Daylight Smiles

Other structure-encoding schemas are developed by software vendors and academia such as Daylight Smiles, CambridgeSoft ChemDraw Exchange (CDX), and Chemical Markup Language (CML), and they all have advantages and disadvantages. The MDL CT File Format is the only one that is supported by almost all chemical informatics software vendors. 

SMILES has seen many extensions since 1988. The present definition, with examples, can be found at http f/w m>.daylight.com/dayhtml/smiles/index.html. 

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). 

The compact textual coding requires no graphical input and additionally permits a fast transmission. These are important advantages of using SMILES in chemical applications via the Internet and in online services. SMILES is also used for the input of structures in the Daylight Toolkit [22]. 

SMILES. smi SMILES the most widely used Unear code and file format nmm.daylight.com 20, 21... 

Daylight Chemical Information Systems Inc. SMILES home page. http //www.daylight.com/dayhtml/ smiles/index.html. 

SMILES Manual, Daylight Chemical Information Systems Inc., 27401 Los Altos - Suite 360, Mission Viejo, CA 92691. 

Daylight has extended SMILES rules to accommodate general descriptions of molecular patterns and chemical reactions (13). These SMILES extensions are called SMARTS and SMIRKS. SMARTS is a language for describing molecular patterns while SMIRKS defines rules for chemical reaction transformations. 

The night fled, the lamp burned out, and chinks of daylight came to smile through chinks in the drapes. My knee hurt. The rest of me felt much better. 

Back out in the crisp reality of daylight, still in her crouch, she felt a twinge of fear. But she looked at her horse and Bailador was as calm as ever. She smiled at the animal, reassured. The fear belonged to neither of them. 

One of the common character formats or chemical nomenclature of a valence model which is recognizable by a number of 2D-structure drawing programs is SMILES (Weininger, 1988). A full SMILES language tutorial can be accessed at http // www.daylight.com/dayhtml/smiles/. The general rules for biochemical compounds are as follows ... 

Imports data in SD file format, MDL molfile format, SMILES text strings, Daylight Chemical Information Systems Inc. s Thor Data Tree (TDT) format, and Tripos Inc. s Sybyl Line Notation (SLN) format. 

In order to calculate a physicochemical property, the structure of a molecule must be entered in some manner into an algorithm. Chemical structure notations for input of molecules into calculation software are described in Chapter 2, Section VII and may be considered as either being a 2D string, a 2D representation of the structure, or (very occasionally) a 3D representation of the structure. Of this variety of methods, the simplicity and elegance of the 2D linear molecular representation known as the Simplified Molecular Line Entry System (SMILES) stands out. Many of the packages that calculate physicochemical descriptors use the SMILES chemical notation system, or some variant of it, as the means of structure input. The use of SMILES is well described in Chapter 2, Section VII.B, and by Weininger (1988). There is also an excellent tutorial on the use of SMILES at www.daylight.com/dayhtml/smiles/smiles-intro.html. 

The name SMILES comes from Simplified Molecular Input Line Entry System (Weininger 1988). It is a linear format for description of molecules and reactions developed by Daylight Chemical Information Systems, Inc. SMILES was designed with the intention to be both human readable and writable, which makes it unique among the other chemical formats described in this chapter. 

SMILES is a line notation developed in the 1980s and since modified and extended by others, particularly Daylight Chemical Information Systems, Inc. 

Figure 6.12. Examples of SMILES notations for two compounds obtained using CACTVS and Daylight.

SMARTS, a language created for matching substructures of chemical files created by Daylight Chemical Information Systems, Inc. alongside the SMILES format. 

Previously, the calculation of logP could be performed from SMILES strings at the Daylight site (http //www.daylight. com/daycgi/clogp), however, there was no facility for calculation based on molecular structure. 

Depict This service accepts a SMILES string as Input and returns an HTML page with an embedded image. Unfortunately, there Is no control on the output style and image size. http //www. daylight, com/daycgi/depict... 

SMILES is a trademark and SMARTS is a registered trademark of Daylight Chemical Information Systems Inc., Aliso Viejo, California. 

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