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Molecule FYI-1000040
Molecule Summary: ID: FYI-1000040 SMILES: c1ccccc1 Received at FYIcenter.com on: 2020-04-21
2020-04-21, 650👍, 0💬

List of Open Babel Commands
How many command line tools are provided in the Open Babel package? By default, Open Babel package provides the following command line tools: babel (obabel) - Convert chemistry and molecular modeling data files. obchiral - Print molecular chirality information. obconformer - Generate conformer coord...
2020-11-22, 646👍, 0💬

Open Babel Options on SDF/Mol Files
What options are offered in Parity Code to support stereoinformation in SDF/Mol V2000 and V3000 files generated by Open Babel? Here is the documentation of Open Babel 2.4.1 with options listed to support stereoinformation in SDF/Mol V2000 and V3000 files: fyicenter$ obabel -V Open Babel 2.4.1 -- May...
2021-03-07, 638👍, 0💬

Molecule FYI-1000044
Molecule Summary: ID: FYI-1000044 SMILES: C1=CC=CC=C1 Received at FYIcenter.com on: 2020-04-21
2020-04-21, 638👍, 0💬

Molecule FYI-1000155
Molecule Summary: ID: FYI-1000155 SMILES: CC Received at FYIcenter.com on: 2020-06-17
2020-08-03, 628👍, 1💬

Skeletal Formula Notations
What notations are used in molecule skeletal formula? There are a number of notations are used Skeletal Formula to simiplify molecule diagrams. 1. Carbon Element Symbols Removed - Since carbon elements are so common in molecules, carbon element symbols are removed from Skeletal Formula diagrams. Whe...
2020-08-03, 626👍, 1💬

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, 625👍, 0💬

dtp.cancer.gov Basic Chemical Database
What is dtp.cancer.gov Basic Chemical Database? chedtp.cancer.gov Basic Chemical Database offers 4 ways to search for DTP open compound collection of 250,000 molecules: Structure search Basic chemical data search Chemical names search Smiles search Molecule Online Database - dtp.cancer.gov For more ...
2020-04-17, 625👍, 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, 624👍, 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 InChi Key on JSME Build Mo...
2020-08-03, 615👍, 1💬

Molecule FYI-1000069
Molecule Summary: ID: FYI-1000069 SMILES: Nc1cc[nH]c(=O)n1 Received at FYIcenter.com on: 2020-05-18
2020-05-18, 612👍, 0💬

Introduction to SDF/Mol V3000 File Format
Where to find FAQ (Frequently Asked Questions) in understanding what is SDF/Mol V3000 file format? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team in understanding what is SDF/Mol V3000 file format. What Is SDF/Mol V3000 File Format Tools for SDF/...
2022-07-26, 608👍, 0💬

Stereoinformation in SDF/Mol V3000 Files
How Stereoinformation is stored in in SDF/Mol V3000 files? Similar to SDF/Mol V2000, stereoinformation can be stored in SDF/Mol V3000 files in 3 ways: 0D, 2D, and 3D. 0D: Stereoinformation in 0 dimension is defined by parity at atom lines as "CFG=n" options. 2D: Stereoinformation in 2 dimension is d...
2021-02-06, 606👍, 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, 601👍, 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, 598👍, 0💬

Similarity Search with Open Babel
Where to find FAQ (Frequently Asked Questions) on Similarity Search with Open Babel? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on Similarity Search with Open Babel. "babel -o fpt ..." Command - Similarity Search Fingerprint Types Supported i...
2020-12-22, 591👍, 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, 583👍, 0💬

Molecule Online Dabases
Where to find FAQ (Frequently Asked Questions) on molecule online databases? I want to use them to search molecules and their properties. Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on molecule online Databases. pubchem.ncbi.nlm.nih.gov Molecu...
2020-04-17, 581👍, 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, 578👍, 0💬

"obconformer" - Generate Best Conformer
What Is "obconformer" command? How to use it to generate the best conformer from a base molecule? "obconformer" command is a command line tool provided in the Open Babel package that allows you to generate the best conformer from a base molecule. Here is the user manual of the "obconformer" command....
2020-11-22, 578👍, 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, 577👍, 0💬

pubchem.ncbi.nlm.nih.gov/edit3 - Draw/View Molecules
What is pubchem.ncbi.nlm.nih.gov/edit3 ?pubchem.ncbi.nlm.nih.gov/edit3 is a Website that offers PubChem Sketcher as an online tool to draw and view molecules. PubChem Sketcher was designed to be as Browser- and platform-independent as possible and should work on any recent Web browser on MS Windows,...
2020-04-16, 577👍, 0💬

Build Molecule Pattern in JSME
How to build a molecule pattern in JSME editor? I also want to save it a SMARTS string to do substructre search. If you want to build a molecule pattern in JSME, you can follow this tutorial. 1. Follow the previous tutorial to install JSME on your Web server. 2. Run the demo page on the Apache Web s...
2020-05-18, 576👍, 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, 574👍, 0💬

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