''smile is sadaqah''
The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of chemical molecules using short ASCII strings. SMILES strings can be imported by most molecule editors for conversion back into two-dimensionalthree-dimensional models of the molecules. drawings or
The original SMILES specification was developed by Arthur Weininger and David Weininger in the late 1980s. It has since been modified and extended by others, most notably by Daylight Chemical Information Systems Inc. In 2007, an open standard called "OpenSMILES" was developed by the Blue Obelisk open-source chemistry community. Other 'linear' notations include the Wiswesser Line Notation (WLN), ROSDAL and SLN (Tripos Inc).
In July 2006, the IUPAC introduced the InChI as a standard for formula representation. SMILES is generally considered to have the advantage of being slightly more human-readable than InChI; it also has a wide base of software support with extensive theoretical (e.g., graph theory) backing.
ADVANTAGE:
SMILES requires no special constructs, nor any special data type. Every character in it is part of the original specification of the American Standard Code for Information Interchange. A SMILES structure can reside in a database as a "varying character" or "string" data type. Moreover, any plain-text editor can produce a SMILES structure.
MORE ABOUT SMILE:
SMILES contains the same information as might be found in an extended connection table. The primary reason SMILES is more useful than a connection table is that it is a linguistic construct, rather than a computer data structure. SMILES is a true language, albeit with a simple vocabulary (atom and bond symbols) and only a few grammar rules. SMILES representations of structure can in turn be used as "words" in the vocabulary of other languages designed for storage of chemical information (information about chemicals) and chemical intelligence (information about chemistry).
Part of the power of SMILES is that unique SMILES exist. With standard SMILES, the name of a molecule is synonymous with its structure; with unique SMILES, the name is universal. Anyone in the world who uses unique SMILES to name a molecule will choose the exact same name.
One other important property of SMILES is that it is quite compact compared to most other methods of representing structure. A typical SMILES will take 50% to 70% less space than an equivalent connection table, even binary connection tables. For example, a database of 23,137 structures, with an average of 20 atoms per structure, uses only 1.6 bytes per atom when represented with SMILES. In addition, ordinary compression of SMILES is extremely effective. The same database cited above was reduced to 27% of its original size by Ziv-Lempel compression (i.e. 0.42 bytes per atom).
These properties open many doors to the chemical information programmer. Examples of uses for SMILES are:
- Keys for database access
- Mechanism for researchers to exchange chemical information
- Entry system for chemical data
- Part of languages for artificial intelligence or expert systems in chemistry
SMILESTM as a simple yet comprehensive chemical language in which molecules and reactions can be specified using ASCII characters representing atom and bond symbols. SMILESTM contains the same information as is found in an extended connection table but with several advantages. A SMILESTM string is human understandable, very compact, and if canonicalized represents a unique string that can be used as a universal identifier for a specific chemical structure. In addition, a chemically correct and comprehensible depiction can be made from any SMILESTM string symbolizing either a molecule or reaction.
SMILESTM development was initiated by David Weininger in the late 1980s using the concept of a graph with nodes as atoms and edges as bonds to represent a molecule. Parentheses are used to indicate branching points and numeric labels designate ring connection points. The basic SMILESTM grammar also includes as well as isotopic information, configuration about double bonds, and chirality leading to what is known as isomeric SMILESTM.
SMILESTM development was initiated by David Weininger in the late 1980s using the concept of a graph with nodes as atoms and edges as bonds to represent a molecule. Parentheses are used to indicate branching points and numeric labels designate ring connection points. The basic SMILESTM grammar also includes as well as isotopic information, configuration about double bonds, and chirality leading to what is known as isomeric SMILESTM.
Some simple SMILESTM examples:
Ethanol CCO Acetic acid CC(=O)O Cyclohexane C1CCCCC1 Pyridine c1cnccc1 Trans-2-butene C/C=C/C L-alanine N[C@@H](C)C(=O)O Sodium chloride [Na+].[Cl-] Displacement reaction C=CCBr>>C=CCI
Since its inception, SMILESTM has been modified and expanded by Daylight to include not only new features but two additional chemical languages: SMARTS®, an expansion of SMILESTM allowing specification of molecular patterns and properties for substructure searching with varying levels of specificity, and SMIRKS®, a restricted version of reaction SMARTS® involving changes in atom-bond patterns that define generic reactions.
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