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rdkit.Chem.Draw - Handle Molecule Images
This chapter provides introductions and tutorial examples on rdkit.Chem.Draw module. Topics include introduction of rdkit.Chem.rdDepictor module; module methods to get molecule images quickly; sub-modules to draw molecule images with better controls. 2022-10-01, 540🔥, 0💬

"obabel --append ..." - Calculate Molecule Properties
This section provides a tutorial example on how to calculate molecule properties and append them to the 'title' field using Open Babel 'obabel' command. 2022-10-01, 535🔥, 0💬

"obabel -i ..." - Input Data Format and Source
This section provides tutorial examples on how to specify input data format and source for the Open Babel 'obabel' command. 2022-10-01, 515🔥, 0💬

Full Version in PDF/EPUB
This section provides information on how to obtain the full version of this book in PDF, EPUB, or other format. 2022-10-01, 514🔥, 0💬

"obabel ... -f # -l #" - Split Large Molecule File
This section provides tutorial examples on how to extract a chunk of molecules from a large molecule file with Open Babel 'obabel' command option arguments. 2022-10-01, 503🔥, 0💬

SDF (Structure Data File)
This chapter provides quick introductions about molecules, molecular formula, atomic bonds and molecule structures. 2023-05-04, 485🔥, 1💬

💬 2023-05-04 Siobhan: This is so helpful to me. Thank you so much!

RDKit rdMolDraw2D.PrepareAndDrawMolecule - Substructure Highlight
This section provides a tutorial example on how to highlight a substructure in a molecule with m.GetSubstructMatch(s) and rdMolDraw2D.PrepareAndDrawMole cule()methods in RDKit library. 2022-10-01, 483🔥, 0💬

rdkit.Chem.Draw.MolDrawing.DrawingOptions Class
This section provides a tutorial example on how to use rdkit.Chem.Draw.DrawingOptions class, presenting a set of molecule drawing options. But I could not find a way to use it. 2022-10-01, 480🔥, 0💬

rdkit.Chem.rdDepictor - Compute 2D Coordinates
This chapter provides introductions and tutorial examples on rdkit.Chem.rdDepictor module. Topics include introduction of rdkit.Chem.rdDepictor module and its main methods to depict a molecule in a 2 dimensional space. 2022-10-01, 461🔥, 0💬

What Is rdkit.Chem.rdDepictor Module
This section provides a quick introduction of the molecule file module of the RDKit library, rdkit.Chem.rdDepictor, which provides functionalities to depict a molecule in a 2 dimensional space. 2022-10-01, 441🔥, 0💬

"obabel ... --gen2D" - Calculated 2D Coordinates
This section provides tutorial examples on how to use Open Babel command '--gen2D' option to calculate 2D coordinates of each atom in the given molecule. 2022-05-20, 428🔥, 0💬

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, 408🔥, 0💬

Molecule Core and Sidechains Decomposition with RDKit
This section provides a tutorial example on decomposing a molecule into a core substructure and its sidechains using RDKit library. 2022-10-01, 400🔥, 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, 381🔥, 0💬

What Is rdkit.Chem.rdmolops Module
This section provides a quick introduction of the rdkit.Chem.rdmolops module in RDKit library, which provides many functionalities to manipulate molecules. 2022-10-01, 361🔥, 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, 353🔥, 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.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, 345🔥, 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, 339🔥, 0💬

Hydrogen Representations in SMILES
This section provides a quick introduction on hydrogen representations in SMILES. Hydrogens are represented explicitly as atoms 'O([H])[H]', explicitly as counts '[OH2]', or implicitly like 'O'. 2022-10-01, 331🔥, 0💬

Chirality Representations in SMILES
This section provides a quick introduction on chirality representations in SMILES. Different types of chirality are represented in as different chiral class codes in an format of [x@ccn]. 2022-10-01, 330🔥, 0💬

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, 325🔥, 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, 314🔥, 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"

About This Book
This section provides some detailed information about this book - __title__. 2022-10-01, 310🔥, 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, 307🔥, 0💬

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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 Reference REST SOAP Sorting Swing TV Series UML Unicode VBScript Web Web-Services Windows WSDL XML XMLPad XSD XSL-FO