General Molecule Tools

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"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, 158👍, 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, 157👍, 0💬

"obrotamer" - Generate Random Rotational Isomers
What Is "obrotamer" command? How to use it to Generate Random Rotational Isomers for a given molecule? "obrotamer" command is a command line tool provided in the Open Babel package that allows you to Generate Random Rotational Isomers for a given molecule. Here is the user manual of the "obrotamer" ... 2020-10-26, 148👍, 0💬

Molecule FYI-1000177
Molecule Summary: ID: FYI-1000177 SMILES: C1CCCC1 Received at FYIcenter.com on: 2020-10-16 2020-10-26, 100👍, 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, 100👍, 0💬

Molecule FYI-1000175
Molecule Summary: ID: FYI-1000175 SMILES: C#Cc1ccc(C(=O)CCCC(C)(C)N)cc1 Received at FYIcenter.com on: 2020-10-13 2020-10-26, 100👍, 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, 169👍, 0💬

Install Open Babel Library RPM Package for CentOS
How to download and install Open Babel library RPM package for CentOS computers? Open Babel library RPM package is the base package that is required to support other Open Babel RPM interface packages. So you should download and install it first as shown in this tutorial. 1. Go back to the Linux pack... 2020-10-20, 164👍, 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, 160👍, 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, 159👍, 0💬

"DNF/YUM search" - No Open Babel Binary Package
Is there any Open Babel binary package ready to be installed with DNF/YUM on CentOS systems? The answer is no. "dnf search" command returns no matches: fyicenter$ yum search babel ============================== =====================Name Exactly Matched: babel babel.noarch : Tools for internationaliz... 2020-10-20, 154👍, 0💬

Molecule FYI-1000174
Molecule Summary: ID: FYI-1000174 SMILES: N#CCCC(Br)(Cc1ccccc1)Cc2ccccc2 Received at FYIcenter.com on: 2020-10-12 2020-10-20, 106👍, 0💬

Molecule FYI-1000173
Molecule Summary: ID: FYI-1000173 SMILES: CC(C)N(C)C(=O)c2ccc(C#CCCc1ccc (Cl)cc1)cc2Received at FYIcenter.com on: 2020-10-12 2020-10-20, 106👍, 0💬

Install Open Babel from Source Code on CentOS
How to download and instal Open Babel from source code on CentOS computers? I want to build the binary programs by myself. If you want to build the Open Babel binary programs from source code yourself, you can follow this tutorial. 1. Go to Open Babel Code Repository at https://sourceforge.net/proje. .. 2020-10-10, 172👍, 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, 168👍, 0💬

Molecule FYI-1000170
Molecule Summary: ID: FYI-1000170 SMILES: FFC=CF Received at FYIcenter.com on: 2020-09-20 2020-10-10, 125👍, 0💬

Molecule FYI-1000172
Molecule Summary: ID: FYI-1000172 SMILES: COc1cc(/C=C/c2cc(/C=C/c3ccc(O) c(OC)c3)[nH]n2)ccc1OReceived at FYIcenter.com on: 2020-10-06 2020-10-10, 116👍, 0💬

Molecule FYI-1000168
Molecule Summary: ID: FYI-1000168 SMILES: F(H)C=C(H)F Received at FYIcenter.com on: 2020-09-20 2020-10-10, 115👍, 0💬

Molecule FYI-1000169
Molecule Summary: ID: FYI-1000169 SMILES: FC=C(H)F Received at FYIcenter.com on: 2020-09-20 2020-10-10, 114👍, 0💬

Molecule FYI-1000171
Molecule Summary: ID: FYI-1000171 SMILES: C1=CC(=C(C=C1C2=C(C(=O)C3=C(C= C(C=C3O2)O)O)O)O)OReceived at FYIcenter.com on: 2020-10-05 2020-10-10, 113👍, 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, 178👍, 0💬

Using Fastsearch Fingerprint Index
Where to find FAQ (Frequently Asked Questions) on Using Fastsearch Fingerprint Index with Open Babel? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on Using Fastsearch Fingerprint Index with Open Babel. "babel ... -o fs" - Generate Fastsearch In... 2020-09-30, 176👍, 0💬

What Is Tanimoto coefficient
What Is Tanimoto coefficient? Tanimoto coefficient is a metric (or score) to measure the similarity of two sets of elements. Tanimoto coefficient can be simply defined as the ratio of the intersection of the two sets over the union of the two sets. More precisely, the Tanimoto coefficient of set A a... 2020-09-30, 160👍, 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, 121👍, 0💬

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General Molecule Tools