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What Is rdkit.Chem.Draw Module
This section provides a quick introduction of the core module of the RDKit library, rdkit.Chem.Draw, which functionalities to create molecule images in different formats as displaying images, internal objects, or external files. 2022-10-01, 558🔥, 0💬

SMILES (Simplified Molecular-Input Line-Entry System)
This chapter provides introductions and tutorial examples on SMILES (Simplified Molecular-Input Line-Entry System). Topics include SMILES representations for atoms, bonds, rings, disconnected structures, charges, directional bonds, isotopes, chiral centers. 2022-10-01, 547🔥, 0💬

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, 537🔥, 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, 532🔥, 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, 514🔥, 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, 513🔥, 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💬

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, 482🔥, 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, 440🔥, 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, 407🔥, 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, 399🔥, 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💬

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, 343🔥, 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, 338🔥, 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, 328🔥, 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, 322🔥, 0💬

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💬

Change Display Command on Open Babel GUI
This section provides a tutorial example on how to change structure display command on Open Babel GUI to use Google Chrome browser. 2022-10-01, 279🔥, 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, 271🔥, 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