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Open Source Code for AlphaFold
This section provides a quick introduction on the open source code for AlphaFold provided at github.net. High level steps are also provided to download and run the open source code. 2022-10-01, ∼569🔥, 0💬

Open Babel: The Open Source Chemistry Toolbox
This chapter provides introductions and tutorial examples on Open Babel, The Open Source Chemistry Toolbox. Topics include installing options; install Open Babel with Anaconda; installation from binary packages on Windows and macOS; installation from source code on CentOS. 2022-10-01, ∼541🔥, 0💬

Compile PyMol Source Code
This section provides a tutorial on how to download PyMol open source edition source code and compile it on macOS. Compilation failed with 'GL/glew.h' file not found. 2023-02-19, ∼528🔥, 2💬

💬 2023-02-19 Herong: Markf, I will try it. Thanks!

💬 2023-02-18 Markf: You need to install the glew-devel library

rdkit.Chem.rdchem.RWMol - The RWMol Class
This section provides a quick introduction of the rdkit.Chem.rdchem.RWMol class, which is a sub-class of rdkit.Chem.rdchem.Mol class with additional read and write functionalities. 2022-10-04, ∼527🔥, 0💬

AlphaFold - Protein Structure Prediction
This chapter provides notes and tutorial examples on AlphaFold as an AI system to predict protein’s 3D structures. Topics include introduction of AlphaFold and its open source package; installing source code and databases; running AlphaFold on Docker platform. 2022-10-01, ∼525🔥, 0💬

Install Open Babel from Source Code
This section provides a tutorial example on how to install Open Babel from source code. But there are multiple required libraries are missing on CentOS 8 Computers for Open Babel 3.1.1. 2022-10-01, ∼525🔥, 0💬

rdkit.Chem.rdchem.Atom - The Atom Class
This section provides a quick introduction of the rdkit.Chem.rdchem.Atom class, which represents an atom with its properties, associated objcts, and operation methods. 2022-10-04, ∼523🔥, 0💬

About This Book
This section provides some detailed information about this book - Cheminformatics Tutorials - Herong's Tutorial Examples. 2022-10-01, ∼518🔥, 0💬

"Open Babel Error in LoadAllPlugins" Error
This section provides a tutorial example on how to resolve the 'Open Babel Error in LoadAllPlugins' error by adding the the BABEL_LIBDIR environment variable. 2023-01-07, ∼503🔥, 0💬

Using Open Babel Command: "obabel"
This chapter provides introductions and tutorial examples on Open Babel 'obabel' command. Topics include command line syntax; '-i/-o' for input and output formats; '-O' for output file; '-a/-x' for extra options specific for an input/output format. 2022-10-01, ∼501🔥, 0💬

rdkit.Chem.rdSubstructLibrary - Substructure Library
This section provides a quick introduction on rdkit.Chem.rdSubstructLibrary module in RDKit library that provides functionalities to do substructure search with a molecule library. 2022-10-01, ∼482🔥, 0💬

Morgan Fingerprint Generator in RDKit
This chapter provides introductions and tutorial examples on Morgan Fingerprint Generator in RDKit. Topics include introduction of RDKFingerprint(), UnfoldedRDKFingerprintCountBas ed(),and GetRDKitFPGenerator() methods, impact of radius, useCounts, useBondTypes, and other options. 2023-04-03, ∼481🔥, 0💬

"obabel -L formats" - List of File Formats Supported
This section provides a list of molecule file formats supported by Open Babel obtained by the 'obabel -L formats' command. 2023-11-28, ∼480🔥, 2💬

💬 2023-11-28 Herong: sh, the error message indicates that Open Babel is not able to read the input file torus.mop as a MOPAC Cartesian file. Here is ...

💬 2023-11-26 sh: Hi , First thanks second I tried obabel torus.mop -o orcainp tor.orcainp but is says "Invalid format in geometry specification"

Generating SVG Pictures with Open Babel
This chapter provides introductions and tutorial examples on Open Babel 'obabel -o svg' command to generate molecule structure images in SVG format. Topics include '-xi', '-xS', '-xX' and '-xC' options to control elements on the output SVG images; '-xPnnn' to control image size. 2022-10-01, ∼473🔥, 0💬

"obabel -:... -o svg" - Generate SVG from SMILES
This section provides a tutorial example how to generate a SVG (Portable Network Graphics) picture of a molecule structure specified as a SMILES string using the Open Babel 'obabel -:... -o svg' command. 2022-10-01, ∼470🔥, 0💬

What Is Morgan Fingerprint Generator in RDKit
This section provides a quick introduction on the Morgan Fingerprint Generator provided in the RDKit library. 2023-04-04, ∼467🔥, 0💬

rdkit.Chem.rdchem.Mol - The Molecule Class
This section provides a quick introduction of the rdkit.Chem.rdchem.Mol class, which represents a molecule with its properties, child objcts, and operation methods. 2022-10-04, ∼467🔥, 0💬

What Is "obabel" Command
This section provides a quick introduction on the 'obabel' command, which reads molecule information in any given format, processes it and generates output in any given format. 2022-10-01, ∼461🔥, 0💬

rdkit.Chem.rdmolops - Molecule Operations
This chapter provides introductions and tutorial examples on rdkit.Chem.rdmolops module. Topics include introduction of rdkit.Chem.rdmolops module methods: CombineMols(), RDKFingerprint(), ReplaceSidechains(), ReplaceCore(), etc.. 2022-10-01, ∼452🔥, 0💬

GetHashedMorganFingerprint() Method in RDKit
This section provides a quick introduction on the rdkit.Chem.rdMolDescriptors.Ge tHashedMorganFingerprint()Method in the RDKit library. 2023-04-04, ∼442🔥, 0💬

GetRDKitFPGenerator() Method in RDKit
This section provides a quick introduction on the rdkit.Chem.rdFingerprintGenera tor.GetRDKitFPGenerator()Method in the RDKit library. 2023-04-04, ∼442🔥, 0💬

Isotope Represenations in SMILES
This section provides a quick introduction on charge represenations in SMILES. Isotopes are represented by prefixing the mass count of the atom in square brackets []. 2022-10-01, ∼440🔥, 0💬

Install Open Babel Binary Package on macOS
This section provides a tutorial example on how to install Open Babel from a binary package on macOS computers. 2022-10-01, ∼431🔥, 0💬

What Is SMILES
This section provides a quick introduction of SMILES (Simplified Molecular-Input Line-Entry System), which is a specification in the form of a line notation for describing molecule structures using short ASCII strings. 2022-10-01, ∼415🔥, 0💬

<< < 1 2 3 4 5 6 7 8 > >>   ∑:170  Sort:Date

Android ASP Astrology Big5 Bitcoin Blowfish Built-in C# Calendar CD-DVD Cheminformatics Chinese Cryptography DES Email Encoding Ethereum Flash GB2312 General H Herong History HTML Java JavaScript JDBC JSP JVM Linux Molecule Movie Music MySQL Neural Network Perl PHP Physics PKI Publication Python REST SOAP Sorting Swing TV Series UML Unicode VBScript Web Web-Services Windows WSDL XML XMLPad XSD XSL-FO