multiatom attachment points and atom numbers

User 870ab5b546

05-04-2013 15:15:53

Consider this structure:


<?xml version="1.0"?>
<cml version="ChemAxon file format v5.10.0, generated by v5.11.5">
<MDocument>
<MChemicalStruct>
<molecule molID="m1">
<atomArray atomID="a1 a2 a3 a4 a5 a6" elementType="C C Pd X P P" sgroupRef="sg1 sg1 0 0 0 0" x2="2.40625 2.40625 0.24062499403953552 2.40625 -1.2113009299968418 -1.2113009299968418" y2="2.117500066757202 0.5775000667572021 1.3956249952316284 1.3475000667572021 2.8475509192680057 -0.05630092880474913"/>
<bondArray>
<bond atomRefs2="a1 a2" order="2"/>
<bond atomRefs2="a4 a3" convention="cxn:coord"/>
<bond atomRefs2="a5 a3" convention="cxn:coord"/>
<bond atomRefs2="a6 a3" convention="cxn:coord"/>
</bondArray>
<molecule id="sg1" role="MulticenterSgroup" molID="m2" atomRefs="a1 a2" center="a4"/>
</molecule>
</MChemicalStruct>
</MDocument>
</cml>

If I ask Marvin to show the atom numbers, it numbers them 1–6, even though there are only five atoms; it numbers the multiatom attachment point as atom number 4, even though it is not an atom.  This behavior needs to change.

ChemAxon a202a732bf

14-05-2013 15:12:08

Hi Bob,

This forum topic got lost somehow in our system as well, sorry about that.


I think I have to give a similar answer as inforum topic



https://www.chemaxon.com/forum/ftopic10396.html&highlight=.


We give index to all our atomic objects like R-atoms, pseudo atoms, list atoms, abbreviation atoms, etc. which are not real chemical elements and multicenters are also represented as atomic objects.


Best regards,


Zsuzsa

User 870ab5b546

14-05-2013 15:23:42










zszabo wrote:

We give index to all our atomic objects like R-atoms, pseudo atoms, list atoms, abbreviation atoms, etc. which are not real chemical elements and multicenters are also represented as atomic objects.


 



I am suggesting that in the Marvin GUI, you omit showing the indices of the multicenters.  All of the other examples you cite represent individual atoms, even though the identity of those atoms may be indeterminate (as in R groups and list atoms) or fictional (as in pseudoatoms).  However, the multicenters are different, in that they add a *new* atom to the structure.  It is very confusing to students (and practicing organic chemists) to see a new "atom" with a new atom index where there should be none.  


If you perceive a need to be able to show the atom indices of multicenters, perhaps you can create an option to show them under View -> Misc -> Atom numbers.  But the default should be *not* to show them.