Atom Biology General Molecule Reaction Tools Trial Virus

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Open Babel Command Files on macOS
What are Open Babel commands and files installed by the macOS binary package? If you install Open Babel 2.3.1 with the pre-compiled binary package on a macOS computer, you will get a number of Open Babel commands. All Open Babel command files are located in the /usr/local/bin directory: fyicenter$ l... 2020-05-24, 1039🔥, 0💬

Running Open Babel on Windows
Where to find FAQ (Frequently Asked Questions) on running Open Babel on Windows? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on running Open Babel on Windows. Install Open Babel Binary Package on Windows Run Open Babel GUI on Windows Structure... 2021-02-17, 1034🔥, 0💬

Stereochemistry with Open Babel
Where to find FAQ (Frequently Asked Questions) on doing Stereochemistry with Open Babel? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on doing Stereochemistry with Open Babel. What Is Stereochemistry Read Stereoinformation from Input Stereo Per... 2022-05-31, 1033🔥, 0💬

"babel" - FP2 Exhaustive Fingerprint Fragments
How to exhaust all possible Open Babel FP2 Fingerprint Fragments in a molecule? The easiest way to exhaust all possible Open Babel FP2 Fingerprint Fragments in a molecule to following this algorithm: Loop through all atoms (except H) in the molecule. Set each atom as the root of a bond-atom tree. An... 2020-12-02, 1033🔥, 0💬

"obabel ... -o svg -xP300" - Scale SVG Image
How to scale and center a molecule SVG image in a given square area? The default behavior of Open Babel 2.4 is different than 2.3 regarding scaling and centering SVG images. With Open Babel 2.4, the molecule SVG image is defaulted in the center of 200x200 square. With Open Babel 2.3, the molecule SV... 2020-07-22, 1029🔥, 0💬

Structure Display Command on Open Babel GUI
How to change the display command on Open Babel GUI? By default, Open Babel GUI uses Firefox to display molecule structure. If you don't have Firefox installed, you will get an error: Obgui Error: Execution of command "firefox ..." failed. System cannot find the file. To fix the problem, you can cha... 2022-05-31, 1017🔥, 0💬

JSME Molecule Editor User Interface
Where to find FAQ (Frequently Asked Questions) on JSME Molecule Editor User Interface? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on JSME Molecule Editor User Interface. JSME User Interface Menu Icons Show InChI and InChIKey on JSME Build Mol... 2020-08-03, 1001🔥, 1💬

"DNF/YUM search" - Open Babel Binary Packages
Is there any Open Babel binary packages ready to be installed with DNF/YUM on CentOS systems? The answer is yes and no, depending on which release of CentOS you are running. If you are running CentOS 8.0, Open Babel binary packages are available: fyicenter$ more /etc/system-release CentOS Linux rele... 2020-10-20, 994🔥, 0💬

Install Open Babel CLI RPM Package for CentOS
How to download and install Open Babel CLI (Command Line Interface) RPM package for CentOS computers? Open Babel CLI RPM package offers a number of pre-build command line tools for you convert and manipulate molecule data from one format to another format using Open Babel library. You can follow thi... 2020-10-10, 980🔥, 0💬

Introduction to Open Babel
Where to find FAQ (Frequently Asked Questions) on basic understanding of Open Babel, Chemistry Toolbox? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on basic understanding of Open Babel, Chemistry Toolbox. What Is Open Babel, Chemistry Toolbox ... 2020-05-21, 978🔥, 0💬

"babel -i fs ... -s query_file" - Exact Match Search
How to perform exact match in fastsearch index file using a "babel" command? If you want to perform an exact match search using the fastsearch index file, you can use the following "babel" command syntax: babel -i fs index_file output_section -s query_file In the above command: "-i fs index_file" - ... 2020-05-25, 976🔥, 0💬

Substructure Search with SMARTS Expressions
How to use SMARTS expressions in a substructure search using "babel" commands? You can use SMARTS expressions in the "-s ..." option in "babel" commands to filter molecules that match given SMARTS expressions. Here are some examples: # C, C and O connected with single bonds fyicenter$ obabel "-:c1cc... 2021-01-09, 963🔥, 0💬

What Is Stereochemistry
What Is Stereochemistry? Stereochemistry is the study of stereoisomers, which are molecules having same atoms and same connectivities, but with different spatial arrangements. Here are some stereoisomers listed in the picture below: Example of Stereoisomers You can do stereochemistry with Open Babel... 2022-11-09, 938🔥, 0💬

JSME User Interface Menu Icons
What are JSME user interface menu icons? JSME user interface menu icons are organized into 3 groups: 1. Action Icons - Located on in the first icon bar on top of the editor. Actions icons allows you to perform the following actions: SMILES - Displays the SMILES string of everything in the editor. De... 2020-05-18, 920🔥, 0💬

JS Loading Error - JSME Instance Named as "jsme"
Why I am getting the JavaScript file loading error, if I name the JSME Instance Named as "jsme"? "jsme" is used in JSME JavaScript code for another object. If you use it to name your new JSME object, it will override the other object and cause JavaScript loading errors. 1. Follow the previous tutori... 2020-05-18, 916🔥, 0💬

"obfit" - Superimpose Two Molecules
What Is "obfit" command? How to use it to Superimpose Two Molecules? "obfit" command is a command line tool provided in the Open Babel package that allows you to Superimpose Two Molecules. Here is the user manual of the "obfit" command. NAME obfit -- superimpose two molecules based on a pattern SYNO... 2020-11-11, 903🔥, 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, 902🔥, 0💬

"babel -ofpt -xs" - Display Fingerprint Fragments
How to Display Fingerprint Fragments using "babel" command? I want to know how many fragments are used when taking the fingerprint of a given molecule. You can using ""-ofpt -xs" options of the "babel" command to Display Fingerprint Fragment information. Here are some examples of molecule fingerprin... 2020-12-02, 897🔥, 0💬

JSME Molecule Editor at FYIcenter.com
What is JSME Molecule Editor at FYIcenter.com? FYIcenter.com maintains a version of JSME Molecule Editor. You can use it to create a new molecule, or edit an existing molecule. JSME, Molecule Editor in JavaScript is a free molecule editor created by Peter Ertl and Bruno Bienfait. It can be used as a... 2021-08-13, 888🔥, 0💬

"babel ... -o svg -xS" - Ball/Stick Depiction in SVG
How to generate a ball and stick depiction of a molecule in SVG with the "babel" command? If you want to a ball and stick depiction of a molecule in SVG format, you can use the "-o svg -xS" option with the "babel" command. For example, the following command generate a ball and stick depiction of of ... 2020-07-15, 887🔥, 0💬

Generate Fingerprint of Single Molecule
How to generate the fingerprint of a single molecule? I want to see the fingerprint value. If you want see the fingerprint value of a single molecule, you can just specify the molecule as the only input molecule to the "babel ... -o fpt " command. Open Babel will output its fingerprint in hexadecima... 2020-12-02, 874🔥, 0💬

Open Babel Installation Options on CentOS
What are the options for installing Open Babel on CentOS computers? There are a number of options for installing Open Babel on CentOS computers: 1. Install Open Babel with a newer software package manager like DNF/YUM. This is the easiest option to install Open Babel on CentOS computers, if someone ... 2020-10-20, 873🔥, 0💬

Fingerprint Types Supported in Open Babel
What Fingerprint Types are Supported in Open Babel? You can get a list of fingerprint types supported in Open Babel by running the "babel -L fingerprints" command: fyicenter$ babel -L fingerprints FP2 Indexes linear fragments up to 7 atoms. FP3 SMARTS patterns specified in the file patterns.txt FP4 ... 2020-12-15, 872🔥, 0💬

"obenergy" - Calculate Molecule Energy
What Is "obenergy" command? How to use it to Calculate Molecule Energy? "obenergy" command is a command line tool provided in the Open Babel package that allows you to Calculate Molecule Energy. Here is the user manual of the "obenergy" command. NAME obenergy -- calculate the energy for a molecule S... 2020-11-11, 859🔥, 0💬

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Atom Biology General Molecule Reaction Tools Trial Virus