Tools for SDF/Mol V3000 File Format

Q

What are tools that support the SDF/Mol V3000 file format?

✍: Guest

A

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
  1 molecule converted

(Convert SDF V3000 to SDF)
fyicenter$ obabel -i sdf test.sd3 -O test.sdf
  1 molecule converted

JSME (Molecule Editor in JavaScript) - Can read and write molecules in SDF/Mol V3000 file format.

cheminfo.org/Chemistry/2D_to_3D - Can create molecules and write them in SDF/Mol V3000 file format.

Tools that does not support SDF/Mol V3000 file format:

PubChem 3D Viewer v2.0 at https://pubchem.ncbi.nlm.nih.gov/pc3d/.
Online SMILES Translator and Structure File Generator at https://cactus.nci.nih.gov/translate/.

⇒ Stereochemistry, Chirality, Parity

⇐ What Is SDF/Mol V3000 File Format

⇑ Introduction to SDF/Mol V3000 File Format

⇑⇑ SDF/Mol File FAQ

2021-04-04, 885👍, 0💬

Install Open Babel Binary Package on Windows
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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, 886👍, 0💬

Run Open Babel GUI on Windows
How to run OpenBabelGUI on Windows computers? Open Babel GUI is the graphical user interface for Open Babel. You can use Open Babel GUI to open a molecule file in any supported format and convert it to any other format. Here is how to Open Babel GUI on Windows. 1. Search for "Open Babel GUI" in "Sta... 2021-03-07, 847👍, 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, 576👍, 0💬

Structure Display Command on Open Babel GUI
How to change the display command on Open Babel GUI? By default, Open Babel GUI uses Firefox to display molecule structure. If you don't have Firefox installed, you will get an error: Obgui Error: Execution of command "firefox ..." failed. System cannot find the file. To fix the problem, you can cha... 2022-05-31, 508👍, 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, 484👍, 0💬

Stereochemistry with Open Babel
Where to find FAQ (Frequently Asked Questions) on doing Stereochemistry with Open Babel? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on doing Stereochemistry with Open Babel. What Is Stereochemistry Read Stereoinformation from Input Stereo Per... 2022-05-31, 482👍, 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, 454👍, 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, 418👍, 0💬

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