Simplified Molecular Input Line Entry Specification SMILES

A somewhat dilferent way to define a molecule is as a simplified molecular input line entry specification (SMILES) structure. It is a way of writing a single text string that defines the atoms and connectivity. It does not define the exact bond lengths, and so forth. Valid SMILES structures for ethane are CC, C2, and H3C-CH3. SMILES is used because it is a very convenient way to describe molecular geometry when large databases of compounds must be maintained. There is also a very minimal version for organic molecules called SSMILES. 

SmiLib v2.0 (5) for rapid combinatorial library generation in Simplified Molecular Input Line Entry Specification (SMILES) (6). 

The introduction of the G-SIMS approach, applied by itself or in combination with Fragmentation Pathway Mapping (FPM) and Simplified Molecular Input Line Entry Specification (SMILES), has, however, opened up the possibility of understanding the various fragment pathways and matching SIMS spectra collected under different analytical conditions. 

SMILES (simplified molecular-input line-entry specification) a way of specifying a molecular formula and connectivity, but not the three-dimensional geometry... 

RMSEte Root mean square error for the test set RMSEtr Root mean square error for the training set SMILES Simplified molecular input line entry specification... 

SMILES simplified molecular input line entry specification... 

Rule scripts operate on substances defined in a data file in either SMILES (simplified molecular input line entry specification) or CMP (compound) format. The conventional SMILES notation as developed by Weininger [28] provides a basic description of molecules in terms of two-dimensional chemical graphs. The CMP file format developed with the OASIS system [29] provides separate logical records for information about connectivity, three-dimensional structure, electronic structure from quantum-chemical molecular-orbital computations, as well as physicochemical and experimental toxicological data. 

The use of Simplified Molecular Input Line Entry System (SMILES) as a string representation of chemical structure makes possible much of what has been discussed in earlier chapters of this book. A chemical reaction could be represented as a collection of SMILES, some identified as reactants and some as products. It is possible to define a table to do this, or perhaps use some arrays of character data types, but a syntax extension of standard SMILES allows reaction to be expressed easily. SMIRKS is an extension of SMILES and SMiles ARbitrary Target Specification (SMARTS). It is used to represent chemical transformations. SMIRKS can also be used in a transformation function to combine SMILES reactants to produce SMILES products. 

SMILES Simplified Molecular Input Line Entry Specification... 

SMILES is an acronym for Simplified Molecular Input Line Entry Specification. The algorithm is a universal nomenclature. It was developed in 1988 by Weininger [15]. Several computer programs use now the SMILES algorithm. We briefly show a few most important rules to represent chemical structures by SMILES. We definitely refer to a more detailed version that is given in the Internet [16]. 

Imaging and Measurement and multiple SIMulationS) SHRIMP Sensitive High Resolution Ion Micro Probe SMILES Simplified Molecular Input Line Entry Specification... 

CAS = Chemical Abstracts Service CIP = Cahn-Ingold-Prelog system of labeling stereogenic atoms and bonds MDLI = Molecular Design Limited, Inc. MIF = molecular information file MOLFile = molecule file SEMA = stereo-chemically extended Morgan algorithm SMD = Standard Molecular Data SMILES = simplified molecular input line entry specification. 

SMILES (Simplified Molecular Input Line Entry Systems) is a line notation system based on principles of molecular graph theory for entering and representing molecules and reactions in computer (10-13). It uses a set of simple specification rules to derive a SMILES string for a given molecular structure (or more precisely, a molecular graph). A simplified set of rules is as follows ... 

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