Subset rules between homology groups

• alkyl, alkenyl and alkynyl are subsets of carbontree

• carboalicyclyl, carboaryl, heteromonoaryl, heteromonoalicyclyl and fused hetero cyclyl are subsets of cyclyl

• alkalimetal, transitionmetal, othermetal, lanthanides and actinides are subsets of metal.

• all of the above groups are subsets of the "any" homology group

Halogen

Halogen elements: F, Cl, I and Br.
JChem's group name: halogen
alias name: HAL

Protecting

Protecting groups' definition file contains several definitions, each for protecting different functional groups. The protected functional group is defined by the neighborhood of the R-atom. When the R-atom has the same neighborhood as the "protecting" pseudo atom, then the group is replaced by the R-atom.

The conversion processes the group definitions in their order in the file. This means that more specific environments should be placed earlier. For example, a carboxyl protecting group definition should precede an alcohol definition, otherwise the alcohol definitions will be applied instead. Currently they are located in the following order:

1. amino

2. carboxyl

3. alcohol

Currently the system can't handle protecting groups having more than one attachment point, or groups where the heavy atoms of the functional group should be changed by the substitution. The readily available definitions contain amine, carboxyl and hydroxyl protecting groups.

JChem's group name: protecting
alias name: PRT

Some examples with different functional groups protected can be found on Table 2.

Table 2. Protecting group examples

Any group

The union of all other homology groups except unknown and protecting. This union is represented by cyclyl, carbonTree, metal and halogen groups. If the group occurs in a ring then represents a ringSegment homology group.

JChem's group name: any
alias names: XX, anygroup

Modifying the Predefined Homology group definitions

The lib directories of the installed MarvinBeans and JChem contain com.chemaxon-enumeration.jar file. The default homology groups are defined there as user-defined groups and as enumeration-only groups.

Modifying the Predefined 'Enumeration-only' groupsDirectory chemaxon/enumeration/homology/enumeration_only in the com.chemaxon-enumeration.jar file. These groups are represented by these definitions during enumeration only.Modifying the new User-defined groupsDirectory chemaxon/enumeration/homology/user_def_groups in the com.chemaxon-enumeration.jar file. These groups are represented by these definitions during search and enumeration as well.

Location of user-defined homology group definition files

The default location of chemaxon_home directory of the user on different platforms:

• Windows: %USERPROFILE%\chemaxon\ (in other words ..\Users\<USERNAME>\chemaxon\)

• Unix/Linux: ~/.chemaxon/

Location of "User-defined" (for search and enumeration) user-defined homology group definition files: chemaxon_home/homology/user_def_groups/

Location of "Enumeration-only" user-defined homology group definition files: chemaxon_home/homology/enumeration_only/

Note: Create the above two directories if they do not exist.

1. Defining NEW User-defined Homology (or Protecting) groups

1. Draw the desired group definition in MarvinSketch and save as mrv; the name of the new group should be specified by the name of the file; the name of the file must be in lower case;
   See example nucleobase.mrv below:

   

2. copy the mrv file into chemaxon_home/homology/user_def_groups/.

The files of enumeration-only type User-defined groups should be placed into the directory chemaxon_home/homology/enumeration_only/.

2. Modifying the Predefined (User-defined) Homology (or Protecting) groups

Modifying these files will affect searching/enumeration in case of User-defined groups and the enumeration in case of the Predefined groups.
The modified definition or the newly added group can also be dependent on the neighborhood (context-sensitive) as in the case of Protecting groups.
The modification of these definitions can be executed:

• the same way as described above for the creation of the NEW User-defined Homology (or Protecting) groups, but the name of the mrv file must be the same as the built-in file name within com.chemaxon-enumeration.jar; copy the mrv file into c hemaxon_home/homology/user_def_groups/

• or by modifying the existing default file from com.chemaxon-enumeration.jar

  1. Copy protecting group definition to the user's chemaxon library: e.g. from .../com.chemaxon-enumeration.jar/chemaxon/enumeration/homology/user_def_groups/protecting.mrv to chemaxon_home/homology/user_def_groups/

  2. Open the newly copied file in the user's directory with MarvinSketch.

  3. A dialog appears asking the index of molecule to open. Enter 1 because this contains the amino protecting group definition. If the proper molecule number is not known, all the definitions can be displayed using MarvinView.

  4. Overwrite the structures, e.g. delete the FMOC group, see Table 4. The new definition will be used in searching and enumeration, see Table 4.

The files of enumeration-only type user-defined groups must be placed into the directory chemaxon_home /homology/enumeration_only/.

If you would like to have different definitions for searching and enumeration of a user-defined group, then a separate file should be specified under the same file name in the "enumeration_only" dictionary as well. In this case the content of the "user_def_groups" will be used during searching and the content of the "enumeration_only" for enumeration.

If a definition is modified it comes into effect immediately, however the addition of a new group requires a restart of the Java Virtual Machine.

Table 4. Modifying amino protecting group definitions.