Hi Gilleain, Thank you for explanations. It seems like I found also the prove of your words in CDK-jchempaint source code in function AtomContainerRenderer.setScale(IAtomContainer), which calculates the bond length based on the given molecule and sets scale parameter to this value (and in my case that was 26.66). I think, the parameter should be renamed to "BondLength" then, as it controls the [magnitude of] distance between atoms.
Zoom in contrast to scale also impacts the size of font used to draw atoms. So in this sense zoom is real visual zoom. Correct me if I ma wrong. On 18.01.2011 17:32, gilleain torrance wrote: > Hi Dmitry, > > The idea is that 'scale' means the amount to transform model > coordinates to get a particular bond length, and 'zoom' is the > transform to the bond length. > > To give a concrete example, lets say we have H2 in a molfile. The > distance between the atoms is 1 unit (not necessarily a real unit, > like picometers). If the bond length is 10 pixels, then the scale is > 10. If the zoom is then 0.9, then the line drawn to represent the bond > will be 9 pixels. > > The reason for this is that models may have different scales, and the > transform uses this to render at a particular bond length. The zoom is > user-settable, and only reflects how to change the bond length. So > really, it is bond length and zoom that are redundant - they are > different ways to think of the same thing, specifically how long the > lines are between atoms. > > gilleain -- With best regards, Dmitry ------------------------------------------------------------------------------ Protect Your Site and Customers from Malware Attacks Learn about various malware tactics and how to avoid them. Understand malware threats, the impact they can have on your business, and how you can protect your company and customers by using code signing. http://p.sf.net/sfu/oracle-sfdevnl _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
