Stereochemistry, Chirality, Parity

Q

Where to find FAQ (Frequently Asked Questions) in understanding how stereochemistry is supported in SDF/Mol file format?

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A

Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team in understanding how stereochemistry is supported in SDF/Mol file format.

What Is Stereochemistry

Stereoinformation Presentation in SDF/Mol File

Parity and Stereo with Open Babel

Open Babel Options on SDF/Mol Files

Stereoinformation in SDF/Mol V3000 Files

Stereochemistry with JSME (Molecule Editor in JavaScript)

⇒ What Is Stereochemistry

⇐ Tools for SDF/Mol V3000 File Format

⇑⇑ SDF/Mol File FAQ

2021-04-04, 954👍, 0💬

Tools for SDF/Mol V3000 File Format
What are tools that support the SDF/Mol V3000 file format? There are a number of online or standalone tools that support the SDF/Mol V3000 file format. Open Babel - Can read and write molecules in SDF/Mol V3000 file format. (Convert SDF to SDF V3) fyicenter$ obabel FYI-001.sdf -o sdf -O test.sd3 -x3... 2021-04-04, 2031👍, 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, 1576👍, 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, 1433👍, 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, 1243👍, 0💬

Stereochemistry, Chirality, Parity
Where to find FAQ (Frequently Asked Questions) in understanding how stereochemistry is supported in SDF/Mol file format? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team in understanding how stereochemistry is supported in SDF/Mol file format. What... 2021-04-04, 955👍, 0💬

Stereoinformation Presentation in SDF/Mol File
How Stereoinformation Is Presented in SDF/Mol and SDF/Mol V3000 Files? Ideally stereoinformation should be stored in atom's coordinates, since SDF/Mol files support x, y, and z, 3-dimensional coordinates. However, not all software supports 3-dimensional coordinates. So SDF/Mol file uses 3 types of p... 2021-03-21, 718👍, 0💬

Wedge/Hash Bond Changed by Open Babel
Why some Wedge/Hash Bonds are Changed by Open Babel? Sometimes, you may have an Wedge/Hash bond in the input data to specify a stereo center. When you convert the input data with Open Babel, you will see that the stereo center is identified with a different Wedge/Hash bond. For example, the followin... 2023-08-17, 685👍, 0💬

Parity and Stereo with Open Babel
Cam Open Babel support stereoinformation represented by the Parity Code and Stereo Code in SDF/Mol files? Yes. Open Babel can support stereoinformation represented by the Parity Code and Stereo Code in SDF/Mol files. But you should use Open Babel 2.4.1 and newer versions. Open Babel 2.3.1 seems to h... 2021-03-07, 653👍, 0💬

Hash Bond with Solid Line
Why Hash Bond with a Solid Line used by Open Babel? Sometimes, when a hash bond is located on a ring structure, Open Babel adds a solid line to the hash bond. Here is an example SDF/Mol file, Hash-with-Solid-Line.sdf, that has 4 stereo centers on a ring structure. Hash-with-Solid-Line FYICenter.com ... 2022-07-26, 636👍, 0💬

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