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Hash Bond with Solid Line
Why Hash Bond with a Solid Line used by Open Babel?
✍: FYIcenter.com
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 15 16 0 0 0 0 0 0 0 0999 V2000 3.6373 2.8000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2124 2.8000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4249 2.1000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8497 2.1000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 2.8000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4249 0.7000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6373 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8497 0.7000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 2.1000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4116 2.4271 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 4.2000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8497 4.9000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6373 4.2000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4249 4.9000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2124 4.2000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2 3 1 0 0 0 0 3 1 1 0 0 0 0 4 5 1 0 0 0 0 1 4 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 4 8 1 6 0 0 0 3 6 1 6 0 0 0 2 9 1 1 0 0 0 5 10 1 6 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 5 11 1 0 0 0 0 14 15 1 0 0 0 0 13 14 1 0 0 0 0 2 15 1 0 0 0 0 M END
If we view this SDF/Mol with Open Babel, JSME and pccdb.org, we get 3 different results:
As you can see, 3 tools behaved differently:
So has bond with a solid line is a way to indicate a single bond on a ring going toward the back of the display screen.
By the way, pccdb.org changed the formation of the ring structure, because our input data does not match the real molecule structure. If we allow Open Babel to regenerate the 2D coordinates, it will give us a structure similar to pccdb.org's result.
fyicenter> obabel Hash-with-Solid-Line.sdf \ -o svg -O output.svg --gen2D fyicenter> chrome output.svg
⇐ Custom Wedge/Hash with SVG output
2022-07-26, 586👍, 0💬
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