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, 1131👍, 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, 1132👍, 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, 787👍, 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, 693👍, 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, 593👍, 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, 524👍, 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, 509👍, 0💬

Stereo Perception Performed by Open Babel
What is stereo perception performed by Open Babel? Stereo perception performed by Open Babel is the process of constructing stereo centers with stereoinformation received from input data. Stereo perception is performed in the following order of precedence: 1. Constructing stereo centers with 3D ster... 2022-11-16, 504👍, 0💬

Read Stereoinformation from Input
How stereoinformation is being read from input data by Open Babel? Most molecule data files store stereoinformation in 3 ways: 0D, 2D, and 3D. 0D: Stereoinformation in 0 dimension is defined by parity (or chirality) at atom level. 2D: Stereoinformation in 2 dimension is defined by bond style as wedg... 2022-11-16, 499👍, 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, 485👍, 0💬

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