JSME Molecule Online Editor
How to create and edit a molecule structure with JSME molecule editor? To help you to create and edit a molecule structure, FYIcenter.com provides this JSME Molecule Online Editor tool. All you need to do is to click a menu icon and starts to draw a molecule by adding one part at a time. When you ar... 2020-11-11, 1169👍, 0💬
What Is Radical Molecule
What is Radical Molecule? A Radical molecule, also called free radical, is molecule that has one or more radical centers. A Radical center is an atom in a molecule that has an unpaired valence electron, or odd number of valence electrons (including both bounded and unbound electrons). When writing t... 2020-08-03, 633👍, 1💬
sdf2svg - PHP Script to Convert SDF to SVG
How to convert Convert SDF to SVG (Scalable Vector Graphics) using "sdf2svg" PHP script? I want to see the molecule structure as a SVG file. If you want to convert molecule structures in SDF format to SVG (Scalable Vector Graphics) format to be viewed on Web pages directly, you can download and inst... 2020-04-16, 628👍, 0💬
Constitutional Isomer Example
What are examples of Constitutional Isomers? The picture below gives an example of Constitutional Isomers: Constitutional or Structure Isomers The molecule on the left is N-Butane, also known as Normal Butane, which is a flammable, colorless, mostly nontoxic gas with a natural gas odor. The molecule... 2020-08-03, 617👍, 1💬
Save Molecule from JSME to Server
"obminimize" - Optimize Geometry/Energy of Molecule
What Is "obminimize" command? How to use it to optimize the geometry and minimize the energy for a given molecule? "obminimize" command is a command line tool provided in the Open Babel package that allows you to optimize the geometry and minimize the energy for a given molecule. Here is the user ma... 2020-11-11, 599👍, 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 > openb... 2020-05-24, 581👍, 0💬
JSME Molecule Editor Options
What JSME Molecule Editor Options? JSME Molecule Editor Options are parameters that can be passed to the editor through the API to change it behavior. Here are the options supported by JSME: xbutton, noxbutton - show / hide the X button (default is xbutton) rbutton, norbutton - show / hide the R but... 2020-05-18, 570👍, 0💬
What Is Formal Charge
What is Formal Charge of an atom in a molecule? And what is the total formal charge of a molecule? The formal charge of an atom in a molecule is defined by the formula below: Fc (Formal charge) of atom = Ve - Ue - Be/2 where: Ve = number of valence electrons Ue = number of unbonded electrons Be = nu... 2020-05-29, 567👍, 0💬
Molecule Online Tools
Where to find FAQ (Frequently Asked Questions) on molecule online tools? I want to use them to create and visualize molecules. Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on molecule online tools. Molecular Formula Validator and Parser Molecul... 2020-04-16, 566👍, 0💬
PyMol Screen Layout
What information is displayed in each area on PyMol Screen? Once PyMol is started, you should see two windows displayed: External GUI - A Graphical User Interface window with the following areas: 1. Output message area - An area where output messages are displayed. Initially, the output area display... 2020-08-03, 561👍, 1💬
"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, 560👍, 0💬
"babel ... -o svg -xP300" Bug - width="px" height="px"
Why "babel ... -o svg -xP300" command is not able scale a molecule SVG image? The "babel ... -o svg -xP300" command has a code bug that results incorrect attributes, width="px" height="px", in the top level "svg" element. in both Open 2.3 and 2.4 releases. However, "obabel ... -o svg -xP300" command... 2020-07-22, 551👍, 0💬
What Is Atomic Bond
What Is Atomic Bond? Atomic Bond is a physical process that ties atoms together to form a molecule. There are 3 primary types of atomic bonds that involve the outer electrons of atoms. Ionic Bond - Electrons can be transferred from one atom to another. For example, Sodium (Na) atom transfers one ele... 2020-04-16, 529👍, 0💬
Substructure Search with Wildcard Bond "~"
How to use Wildcard Bond in a substructure search using "babel" commands? You can use "~" in a SMARTS string as a wildcard bond to represent "ANY" bond in a substructure search using "babel" commands. Here are some examples of substructure matching with a wildcard bond "~" in the molecule pattern: f... 2020-06-08, 528👍, 0💬
chemdb.niaid.nih.gov - Molecule Compounds Against HIV
What is chemdb.niaid.nih.gov's Molecule Compounds Against HIV? chemdb.niaid.nih.gov offers a searchable database of over 40,000 Molecule Compounds Against HIV. You can search the database by structure, molecule names, chemical properties, or HIV targets. Molecule Online Database - chemdb.niaid.nih.g... 2020-04-17, 527👍, 0💬
Introduction to JSME
molview.org - Draw/View/Search Molecules
What is molview.org? molview.org is a Website that offers MolView as an open source web application, and an online tool to draw, view and search molecules. MolView is an intuitive, Open-Source web-application to make science and education more awesome! MolView is mainly intended as web-based data vi... 2020-04-16, 516👍, 0💬
Scaling SVG Images using "viewBox" Attribute
What is the meaning of the <svg viewBox="..." ...> attribute? I want to understand how it is used to scale up the image. The <svg viewBox="..." ...> attribute defines view box properties which work together to scale and translate a SVG image. View Port Properties - Specif... 2020-08-03, 502👍, 1💬
"babel ... -o svg -xX" - Hide Implicit H in SVG
How to hide those H symbols (Hydrogen symbols) implicitly added to non-carbon terminal atoms in SVG with the "babel" command? If you want to hide those Hydrogen symbols implicitly added to non-carbon terminal atoms in SVG format, you can use the "-o svg -xX" option with the "babel" command. Here is ... 2020-07-22, 501👍, 0💬
pubchem.ncbi.nlm.nih.gov Molecule Database
What is pubchem.ncbi.nlm.nih.gov Molecule Database? pubchem.ncbi.nlm.nih.gov Molecule Database is the world's largest collection of small molecules with fewer than 1000 atoms and 1000 bonds. You can search pubchem.ncbi.nlm.nih.gov Molecule Database by: Chemical names Molecule formula SMILES and InCh... 2020-08-03, 499👍, 1💬
Introduction to SDF/Mol File Format
Where to find FAQ (Frequently Asked Questions) in understanding what is SDF/Mol 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 file format. What Is SDF/Mol File Format SDF File Format Specification Wh... 2020-04-16, 494👍, 0💬
How to generate the molecule structure in SDF format from a SMILES string? To help you to generate t...
What is Radical Molecule? A Radical molecule, also called free radical, is molecule that has one or ...
How to view the molecule structure specified in a SDF/Mol file? To help you to view the molecule str...
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