As already said, MOLGEN has as input
Once you have entered the chemical formula, it is checked if molecular graphs with this sequence of numbers and valences of atoms can exist. If this is not the case you will get a corresponding error message.
The next step is the input of prescribed and of forbidden substructures. We would like in particular to outline that there are three types of substructures that can be entered optionally, namely:
The mathematical concept behind MOLGEN is a mixture of combinatorial and algebraic methods. In particular orderly generation is intensively used, details are given in . Its application in molecular structure elucidation stands or falls with the input. The main emphasis should lie on the macroatoms, since a big set of prescribed and nonoverlapping substructures reduces the problem of generation considerably, while the goodlist and the badlist can be applied only after the generation.
The macroatoms in fact shrink to a point in the eyes of the generator. For example, if you use the skeleton of the dioxin molecule (see fig. 1), say, as a macro-atom, it shows up as a single point in the generated graphs, which is a single graph in this particular example, and so, here the generator needs to construct one graph only, instead of 22. Of course, the full set of isomers is obtained afterwards by the so-called expansion of the macroatoms, including an isomorphism check. But this separation of generation and expansions splits the total problem into two pieces, which increases the reach considerably.
The aim of structure elucidation is to obtain the complete set of molecular graphs that correspond to given data, and this set of candidates should be as small as possible, which means that we have to interpret the data carefully to get - first of all - the biggest possible set of macroatoms. An example is given below.
Table 1 gives an impression of what happens if only the chemical formula is entered. The reader immediately sees how complex the problem is and that he should try to find further conditions very intensively.
Table 1: Each table entry contains the number of isomers and the CPU-time in seconds. The row index denotes the number of C-atoms, the column index the number of H-atoms. The times were computed on a HP-9000/705, which is approximately as fast as a 486DX2/66 PC running OS/2.
The table 1 shows that it is very important to impose as many
restrictions as possible in order to make the generator construct as few
as possible molecular graphs. Therefore, besides the restrictions by
giving prescribed and forbidden substructures, you can also enter
conditions on the size of rings, where you may in fact enter an interval, say
from 4 to 6 in order to exclude, say, 3-rings in a molecule with the
gross formula Moreover, you may also restrict the multiplicity of
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