General Molecule Tools

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"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, 242👍, 0💬

What Is Molecule
What Is Molecule? A Molecule is a group of two or more atoms that form the smallest identifiable unit into which a pure substance can be divided and still retain the composition and chemical properties of that substance. Examples of molecules: Hydrogen gas molecule has 2 hydrogen atoms bonded togeth... 2020-04-16, 242👍, 0💬

Introduction to JSME
Where to find FAQ (Frequently Asked Questions) on basic understanding of JSME, Molecule Editor in JavaScript? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on basic understanding of JSME, Molecule Editor in JavaScript. What IS JSME - Molecule Ed... 2020-05-18, 241👍, 0💬

"babel -h" Command - Add Hydrogens to Molecule Data
How to add hydrogen atoms to molecule data during data conversion? Most molecules contains many hydrogen atoms. When molecules are written in many data formats, those hydrogen atoms are removed. We normally can read molecule structure without hydrogen atoms. But if you want to add those removed hydr... 2020-07-15, 239👍, 0💬

Install JSME on Apache Web Server
How to install JSME on an Appache Web server? If you want to install JSME on a Web server for others to try it remotely, you can follow this tutorial to install it an an Apache Web server. 1. Follow the previous tutorial to download and install JSME on your local computer in the "./JSME_2017-02-26" ... 2020-05-18, 237👍, 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, 236👍, 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, 231👍, 0💬

Install Open Babel Binary Package on macOS
How to Install Open Babel binary package on macOS computers? The easiest option to install Open Babel on macOS computers is to install the Open Babel pre-compiled binary package as shown in this tutorial. 1. Go to Open Babel download Website at SourceForge.net. 2. Click to open "Files &gt; openb... 2020-05-24, 231👍, 0💬

Substructure Search with Open Babel
Where to find FAQ (Frequently Asked Questions) on Substructure Search with Open Babel? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on Substructure Search with Open Babel. "babel -s ..." Command - Substructure Search Substructure Search with Wi... 2020-06-08, 230👍, 0💬

"babel ... -o svg -xd -xP300" Bug - Option -d takes a parameter
Why "babel ... -o svg -xd -xP300" command is giving the "Option -d takes a parameter" error in Open Babel 2.4? It seems to be another code bug in the "babel" command in Open Babel 2.4 release. "-xd" option for "svg" output format should not require any parameters according the help document: "d - do... 2020-07-15, 228👍, 0💬

Understanding "babel" Command Line Syntax
Where to find FAQ (Frequently Asked Questions) on understanding "babel" Command Line Syntax? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on understanding "babel" Command Line Syntax. What Is "babel" Command "babel" Command - Input Data Source ... 2020-05-24, 226👍, 0💬

What Is Ion
What Is Ion? An ion is a molecule that has a net electrical charge. Since the charge of the electron (considered negative by convention) is equal and opposite to that of the proton (considered positive by convention), the net charge of an ion is non-zero due to its total number of electrons being un... 2020-05-29, 223👍, 0💬

"babel ... -f # -l #" - Split Large Molecule File
How to split a file with a large number of molecules? You can split a file with a large number of molecules into smaller files by extracting a chunk of molecules to the output using the "-f #" and "-l #" options. The "-f #" option specifies the index of the first molecule to be extrancted. The "-l #... 2020-09-30, 222👍, 0💬

Open Babel File Location on macOS
Where are Open Babel files located on my macOS computers? If you install Open Babel 2.3.1 with the pre-compiled binary package on a macOS computer, you can find its program file location with the "which" command: fyicenter$ which babel /usr/local/bin/babel fyicenter$ ls -l /usr/local/bin/babel -rwxr... 2020-05-24, 221👍, 0💬

Install PyMol Open Source Edition on macOS
How to download and install PyMol Open Source edition on macOS? If you want to try the open source edition of PyMol on macOS, you have 4 installation options. 1. Using Homebrew package manager - If you have Homebrew installed on your macOS, you can try the following command to install PyMol open sou... 2020-04-16, 219👍, 0💬

Substructure Search with Wildcard Atom "*"
How to use Wildcard Atom in a substructure search using "babel" commands? You can use "*" in a SMARTS string as a wildcard atom to represent "ANY" atom in a substructure search using "babel" commands. Here are some examples of substructure matching with a wildcard atom "*" in the molecule pattern: f... 2020-06-08, 218👍, 0💬

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, 216👍, 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, 215👍, 0💬

Show InChi and InChi Key on JSME
How to display the InChi string and InChi Key of the molecule in JSME editor? JSME does not offer any API methods to export the InChi string and InChi Key of the molecule in the editor. But you can display them on the editor UI. 1. Follow the previous tutorial to install JSME on your Web server. 2. ... 2020-05-18, 215👍, 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 orginal molecule data files in the original location, because the index file has references to the original data files. If those original data... 2020-08-25, 214👍, 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, 214👍, 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, 214👍, 0💬

Molecule FYI-1000155
Molecule Summary: ID: FYI-1000155 SMILES: CC Received at FYIcenter.com on: 2020-06-17 2020-08-03, 213👍, 1💬

What Are Valence Electrons
What Are Valence Electrons of an Atom? Valence Electrons of an Atom are electrons located on the most outer shell of the atom. The number of Valence Electrons of an atom is very important chemical property of the atom. There is no easy way to calculate the number of Valence Electrons of an atom. But... 2020-05-29, 213👍, 0💬

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General Molecule Tools