Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
StoneMIND Collector - Information Extraction System
This section provides a quick introduction of StoneMIND Collector, a free OCSR (Optical Chemical Structure Recognition) software provided by Stonewise.
What Is StoneMIND Collector? - StoneMIND Collector is an information extraction system that allows you to extract chemical structures from patents and essays using OCSR (Optical Chemical Structure Recognition) and IUPAC (International Union of Pure and Applied Chemistry) methods. Results can be exported in computer-friendly formats (sdf/mol/smiles/xls) to set up your own chemical information database.
StoneMIND Collector can be used free of charge in two ways:
1. Client Module - Runs locally on your Windows or Mac computer. It allows you to take a screenshot of any 2D molecule diagram or IUPAC name, and perform optical recognition. The resulting molecule structure can revised and saved in SMILES or SDF format.
2. Web Interface - Runs remotely on Stonewise server. It allows you to upload an image or PDF file with molecule diagrams or IUPAC names, and perform optical recognition. The resulting molecule structures can revised and saved in SMILES or SDF format. The Web interface offers additional functionalities to do batch extraction of patents or essays.
For more information, visit Stonewise Website at https://www.stonewise.ai/mol_product.
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