Saving old coords

Hello,

I am using ChemAxon in order to standardize, protonate & generate new conformers from 3D SDF structures files.

I need to save the old coordinates of my structures. My problem is that atom number & order change after processing the files.

Since the order can change, a plain concanenation of input coords is not possible.

I tried to add a property for each input atom but it seems I can't retrieve it in the final object

A Hasmap could store old coords from input atoms but I need a key for each atom which is constant after the process : hashcode(), toString ... cannot be used

Is there a way to do that ? (eg : a method which give an uniq key for an atom)

TIA for your answer

H

Hi,

Try something like this:

Map the input structures in your file

standardize -c map nci10.sdf -f sdf -o nci10mapped.sdf

Standardize your molecules, generate their protonated form (major microspecies) at pH 7.4, and then generate the 3D structures (lowest energy conformer) of the protonated molecules.

standardize -c "" nci10mapped.sdf -f sdf | cxcalc majormicrospecies -H 7.4 -f sdf | cxcalc -o majorms3d.sdf leconformer -f sdf 

You can use atom maps to identify atoms in mapped input file (nci10mapped.sdf) and in result file (majorms3d.sdf).

I hope this helps.

Zsolt

Ty for the fast answer. I will continue in this direction (set/get AtomMap) ... specially for heavy atoms which must be present in both structures (pre/post process)