Pseudo Atom¶
- Checker searches for pseudo atoms in the molecule. A list of excluded atom labels can be specified, the checker will not find (and fix) pseudo atoms with labels that are indicated in this list.
-
Fixer offers:
-
converting to abbreviated group if the name is in the abbreviated group list (e.g., Et for ethyl) * (
pseudotogroup); -
converting to carbon atom (
converttocarbon); -
deleting atom (
removeatom).
-
Example :
Pseudo Atom Checker (pseudoatom) |
Warning: | Fix | ||
|---|---|---|---|---|
Convert Pseudo Atom to Group (pseudotogroup) |
Convert to Carbon (converttocarbon) |
Delete Atom (removeatom) |
||
| Detect Pseudo Atom |  ex_pseudo_ch |
 not available |
 ex_pseudo_f |
 ex_pseudo_f |
| Detect Pseudo Atom |  ex_pseudo_ch |
 ex_pseudo_f |
 ex_pseudo_f |
 ex_pseudo_f |
| Detect Pseudo Atom with excluded list(pseudoatom:excluded='PG') |  |
 |
 |
 |
*Note** : User defined abbreviated groupsare also available to be applied as recognizable abbreviated group set.