Thu, 08 Oct 2026 00:00:00 +0000

Description

SXM Image Analyzer is a Streamlit app for quickly viewing and cleaning up scanning probe microscopy (SPM/STM) images saved in the Nanonis .sxm format, with no local installation needed. Upload a .sxm file (up to 200 MB) to see the image and its acquisition metadata right away.

Open the app directly via the site link.

Features

Original image

View the raw topography image as recorded.
Download the unfiltered image (PNG), the scan metadata (TXT) and the STM data grid (NPZ) for further analysis in Python.

Processing

Use the Process tab to enhance the image interactively:

FFT filtering with Gaussian, Blackman–Harris or exponential windows and an adjustable width (σ), to remove high-frequency noise.
Unsharp masking with adjustable radius and amount, to sharpen molecular and atomic features.
Image transforms: contrast inversion and cosine transform.

The processed image, processed raw image and metadata can be downloaded.

Analysis (coming soon)

Dedicated analysis modes for specific adsorbates are under development: chitosan, RNA, proteins, chlorophyll and glycolipids.

Tutorial

A step-by-step notebook showing how to load .sxm files and apply these filters in Python is available on GitHub.

Web App | My CV

Sugar SMILES Finder

Description

Simple search

Advanced search

Source code

References

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SXM Image Analyzer

Description

Features

Original image

Processing

Analysis (coming soon)

Tutorial

Did you find this page helpful? Consider sharing it 🙌