strange clean3d behaviour

Hello





I have a simple test of cyclic hydrocarbons which I feed to the fast 3D model builder:

Code:

//mol3d.hydrogenize(true); mol3d.clean(3, "S{fast}");

Benzene till Naphtalene are built correctly but cyclohexane appears completely flat, hydrogenized or not. Only a fine build makes the correct structure. Is this a bug?





Otherwise it is working very well and very fast. Thanks for the good job.


lorenz

Test set:


C1CCCCC1


C1=CC=CC=C1


C1CCC2CCCCC2C1


C1=CC2=C(C=C1)C=CC=C2

When using S{fast} option Clean3D invokes a fast coordinate generation process which not always lead to a low energy 3D conformer. (This is the case with cyclohexane) I recommend to use default settings (giving empty option string).





By the way the Cleaning Options document is not updated, so mentioning S{...} options is a bug. You can access a detailed list of options with command line tool molconvert -H3D





If you have any further questions about Clean3D, feel free to ask them.