B(OH)2 Leftname not working..and how to point bond to B?

User 9d72be7cd4

05-05-2007 01:47:39

Created a abbrevgroup for B(OH)2





I can add it to a molecule, it connect correctly, expands and contract correctly, but leftname function is not working when I rotate it.





Here is the entry in mydefault.abbrevgroup





Code:
B(OH)2   OBO   2   leftname=(OH)2B






I've also tried :





Code:
B(OH)2   B(O)O   1   leftname=(OH)2B






and:


Code:
B(OH)2   B(O)O   1   1   leftname=(OH)2B






What is the second number for anyway?





Secondly, the bond points to the center of the group label, making the bond disappear in certain orientations. (See Attachment)





All other leftname / rightname groups function as intended.





Any ideas on where to look for a problem? Or is my smiles or abbrevgroup entry somehow munged?





Using MarvinBeans 4.1.7, all this done in MarvinSketch





Thanks for any help!





NCM


FSCI

User 9d72be7cd4

08-05-2007 17:13:17

Anyone move versed in Abbrevgroups want to weigh in?





I'm not seeing why this is not working - I can add this custom abbrevgroup to a molecule by typing it, but it doesn't behave like other original abbrevgroups.





Am I forming my smile string wrong?





Any hints appreciated!





This is my last major hurdle to making MarvinSketch mainstream in our organization as we utilize LOTS of groups we'd like to add to the abbrevgroup file.





Hard to understand why the leftname/rightname and visual attachment to the B in B(OH)2 is not working with this custom abbrevgroup - despite trying several different smiles strings.





Thanks for any further insight,





NCM


FSCI

User 9d72be7cd4

09-05-2007 20:32:16

SOLVED - Was a Typo





used leftname instead of leftName (notice the cap "N")





Interesting that the letter of the label the bond points to is affected by the leftName function working. It now points correctly to the B just by fixing leftname to leftName





NCM


FSCI

User 870ab5b546

13-05-2007 00:36:01

A second number is used when a group has two attachment points, like Ala.

ChemAxon 7c2d26e5cf

14-05-2007 10:00:06

Bob's answer is correct. Thanks Bob.


You can read more about this format in the documentation: ChemAxon SMILES Abbreviated Group