SMILES atomic symbol

Stereochemistry can also be expressed in the SMILES notation [113]. Depending on the clockwise or anti-clockwise ordering of the atoms, the stereocenter is specified in the SMILES code with or respectively Figure 2-78). The atoms around this stereocenter are then assigned by the sequence of the atom symbols following the identifier or (g). This means that, reading the SMILES code from the left, the three atoms behind the identifiers ( ) or ( )( )) describe the stereochemistry of the stereocenter. The sequence of these three atoms is dependent only on the order of writing, and independent of the priorities of the atoms. 

SMILES is based on die natural grammer of atomic symbols and symbols for bonds. The most important rules are as follows ... 

The Simplified Molecular Input Line Entry System (SMILES) is frequently used for computer-aided evaluation of molecular structures [1-3]. SMILES is widely accepted and computationally efficient because SMILES uses atomic symbols and a set of intuitive rules. Before presenting examples, the basic rules needed to enter molecular structures as SMILES notation are given. 

SMILES (Simplified Molecular Input Line Entry System) was invented by Weininger5 to facilitate the representation and manipulation of molecular structures using computers. It uses standard atomic symbols to represent atoms and the symbols - for single bond, = for double bond, and for triple bond. Hydrogen atoms can be represented explicitly but are almost always represented implicitly using normal conventions of valence bond theory. Single bonds need not be explicitly written. For example, propane is C-C-C or simply CCC. Methylamine is CN, and C N is hydrogen cyanide. Propene is C=CC. For more complex structures with branched bonds, parentheses are used. For example, CC(C)0 is isopropyl alcohol, whereas CCCO is propanol. 

Benzene is typically thought of as a combination of two equivalent resonance structures. These could be written as the SMILES C1=C-C=C-C=C1 and C1-C=C-C=C-C=1. In order to have just one representation for benzene and other aromatic systems, SMILES handles these aromatic systems specially, treating the atoms in an aromatic ring as a special aromatic type and the bonds as a special aromatic type. The lowercase symbol is used to denote an aromatic atom in SMILES and SMARTS. The SMILES for benzene then becomes clcccccl. A bond between aromatic atoms is an aromatic bond, unless otherwise spelled out. For example, biphenyl can be written as clcccccl-clcccccl. 

Each row in the coordtest table represents a molecule. The smiles column is a string of atom symbols and bonds and the coord column is an array of atom coordinates. How is it possible to keep the ordering of atoms in the smiles string in sync with the ordering of atom coordinates in the coord array When the coordinates are initially entered from the external source, they are likely to be in a common chemical file format. The program that converts from that file format to SMILES would have to output the atom coordinates in the same order as the atoms in the SMILES. 

It would be possible to create tables using columns to store the atomic symbols and bond information found in molecular structure files, reflecting the column style format of the file itself. Instead, a SMILES representation of this valence bond information is preferred. SMILES is a compact text string containing the same information as the columns of atom symbols and bonds. It can also be used directly in the search functions described in earlier chapters. It is desirable to parse the molecular properties in molecular structure files in order to store them in data columns for possible searching... 

It may seem that some information will have been lost if the original molfile is discarded. For example, the list of atomic symbols and bonds is not stored directly in the vla4.structure table. The cansmiles string, however, does contain this information. It may be necessary for some purposes to extract this information, for example, when an external program does not read SMILES but instead requires a list of atomic symbols and bonds. This is discussed more in the next section. A connection table can... 

These simple rules allow very rapid encoding of most chemical structures and need only a few simple additions to cope with other atoms, charges, isomers, etc. Specification of atoms not in the organic subset, for example, is coded by use of an atomic symbol within square brackets. An extensive description of the SMILES system is given by Weininger and Weininger (1990). 

The atom symbols in the SMILES string are numbered sequentially and a connection table is constructed which indicates which atoms are bonded to each other. 

Bonds Single bonds are omitted double, triple, and aromatic bonds are indicated by the symbols " = " and " ", respectively. In contrast to SMILES, aromaticity is not an atomic property,... 

Another approach for representing 2D chemical structures is the linear notation. Linear notations are strings that represent the 2D structure as a more or less complex set of characters and symbols. Characters represent the atoms in a linear manner, whereas symbols are nsed to describe information about the connectivity [3]. The most commonly nsed notations are the Wiswesser line notation (WLN) and the simpUfled molecnlar inpnt line entry specihcation (SMILES) [2]. The WLN, invented by William J. Wiswesser in the 1949, was the hrst line notation capable of precisely describing complex molecnles [4]. It consists of a series of uppercase characters (A-Z), numerals (0-9), the ampersand ( ), the hyphen (-), the oblique stroke (/), and a blank space. 

Simplified Molecular Input Line Entry Specification (SMILES) is a simplistic line notation for describing chemical structnres as a set of characters, numbers, and symbols that represent atoms, bonds, and stereochemistry. 

Although SMILES is an entirely equivalent way of storing a connection table of atoms and bonds, it is sometimes desirable to create a traditional connection table, for example, when an external program requires it. The extension functions smiles to symbols and smiles to bonds accept a SMILES string and produce an array of either symbols or bonds. These are discussed in a later section of this chapter. Several implementations of these functions are shown in the Appendix. 

In a molecular structure file, an atom record typically contains all of the information about that atom the atomic number or symbol, the charge, coordinates, etc. When such a file is parsed into a SMILES string and an array of coordinates, it is important to be able to associate the proper coordinate with the proper atom. The use of canonical SMILES ensures this. Because canonical SMILES defines a unique order of the atoms in a molecule, that order is used to store the coordinates. Later sections of this chapter will discuss ways in which atomic coordinates might be stored in columns of a table. 

Single, double, triple, and aromatic bonds are represented by the symbols —, =,, and However, the bond type may be omitted when suggestive, and sp2-hybridized bonded atoms can be written in lower case letters. So C=C—C=C means 1,3-butadiene, which is equivalent to cccc. Branches are indicated by parentheses, e.g., CC(C)C(=0)0 is isobutyric acid. To specify rings, the atom that closes the ring is numbered and specified, as ClCCCCCl for cyclohexane and clcc2ccccc2ccl for naphthalene. The SMILES notation can be used in chemical structure drawing programs for quick input of a structure by the skilled user. 

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