General Molecule Tools

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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, 211👍, 0💬

Open Babel History and Releases
When Open Babel was first developed? And how many Open Babel releases are there? The original Babel was written by Pat Walters and Matt Stahl in 2001, based on the "convert" program by Ajay Shah. The original Babel is a remarkable chemistry file convesion tool. Pat Walters and Matt Stahl rewrote Bab... 2020-09-15, 209👍, 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, 235👍, 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, 229👍, 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, 226👍, 0💬

"babel ... -o fs" - Generate Fastsearch Index
What is Open Babel Fastsearch Index file? How to generate it with the "babel" command? Fastsearch index file is an Open Babel specific binary file that stores pre-calculated fingerprints and their indexes for multiple molecules. Fastsearch index file can improve similarty search significantly faster... 2020-08-25, 224👍, 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, 224👍, 0💬

Molecule FYI-1000165
Molecule Summary: ID: FYI-1000165 SMILES: Received at FYIcenter.com on: 2020-08-17 2020-08-25, 186👍, 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, 336👍, 1💬

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, 281👍, 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, 301👍, 1💬

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, 273👍, 1💬

What Is Isomer
What is Isomer? An Isomer is molecule that has the same the same chemical formula as another molecule, but with a different molecule structure than the other molecule. There are several types of isomers: 1. Constitutional Isomers - Isomers that differ in connectivity are called constitutional isomer... 2020-08-03, 465👍, 1💬

Enantiomers Isomer Example
What are examples of Enantiomers Isomers? The picture below gives an example of Enantiomers Isomers: Stereoisomers &gt; Enantiomers (Mirror Images) The molecule on the left is (R)-Lactic Acid with a chiral C in (R)-configuration, or right-hand configuration, or clockwise configuration. The molec... 2020-08-03, 396👍, 1💬

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, 282👍, 1💬

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, 324👍, 1💬

Molecule FYI-1000155
Molecule Summary: ID: FYI-1000155 SMILES: CC Received at FYIcenter.com on: 2020-06-17 2020-08-03, 242👍, 1💬

Scaling SVG Images using "viewBox" Attribute
What is the meaning of the &lt;svg viewBox="..." ...&gt; attribute? I want to understand how it is used to scale up the image. The &lt;svg viewBox="..." ...&gt; attribute defines view box properties which work together to scale and translate a SVG image. View Port Properties - Specif... 2020-08-03, 320👍, 1💬

💬 2020-08-03 chelseaclark: The success of any ion channel research program involves complex decisions that require specific expertise to address the comple...

"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, 351👍, 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, 318👍, 0💬

"babel ... -o svg -xC" - Hide Terminal C in SVG
How to hide those C symbols for terminal carbon atoms in SVG with the "babel" command? If you want to hide those C symbols for terminal carbon atoms in SVG format, you can use the "-o svg -xC" option with the "babel" command. Here is how the "-xC" option is described in Open Babel help documebnt: "C... 2020-07-22, 284👍, 0💬

"obabel ... -o svg -xP300" - Scale SVG Image
How to scale and center a molecule SVG image in a given squar area? The default behavior of Open Babel 2.4 is different than 2.3 reguarding scalling 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 S... 2020-07-22, 275👍, 0💬

"babel ... -o svg" - Two "svg" Tag Levels
Why am getting two "svg" tag levels in SVG source code generated by the "babel" command? If you are using Open Babel 2.4.1 or higher, you will notice that there are two "svg" tag levels in SVG source code generated by the "babel" command. The main reason for using two "svg" tag levels for including ... 2020-07-22, 265👍, 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, 252👍, 0💬

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General Molecule Tools