Atom Biology General Molecule Reaction Tools Trial Virus

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Search Open Babel RPM Packages for CentOS
How to search for Open Babel RPM binary packages for CentOS computers? You can follow this tutorial to search for Open Babel RPM binary packages for CentOS computers. 1. Before searching the Internet for any RPM binary packages, you need to know the architecture type of your computer. This can be do... 2020-10-20, 1284🔥, 0💬

"obprobe" - Create Electrostatic Probe Grid
What Is "obprobe" command? How to use it to optimize the geometry and minimize the energy for a given molecule? "obprobe" command is a command line tool provided in the Open Babel package that allows you to Create Electrostatic Probe Grid for a given molecule. Here is the user manual of the "obprobe... 2020-10-26, 1279🔥, 0💬

"babel" Command Option Argument Syntax
How to write "babel" command option argument properly? What's the difference between "-isdf" and "-i sdf"? There is no difference between "-isdf" and "-i sdf". Both are valid "babel" option "-i" with an argument of "sdf". If a "babel" command option takes an argument, you can specify the argument in... 2020-12-26, 1277🔥, 0💬

"babel ... -o svg -xi" - Show Atom Indices in SVG
How to show atom indices in a molecule SVG picture? I want to see in what order each atom is listed in the SMILES string. The SMILES string list each atom a molecule is a specific sequence. You can use the "-xi" option when generating the SVG file to show the index of each atom corresponding to the ... 2021-02-04, 1269🔥, 0💬

Substructure Search with Fingerprints
Can I do Substructure Search with fingerprints using Open Babel? Yes, you can do Substructure Search with fingerprints using Open Babel. All you have to do is to take substructure as the query molecule and run a similarity search using the fingerprint output option "-o fpt ". When Open Babel calcula... 2020-12-02, 1267🔥, 0💬

"babel ... -o svg" - Generating SVG Pictures
Where to find FAQ (Frequently Asked Questions) on using Open Babel to generate SVG Pictures from molecule input data? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on using Open Babel to generate SVG Pictures from molecule input data. "babel -o ... 2021-07-19, 1255🔥, 0💬

"babel -x..." Command - Extra Output Writing Options
How to pass extra options for "babel" to write output data of a specific format? If you want to pass extra options for "babel" to write output data of a specific format, you need to use one or more "-x..." options in the "babel" command line as shown in the following syntax: babel input_section outp... 2020-07-15, 1252🔥, 0💬

"babel -i fs ... -s SMILES" - Substructure Search with Index
How to perform a substructure search using the fastsearch index file with the "babel" command? If you want to perform a substructure search using the fastsearch index file, you can use the following "babel" command syntax: babel -i fs index_file output_section -s SMILES In the above command: "-i fs ... 2020-05-25, 1251🔥, 0💬

"obgrep" - Search Molecules using SMARTS
What Is "obgrep" command? How to use it to Search Molecules using SMARTS strings? "obgrep" command is a command line tool provided in the Open Babel package that allows you to Search Molecules using SMARTS strings. "obgrep" command does the same job as the "babel ... -s ..." with more options. Here ... 2020-11-11, 1248🔥, 0💬

Stereo Perception Performed by Open Babel
What is stereo perception performed by Open Babel? Stereo perception performed by Open Babel is the process of constructing stereo centers with stereoinformation received from input data. Stereo perception is performed in the following order of precedence: 1. Constructing stereo centers with 3D ster... 2022-11-16, 1240🔥, 0💬

"babel ... -o svg" - Two "svg" Tag Levels
Why am getting two "svg" tag levels in SVG source code generated by the "babel" command? If you are using Open Babel 2.4.1 or higher, you will notice that there are two "svg" tag levels in SVG source code generated by the "babel" command. The main reason for using two "svg" tag levels for including ... 2020-07-22, 1235🔥, 0💬

"obchiral" - Print Chirality Information
What Is "obchiral" command? How to use it to Print Chirality Information? "obchiral" command is a command line tool provided in the Open Babel package that allows you to calculate and print molecule chirality information. Here is the user manual of the "obchiral" command. NAME obchiral -- print mole... 2020-11-22, 1224🔥, 0💬

"babel -s ..." Command - Substructure Search
How to use "babel -s ..." command to do substructure search? You can do substructure search using the "-s ..." option of the "babel" command with the following syntax: babel input_section output_section -s smarts_string The smarts_string specifies a SMARTS string that represents a molecule pattern. ... 2020-06-08, 1223🔥, 0💬

"babel -... --..." Command - Generic Conversion Options
What are generic conversion options that I can use on "babel" commands for all input and output formats? "babel" commands supports a number of generic conversion options that applies all input and output formats as listed below: --addtotitle Append text to the current molecule title --addformula App... 2021-07-19, 1220🔥, 0💬

What Is Ketcher Editor Interface
What is Ketcher Editor interface? Ketcher Editor interface is part of the Ketcher JavaScript API that allows you to interact with Ketcher editor UI elements. To access Ketcher Editor interface, you need to access the "ketcher" object as a property of the content "window" object of the "iframe" where... 2023-12-08, 1213🔥, 0💬

Ketcher User Interface Menu Icons
What are Ketcher user interface menu icons? Ketcher user interface menu icons are organized into 4 toolbars: 1. Action toolbar - Displayed horizontally at the top of the window, the main toolbar contains the following buttons to perform different actions: Clear canvas - Removes everything in the edi... 2023-11-06, 1213🔥, 0💬

"babel" Command - Input Data Source and Format
How to specify Input Data Source and Format for a "babel" command? "babel" command arguments and options are organized into 3 sections as shown in the following syntax to convert chemical data from input to output with specified options. babel input_section output_section option_section You use inpu... 2021-07-19, 1206🔥, 0💬

"babel -i fs ... -s query_file" - Substructure Search
Why am I getting no results with "babel -i fs ... -s query_file" command? It should perform a substructure search in a fastsearch index file. According to the "babel -H fs" help document, you can perform a substructure search in a fastsearch index file with the query molecule stored in a file in any... 2020-05-25, 1205🔥, 0💬

"babel -i fs ..." - Fingerprint Index Based Search
How to perform a Fingerprint Index Based Search with the "babel" command? You can perform a Fingerprint Index Based Search with the "babel" command using the "-i fs" option to specify the fingerprint index file as the input. For more information, read the help document on fastsearch index file forma... 2020-08-25, 1202🔥, 0💬

Write Stereoinformation to Output
How stereoinformation is being written to output data by Open Babel? Stereoinformation is being written to output data based on stereo centers maintained by Open Babel according the following rules: 1. 3D Stereoinformation - By default, 3D coordinates are copied over from input data to output data w... 2023-08-17, 1200🔥, 0💬

"babel -d" Command - Delete Hydrogens from Molecule Data
How to delete hydrogen atoms from molecule data during data conversion? If hydrogen atoms of a molecule are included in the input data source, you can use the "babel" generic option "-d" remove those hydrogen atoms during the molecule data conversion process. Here is an example of using the "-d" opt... 2020-07-15, 1200🔥, 0💬

"babel -a..." Command - Extra Input Reading Options
How to pass extra options for "babel" to read input data of a specific format? If you want to pass extra options for "babel" to read input data of a specific format, you need to use one or more "-a..." options in the "babel" command line as shown in the following syntax: babel input_section output_s... 2020-07-15, 1194🔥, 0💬

"Difficulty opening ..." Error Using Fastsearch Index
Why am I getting this "Difficulty opening ..." error using Fastsearch Index files? When you are using a fastsearch index file as the input, you must keep the original molecule data files in the original location, because the index file has references to the original data files. If those original dat... 2020-08-25, 1186🔥, 0💬

Running Open Babel on CentOS
Where to find FAQ (Frequently Asked Questions) on running Open Babel on CentOS? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on running Open Babel on CentOS. Open Babel Installation Options on CentOS "DNF/YUM search" - No Open Babel Binary Pack... 2020-10-20, 1179🔥, 0💬

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Atom Biology General Molecule Reaction Tools Trial Virus