Standardizer order

Hi,





I am running Standardizer on a dot separated list of smiles and have noticed that the ouput order is sometimes changed even no standardization has taken place.

Code:

select jc_standardize ('CCN1CCC(=O)C(\C1)=C/N(C)C.CCOC(=O)CC(N)=O','config:aromatize:d')from dual --- OUTPUT --- CCOC(=O)CC(N)=O.CCN1CCC(=O)C(\C1)=C/N(C)C

The next example is not affected

Code:

select jc_standardize ('NC(=N)CC.CC(=O)CC(=O)C','config:aromatize:d')from dual --- OUTPUT --- CCC(N)=N.CC(=O)CC(C)=O

Is this expected? Is there a way to prevent this from happening?





Thanks


Catherine





PS I am using JChem 3.1.7

Hi,





The SMILES generation code also takes care for the number of nodes in the molecule.


So the order of the fragment molecules in the generated SMILES will depend on number of atoms in the fragment molecule.


This is necessary for uniqueness.





Take the following SMILES:


CCN1CCC(=O)C(\C1)=C/N(C)C.CCOC(=O)CC(N)=O.C


The molecule contains 3 fragments.


The first one is the largest:


CCN1CCC(=O)C(\C1)=C/N(C)C


the second one is smaller:


CCOC(=O)CC(N)=O


and the last one contains only one atom:


C


So the generated SMILES will have just the opposite order:


C.CCOC(=O)CC(N)=O.CCN1CCC(=O)\C(C1)=C/N(C)C





To avoid this, you should generate SMILES for each fragment.





All the best


Andras

Thanks a lot, I understand why it's happening.


Catherine