Re: [Cdk-user] Aligning Reaction using Fixed Substructure

Nice, For historical reasons, CDK uses unit bond length 1.5 instead of 1. Something to do with C-C bonds but that really only makes sense for 3D. Rescale it like this: GeometryUtil.scaleMolecule(fixedSubstructure, 1.5/GeometryUtil.getBondLengthMedian(fixedSubstructure)); Also I presume you want

Re: [Cdk-user] Aligning Reaction using Fixed Substructure

Yes, reactions are aligned left to right automatically when atom-maps are present. For example: [image: image.png] (CDK Depict

[Cdk-user] Aligning Reaction using Fixed Substructure

Hi, I'm wondering if it's possible to align a Reaction using a fixed substructure similar to the methods covered here: http://ctr.wikia.com/wiki/Align_the_depiction_using_a_fixed_substructure Is this possible using CDK? Thanks in advance, Ross --