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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, 372👍, 0💬

Molecule FYI-1000179
Molecule Summary: ID: FYI-1000179 SMILES: CNC[C@H](O)C1=CC(O)=C(O)C=C1 Received at FYIcenter.com on: 2020-10-16
2020-11-11, 371👍, 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, 371👍, 0💬

Molecule FYI-1000166
Molecule Summary: ID: FYI-1000166 SMILES: FC(F)=C(H)F Received at FYIcenter.com on: 2020-09-20
2020-09-30, 368👍, 0💬

"babel -i fs ... -s ... -at n" - Top n Similarity Search
How to perform a top 10 similary search using the fastsearch index file with the "babel" command? If you want to perform a top n similary search using the fastsearch index file, you can use the following "babel" command syntax: babel -i fs index_file output_section -s query_molecule -at n -aa In the...
2020-08-25, 368👍, 0💬

Introduction to Molecules
Where to find FAQ (Frequently Asked Questions) in understanding what is molecule and its basic properties? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team in understanding what is molecule. What Is Molecule What Is Molecular Formula What Is Atomic...
2020-04-16, 368👍, 0💬

Open Babel Installation Options on macOS
What are the options for installing Open Babel on macOS computers? There are a number of options for installing Open Babel on macOS computers: 1. Install Open Babel with a pre-compiled binary package. Open Babel 2.3.1 macOS binary package is available. This is the easiest option to install Open Babe...
2020-09-15, 366👍, 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, 366👍, 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, 365👍, 0💬

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, 364👍, 0💬

Migrate JME Applet to JSME JavaScript
How to migrate my old JME Applet Web pages to use JSME JavaScript? If you have old Web pages that use the JME Applet molecule editor, you migrate your old pages to use JSME by making 2 changes: 1. Load JSME JavaScript library using a "script" tag in the "head" tag. &lt;script type="text/javascri...
2020-05-18, 364👍, 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, 363👍, 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, 363👍, 0💬

"obrotate" - Rotate Dihedral Angles with SMARTS
What Is "obrotate" command? How to use it to batch-rotate dihedral angles matching SMARTS patterns? "obrotate" command is a command line tool provided in the Open Babel package that allows you to batch-rotate dihedral angles matching SMARTS patterns. Here is the user manual of the "obrotamer" comman...
2020-10-26, 361👍, 0💬

Load Molecule Strcuture from File
How to load a molecule structure from a file into PyMol? In order to visualize a molecule in PyMol, you need to load the molecule structure from a file first. 1. Start PyMol and click the "File &gt; Open" menu. You see the file open dialog box. 2. Find and select the "Molecule-HY-001.sdf" file, ...
2020-04-16, 360👍, 0💬

Install PyMol Incentive Edition on MacOS
How to download and install PyMol Incentive edition on macOS? Downloading and installing PyMol Incentive edition on macOS is straightforward and easy as shwon in the following steps: 1. Go to PyMol Website at pymol.org. 2. Download and save the macOS DMG Disk Image file: PyMOL-2.3.3_107-MacOS-py37.d.. .
2020-04-16, 360👍, 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, 359👍, 0💬

Molecule FYI-1000176
Molecule Summary: ID: FYI-1000176 SMILES: COCC(=O)Cc1ccc(CC#N)cc1 Received at FYIcenter.com on: 2020-10-14
2020-10-26, 359👍, 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, 359👍, 0💬

List of File Formats Supported by Open Babel
How to get a list of File Formats Supported by Open Babel? You can use "babel -L formats" command to get a list of File Formats Supported by Open Babel: fyicenter$ babel -L formats abinit -- ABINIT Output Format [Read-only] acr -- ACR format [Read-only] adf -- ADF cartesian input format [Write-only]...
2020-07-15, 358👍, 0💬

"babel -ofpt -xs" - Display Fingerprint Fragments
How to Display Fingerprint Fragments usig "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 fingerprint...
2020-12-02, 357👍, 0💬

Molecule FYI-1000180
Molecule Summary: ID: FYI-1000180 SMILES: O=C1N[C@H](C)CNC2=C1SC(C=C3)=C 2C4=C3N=C(OC5=NC(Cl)=NC=C5COCC )C=C4Received at FYIcenter.com on: 2020-10-25
2020-11-11, 357👍, 0💬

What Is "babel" Command
What Is "babel" Command? How to get command line help for Open Babel? "babel" Command is the command to invoke Open Babel different functionalities by specifing different command options. You can use "babel -H" command to get help information on Open Babel command: fyicenter$ babel -H Open Babel con...
2020-09-15, 357👍, 0💬

"babel -i fs ... -s ... -at score_range" - Similarity Search
How to perform a similary search in a given score range using the fastsearch index file with the "babel" command? If you want to perform a similary search in a specific score range using the fastsearch index file, you can use the following "babel" command syntax: babel -i fs index_file output_sectio...
2020-08-25, 357👍, 0💬

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