- 1.7
- 1.6
- 1.5
- Beta
- Examples (for 1.6a)
- Misc
In a forcefield with many defined types, more than one type may match an atom in a molecule. In order to best assign types to atoms, Aten scores each type description according to the number of terms defined within it, one point for each term satisfied. Once a matching type for an atom is located in the forcefield it is assigned to that atom, but the search for a better-scoring type continues. If a match with a higher score is found it replaces the previously-assigned type. If a match with the same score is found, the previous type is not replaced.
When a type description is tested for a given atom, it accumulates points for each term in the description that is satisfied by the environment of the atom. As soon as a term is found that is not satisfied, however, the score is reset to -1 and the match will fail. All terms in a type description must be satisfied in order for the type to be assigned to an atom.
A type description containing no terms has a maximum score of 1 (coming from a match of the element type). Hence:
99 Cgen C "" # Generic carbon
matches any carbon in any system, but will be replaced fairly easily by other types since it has such a low score.
For a type in which all terms are matched successfully, one point is scored for each individual term. All of the following types have a potential maximum score of 3 (don't forget, one point comes from matching the element):
100 C1 C "nbonds=2,linear" # Carbon A 101 C2 C "-C,-C" # Carbon B 102 C3 C "-C(n=2)" # Carbon C 102 C4 C "=C" # Carbon D
Moreover, they all potentially match the same atom (for example the central carbon in 1,2-propadiene). Since they have the same score, the first type C1 will match and persist over the other three, since only types with higher (not equivalent) scores can replace it.