Unique SMILES

A special extension of SMILES is USMILES (sometimes described as Broad SMILES) [23-25]. This Unique SMILES of Daylight is a canonical representation of a structure. This means that the coding is independent of the internal atomic numbering and results always in the same canonical, unambiguous, and unique description of the compound, granted by an algorithm (see Section 2.5.2). 

A SMILES code [22], MDL Molfile [50], or JME s own compact format (one-line representation of a molecule or reaction including the 2D coordinates) of created molecules may be generated. The created SMILES is independent of the way the molecule was drawn (unique SMILES see Section 2.3.3). Extensions to JME developed in cooperation with H. Rzepa and P. Murray-Rust also allow output of molecules in the CML format [60]. 

The structure of a compound including its stereochemistry can be specified with the graphical molecule editor J M E which converts it into a stereochemically unique SMILES string as search item. Figure 10.3-24a shows how I-glutamatc can be input as query,... 

Weininger D, Weininger A, Weininger L (1989) SMILES. 2. Algorithm for generation of unique SMILES notation, J. Chem. Inf. Comput. Sci. 29 97-101. 

WOMBAT2004.1 [10] contains 76165 entries (68 543 unique SMILES [11,12]), covering 3039 series from over 3000 papers and 143 000 achvities for 630 targets. AH biological achvihes are automatically converted to the negahve logjQ of the molar concentrahon. 

To obtain a unique SMILES notation, computer programs such as the Toolkit include the CANGEN algorithm [1] which performs CANonicalization, resulting in unique enumeration of atoms, and then GENerates the unique SMILES notation for the canonical structure. In the case of pyridine, this is notation (III). Any molecular structure entered in the Toolkit is converted automatically into its unique representation. 

The presence of a branch in the structure raises the question of where to start coding. With the SMILES system it does not matter where one starts. A SMILES interpreter will produce the same structure from any valid SMILES coding for a compound. In some circumstances, such as the system s use in databases, it is necessary to have a unique SMILES string for a molecule. Using a set of rules it is possible to uniquify a SMILES string. 

Weininger, D., Weininger, A. and Weininger, J.L. (1989). SMILES. 2. Algorithm for Generation of Unique SMILES Notation. J.Chem.Inf.Comput.ScL, 29, 97-101. 

WOMBAT 2006.1 contains 154 236 entries (136 091 unique SMILES Simplified Molecular Input Line Entry System [17, 18]), covering 6801 series from over 6791 papers with more than 307 700 activities for 1320 unique targets. All biological activities are automatically converted to the — log10 of the molar concentration, regardless of activity type. Numerical values for activity are stored in three fields the additional two fields capture the experimental error, when reported1 . Besides exact numeric values (the vast majority), WOMBAT... 

Weininger D, A Weininger and J L Weirunger 1989 SMILES 2 Algorithm for Generation of Unique SMILES Notation Journal of Chemical Information and Computer Science 29 97-101. 

Table 7. Log P calculation of chlorpromazine (4) by the program CLOGP [253]. Input of the structure in SMILES code cl2cc(Cl)ccc2Sc3ccccc3NlCCCN(C)C unique SMILES code, generated by the program CN(C)CCCN2cIccccclSc3ccc(Cl)cc23 (reproduced from ref. [253] with permission...

An alternative, and highly efficient, structure search uses a hashing function, a computational procedure that takes some data record, such as a connection table or unique SMILES, and converts it to the computer address at which that record is stored." Although hashing functions may lead to more than one record with the same address, the detailed molecular comparisons need to be carried out for just those few molecules." " Because of canonicalization and hashing functions, identity searching is generally very fast. 

The program ONESMILE removes duplicate structures from a sorted list of SMILES. Thus, after the MODSMI transformations, sorting and ONESMILE would be used to produce a file of the unique molecules. Notice that this is possible only because all MODSMI operations produce the unique SMILES with the result that each particular molecular structure is represented by the same SMILES string regardless of the order of the atoms in the structure from which it originated. 

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