identical UID for different fragments

Hi, I used the recap fragmenter to generated fragments. I found two fragments with slight different structures were assigned with the same UID. 

Accoding to the documentation on this page: http://www.chemaxon.com/jchem/doc/user/fragment_recap.html, the UID identifier should not be the same for different structures, right? 

Quote: 

The following cleavage data is stored in SDF tags (molecule properties) for each fragment, if specified in the configuration:

• unique fragment ID (Uid): the reaction indices with atom maps for each atom, separated by semicolons, in canonincal atom order - that is, two fragment IDs coincide if and only if the fragments represent the same molecular structure with corresponding cleavage data

Here is the smiles of the molecule that was fragmented: 

C[C@@]1(COC(=O)c2cccnc2)[C@@H](CC[C@]3(C)[C@@H]1CCC(=C)[C@H]3\C=C\C4=C\C(=C\c5occc5)\OC4=O)OC(=O)c6cccnc6

the configuration file was attached. The command used was:

fragment -c ../chemaxon/Fragmenter.xml "C[C@@]1(COC(=O)c2cccnc2)[C@@H](CC[C@]3(C)[C@@H]1CCC(=C)[C@H]3\C=C\C4=C\C(=C\c5occc5)\OC4=O)OC(=O)c6cccnc6" > test.cxsmiles

If you look at the fragnment #8 and #12, they have the same UID but the structure are slight different. Is this a bug? 

Hi,

No, it's not a bug, the documentation is not correct.

Unfortunately the "UID" field was not named correctly, as it contains a cut ID. By "unique fragment ID" we mean the cxsmiles and the cut ID. So int this case the "unique fragment ID" of fragment #8 is

C[C@@H]1CCC[C@@H]2[C@](C)(CO)[C@@H](CC[C@@]12C)OC(=O)c1cccnc1 |$_AV:olefin:1;;olefin:1;;;;;;;ester:2;;;;;;;;;;;;;;$|    5:1;;;;;;;;;;;;;;;;;1:2;;;;5:1;;

and the "unique fragment ID" of fragment #12 is

C[C@@H]1CCC[C@@H]2[C@](C)(COC(=O)c3cccnc3)[C@H](O)CC[C@@]12C |$_AV:olefin:1;;olefin:1;;;;;;;;;;;;;;;;;ester:2;;;;$|    5:1;;;;;;;;;;;;;;;;;1:2;;;;5:1;;

These two unique ID-s are different.

We will fix the documentation, and we will rename the "UID" field.

Sorry for the inconvenience.

Zsolt

Thanks for the clarification!