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Tautomer SMILES

The transformation used above to enumerate tautomers would lead to identical products when applied to symmetrically substituted pyrazoles. The set of structures generated in the enumeration process is converted to a sorted list of canonical SMILES [23] from which duplicates are easily eliminated. Structures registered in alternative tautomeric forms are converted to identical lists of SMILES that can each be represented by their common first member. This effectively extends the definition of canonical SMILES to cover an ensemble of tautomeric forms and makes it possible to check for duplicate structures without having to register multiple forms [16, 26]. [Pg.281]

While the several resonance forms for aromatic systems are neatly solved using aromatic atom types in SMILES, the issue of multiple tautomers cannot be handled as neatly. This is a good thing. After all, it is quite possible to distinguish two different tautomers experimentally and measure different properties that may need to be stored in a database. On the other hand, it is not possible to distinguish two different resonance forms experimentally. Every equivalent resonance form for a structure ought to be considered to be the same structure. Resonance is simply a theoretical concept. [Pg.77]

It is sometimes necessary to be able to recognize one structure as a tautomer of another. This could be because a user entered one tautomer and expects to find data for other tautomers, especially in cases where the tautomers are in approximately equal abundance under normal laboratory conditions. It may even be that data is stored for a compound before knowing to which tautomer the data refers. In many cases, experimental data will be measured for a mixture of tautomers, yet it will be assigned to one tautomer. There is no simple solution for handing tautomers in SMILES or in a relational database. If two or more structures are tautomers of each other, this might be recorded in another table related to the table containing the SMILES. [Pg.78]

Finally, there are algorithms available for simply recognizing when two structures are tautomers. This is sufficient to locate all isomers in a database. In general, two structures are considered to be structural isomers if they share the same molecular formula. Tautomers are a special type of structural isomer in which the connectivity of the atoms, as well as the molecular formula, is the same. For example, butane (smiles CCCC) and isobutane (smiles CC(C)C) are strucural isomers but not tautomers. Butyraldehyde (smiles CCCC=0) and but-l-en-l-ol (smiles CCC=CO) are structural isomers as well as tautomers. A direct comparison of the molecular formulae readily shows the structural isomerism. There is a text graph representation that can allow easy detection of tautomers. [Pg.78]

There is some overhead in the use of indexes, constraints, triggers, etc. as discussed here. The overhead is incurred when rows are inserted or updated in the table. However, the value of this approach is that the data in the table are well validated and can be searched more reliably and efficiently. Direct lookups of canonical or stereo SMILES is simple and quick because of the index on these columns. Using the fingerprint column speeds up substructure search. Tautomers can be readily selected using the column of simple graphs. [Pg.162]

Figure 2.1 Tautomers and SMILES. Each tautomer is represented by a different SMILES string. This type of difference can lead to inconsistencies between programs. Figure 2.1 Tautomers and SMILES. Each tautomer is represented by a different SMILES string. This type of difference can lead to inconsistencies between programs.
Definition of unambiguous business rules is not always straightforward and in these situations it is useful to generate an ensemble of equivalent structures.If rules to rank the structures in the ensemble can be defined, then it becomes possible to select one of these to represent the ensemble. For example, enumeration of tautomers using Leatherface creates a sorted list of canonical SMILES, the first of which is used to represent the ensemble. This effectively extends the concept of canonicalisation to an ensemble of structures, and the term canonical tautomer may be encountered in the literature. ... [Pg.177]


See other pages where Tautomer SMILES is mentioned: [Pg.279]    [Pg.64]    [Pg.86]    [Pg.78]    [Pg.160]    [Pg.49]    [Pg.40]    [Pg.21]    [Pg.171]    [Pg.371]   
See also in sourсe #XX -- [ Pg.77 , Pg.159 ]




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