electron-flow arrow ending at shortcut group

User 870ab5b546

12-05-2016 15:38:50

It should be possible to draw an electron-flow arrow that ends at a shortcut group, as in the following MRV (that I produced in MarvinSketch). This is an important deficiency in Marvin JS.


<?xml version="1.0" encoding="MacRoman"?>
<cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com/marvin/schema/mrvSchema_14_12_01.xsd" version="ChemAxon file format v14.12.01, generated by v15.11.23.0">
<MDocument>
<MChemicalStruct>
<molecule molID="m1">
<atomArray atomID="a1 a2" elementType="C R" sgroupRef="0 sg1" x2="-7.277777671813965 -5.737777671813965" y2="2.6666667461395264 2.6666667461395264"/>
<bondArray>
<bond id="b1" atomRefs2="a1 a2" order="1"/>
</bondArray>
<molecule id="sg1" role="SuperatomSgroup" title="OTs" leftName="TsO" molID="m2">
<atomArray atomID="a3 a4 a5 a6 a7 a8 a9 a10 a11 a12 a13" elementType="O C C C C C C S C O O" attachmentPoint="1 0 0 0 0 0 0 0 0 0 0" sgroupAttachmentPoint="1 0 0 0 0 0 0 0 0 0 0" x2="-8.405135915470026 -8.405135915470037 -9.738815037298073 -9.738815037298071 -8.405135915470034 -7.071456793641999 -7.0714567936420005 -8.40513591547003 -8.405135915470039 -6.865135915470029 -9.94513591547003" y2="6.726666746139527 0.5666667461395258 1.3366667461395294 2.8766667461395294 3.646666746139527 2.8766667461395246 1.3366667461395245 5.186666746139527 -0.9733332538604751 5.186666746139524 5.18666674613953"/>
<bondArray>
<bond id="b2" atomRefs2="a11 a4" order="1"/>
<bond id="b3" atomRefs2="a4 a5" order="2"/>
<bond id="b4" atomRefs2="a5 a6" order="1"/>
<bond id="b5" atomRefs2="a6 a7" order="2"/>
<bond id="b6" atomRefs2="a7 a8" order="1"/>
<bond id="b7" atomRefs2="a8 a9" order="2"/>
<bond id="b8" atomRefs2="a4 a9" order="1"/>
<bond id="b9" atomRefs2="a7 a10" order="1"/>
<bond id="b10" atomRefs2="a10 a3" order="1"/>
<bond id="b11" atomRefs2="a10 a12" order="2"/>
<bond id="b12" atomRefs2="a10 a13" order="2"/>
</bondArray>
<AttachmentPointArray>
<attachmentPoint atom="a3" order="1" bond="b1"/>
</AttachmentPointArray>
</molecule>
</molecule>
</MChemicalStruct>
<MEFlow id="o2" arcAngle="254.77468199999998" headSkip="0.38" headLength="0.5" headWidth="0.4" tailSkip="0.38" baseElectronContainerIndex="-1" baseElectronIndexInContainer="0">
<MAtomSetPoint atomRefs="m1.a1 m1.a2"/>
<MAtomSetPoint atomRefs="m1.a2"/>
</MEFlow>
</MDocument>
</cml>

ChemAxon f052bdfe3c

20-05-2016 11:11:56

The reason while we did not implemented electron-flow arrow that ends at a shortcut group is that it can lead to some confusion: What should happen if the user ungroups or expands the abbreviated group?


Since that case the electronflow arrow would point to the first attachment point atom to the group, which will not be correct in most of the cases. Or we could just simple eliminate the arrow in these cases, but I am not sure that you would prefer this. Which behaviour would you expect?  I am looking forward to hear your opinion.


 


Best regards,


Efi

User 870ab5b546

20-05-2016 13:18:24

I can't think of a case where the electron-flow arrow would *not* point to the attachment point, if there was only one attachment point. Can you give me an example where it would not have the expected behavior?

User 870ab5b546

02-06-2016 17:24:41

Does your lack of response indicate that you can't think of such a case? I can't.

ChemAxon 5693b0ec15

15-06-2016 09:28:41

Dear Bob,


Of course, when there is an attachment point on an abbreviated group bond formation is expected. However, there are no strict rules how to create abbreviated group or how to assign attachment points to them in Marvin. That is why we think that this feature would create more confusion than benefit. For example many carbocations i.e. tBu+ can be both Lewis and Bronsted acids, can be involved both in substitution and elimination reactions.  Reactions involving rearrangement can make another example.


Best regards,


Nikolett Mihala

User 870ab5b546

15-06-2016 17:44:15

Although it is true that tBu+ can be both a Lewis acid and a Brønsted acid, if anyone points an electron-flow arrow to tBu+, they cannot possibly mean that the arrow points to an H atom of the tBu+ group.


As for attachment points, you can restrict electron-flow arrows to point only to shortcut groups that have exactly one attachment point.


I don't understand your concern about shortcut groups being involved in substitutions, eliminations, and rearrangements. Can you provide specific examples of how an electron-flow arrow pointing to a shortcut group could possibly be interpreted ambiguously?


We have had this feature in MarvinSketch for ages and ages, and we have never encountered any problems. I don't understand why it should suddenly be a problem in MarvinJS.

ChemAxon 76c88f5366

01-07-2016 14:33:57

Hi Bob,


We are working on some new features currently, but when this question will be actual, we will consider your point of view. Thank you for your feedback, it is always valuable for us.


Best regards,
Eszter 

User 870ab5b546

27-07-2016 20:10:02

If you look at the example I gave in the first post in this thread, there is a bond between a shortcut group and an atom, and the electron-flow arrow points from the bond to the shortcut group. This is the most common situation in which we are likely to find electron-flow arrows pointing to shortcut groups, and it is the one we need the most.

ChemAxon 76c88f5366

28-07-2016 09:43:38

Thank you, for the additional information. This helps us to explore all of the possible use cases.