On Jan 20, 2021, at 07:37, Egon Willighagen <[email protected]> wrote:
> Jmol had code to deduce bonds (for files which only have coordinates and no
> bond info, like XYZ), which was ported at some point to the CDK. Here's some
> example code: https://egonw.github.io/cdkbook/missing.html#reconnecting-atoms
Thanks for the pointer, Egon.
I used your book when trying to figure this out. I was blocked because I
couldn't figure out how to then identify double and triple bonds.
Eg, quoting part of RebondTool.java where it makes the bond:
/**
* Returns the bond order for the bond. At this moment, it only returns
* 0 or 1, but not 2 or 3, or aromatic bond order.
*/
private boolean isBonded(double covalentRadiusA, double covalentRadiusB,
double distance2) {
The book's example uses methane, which of course only has single bonds.
Cheers,
Andrew
[email protected]
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