heteroCycle Homology

User bf27213fcf

23-09-2009 21:50:48

Hi Technical Support,

I noticed that the Heterocycle template has 53 heterocyclic compounds in it. However when you use the heteroCycle Homology group the library only has 8 heterocyclic compounds in it.  Why? 

Also I am having trouble customizing rgroups as explained in the link below:


I can copy the homology definition from .../jchem.jar/chemaxon/enumeration/homology/user_def_groups/homology.mrv but I can not find /home/{USER_NAME}/.chemaxon/homology/user_def_groups/  to paste it to. I've looked in C:\Users\my user name\chemaxon but there is no homology folder.



ChemAxon 42004978e8

24-09-2009 09:56:26



When you use heteroCycle in searching on the target side (query side will be supported from version 5.3), then any compount satisfying the condition for a heteroCycle should match on the target heteroCycle. (see http://chemaxon.com/marvin/help/calculations/homologygroups.html - at aliphaticHeterocyclyl)

When you bump into a query that doesn't match heterocycle (the new name is aliphaticHeterocyclyl) but fullfils the condition of the group then please let us know it. Of course the other atoms in the query molecule need also to have a corresponding target atom.

If you chose enumeration of this group then the definitions in the jar file are used. Enumeration of homology groups is of course not exhaustive, it's only a representative set. That's why there are only 8 samples.

Regarding the rewriting of the definition:

The exmple for overriding the definition was given for a specific linux scenario we will write a windows one as well. On Windows the chemaxon directory is "chemaxon" (linux/unix it's ".chemaxon").

So you have to copy it to

C:\Users\my user name\chemaxon
there you have to make the subdirectories: "homology/user_def_groups" and "homology/enumeration_only"
They don't exist as default the user can create them if he wishes to override any definition.
Then you can copy the definition to this directory:
/jchem.jar/chemaxon/enumeration/homology/user_def_groups/<USER_DEF_GROUPNAME>.mrv to
C:\Users\my user name\chemaxon\homology\user_def_group\<USER_DEF_GROUPNAME>.mrv

/jchem.jar/chemaxon/enumeration/homology/enumeration_only/<BUILT_IN_GROUP>.mrv to
C:\Users\my user name\chemaxon\homology\user_def_group\<BUILT_IN_GROUP>.mrv

The former case applies for groups which are represented by the definition in the .mrv file BOTH in searching and enumeration. e.g. halogen can be Cl,F,Br, and I
if you don't like it copy it as described and modify it as you wish.

The second case applies for the built in groups (such as heteroCycle), during searching the matching query structures are recognized algorithmically. The definitions (and their overriding) specify only the enumeration.

Hope this helps.