Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
Use StoneMIND Collector on Windows
This section provides a tutorial example on how to use StoneMIND Collector client on a Windows computer to capture and recognize any molecule diagrams on the screen.
Once you have installed StoneMIND Collector on your Windows computer, you can use it to capture any molecule diagram on the screen and recognize it as a molecule structure.
Here is what I did to see how good this tool is.
1. Open paten WO2001000214A1 PDF file in a browser at https://patentimages.storage.googleapis.com/31/69/21/9231664697ed8a/WO2001000214A1.pdf.
2. Go to page 6 to display the first molecule diagram and keep the scale at 100%.
3. Open StoneMIND Collector client and click "Recognize". I see a screen capture window displayed.
4. Move, click and drag the mouse pointer to capture the molecule diagram on the browser window.
5. Click OK to let StoneMIND Collector recognize the molecule structure.
6. In a moment, StoneMIND Collector displays the result in an structure editor window as shown below.
7. Review the resulting molecule structure. I see that it failed to recognize the top ring, missing X2 atom and its bonds.
8. Increase the molecule diagram size by changing the PDF page display scale 400%. And use StoneMIND Collector to try it again.
9. Review the second result. It failed again on the same ring. But it missed atom X3 this time.
10. Use the structure editor to fix the problem. And save it as a SDF file.
Conclusions.
- StoneMIND Collector Client is easy to use, and fast for a single molecule.
- It's about 97% accurate, missing 1 out of 19 atoms in my test.
Table of Contents
SMILES (Simplified Molecular-Input Line-Entry System)
Open Babel: The Open Source Chemistry Toolbox
Using Open Babel Command: "obabel"
Generating SVG Pictures with Open Babel
Substructure Search with Open Babel
Similarity Search with Open Babel
Fingerprint Index for Fastsearch with Open Babel
Stereochemistry with Open Babel
Command Line Tools Provided by Open Babel
RDKit: Open-Source Cheminformatics Software
rdkit.Chem.rdchem - The Core Module
rdkit.Chem.rdmolfiles - Molecular File Module
rdkit.Chem.rdDepictor - Compute 2D Coordinates
rdkit.Chem.Draw - Handle Molecule Images
Molecule Substructure Search with RDKit
rdkit.Chem.rdmolops - Molecule Operations
Daylight Fingerprint Generator in RDKit
Morgan Fingerprint Generator in RDKit
RDKit Performance on Substructure Search
Introduction to Molecular Fingerprints
►OCSR (Optical Chemical Structure Recognition)
StoneMIND Collector - Information Extraction System
Install StoneMIND Collector Client on Windows
►Use StoneMIND Collector on Windows
Stop StoneMIND Collector on Windows
Use StoneMIND Collector Web Interface
AlphaFold - Protein Structure Prediction