ROSDAL

The ROSDAL (Representation of Organic Structures Description Arranged Linearly) syntax was developed by S. Welford, J. Barnard, and M.F. Lynch in 1985 for the Beilstein Institute. This line notation was intended to transmit structural information between the user and the Beilstein DIALOG system (Beilstein-Ohlme) during database retrieval queries and structure displays. This exchange of structure information by the ROSDAL ASCII character string is very fast. 

The structure diagram is drawn and the atoms are arbitrarily numbered each atom is assigned a unique number), 

Atomic symbols are usually written directly behind the index of an atom. 

Usually only the indices of the carbon atoms are written, not the symbols hydrogen atoms can have, but do not need, an atom number 

Simplifications are allowed, such as writing alternating bonds as -= 

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In Sections 2,.3.1-2.3.4, only the four most popular line notations, Wiswesser (WLN), ROSDAL. SMILES, and Sybyl (SEN), arc discussed. Whereas WLN is now almost obsolete, SMILES is quite an important representation and is widely used (Figure 2-7). 

The ROSDAL syntax is characterized by a simple coding of a chemical structure using alphanumeric symbols which can easily be learned by a chemist [14]. In the linear structure representation, each atom of the structure is arbitrarily assigned a unique number, except for the hydrogen atoms. Carbon atoms are shown in the notation only by digits. The other types of atoms carry, in addition, their atomic symbol. In order to describe the bonds between atoms, bond symbols are inserted between the atom numbers. Branches are marked and separated from the other parts of the code by commas [15, 16] (Figure 2-9). The ROSDAL linear notation is rmambiguous but not unique. 

Figure 2-9. A possible ROSDAL code for phenylalanine in a) a complete and b) a compressed notation.

ROSDAL is used in the Beilstein-DIALOG system [17] as a data exchange format. The code can represent not only full structures and substructures but also some generic structures. 

A structure drawn by a molecular editor such as ISIS Draw) can be translated by the data conversion program AutoNom into a lUPAC name, and vice versa, by exchanging structure information through a ROSDAL string [18, 19]. 

Compared with WLN and ROSDAL, SMILES uses only six basic rules to convert a structure into a character string (Table 2-2). 

Chemical structures can be transformed into a language for computer representation via line notations such as ROSDAL, SMILES, Sybyl. 

J.M. Barnard, C.J. Jochum, S.M. Wel-ford, ROSDAL A universal structure/ substmcture representation for PC-host communication, in Chemical Structure Information Systems Interfaces Communication and Standards, WA. Warr (Ed.), ACS Symposium Series No. 400, American Chemical Sodety, Washington, DC, 1989, pp. 76- 81. 

Figure 9.7. Various linear notation schemes for chemical representation. Some contain only atom types and connectivity (WLN, ROSDAL, SMILES, SLN) and are chemist-readable. Others are compressed versions of molecule file formats (CHIME) and are meant for computer interpretation.

ROSDAL. Linear notation scheme devised by the Beilstein Institute. It can contain just connection table information, or it may also contain atom coordinates. Several chemical information systems can convert ROSDAL strings to other structure file formats. 

Hie HOSE code represents a linear notation of a chemical structure. Other codes are ROSDAL, SYBYL, and SMILES. The latter code is currently the most popular linear notation. 

Key to the implementation of the substructure searching system is a chemical structure representation known as the ROSDAL string. This is an ASCII character string that conveys sufficient information to convey fully a structure representation, including stereochemistry. A subset of a structure, that is to say, a substructure query, can also be represented by the ROSDAL string. Use of the ROSDAL string provides two immediate advantages for any new substructure... 

One advantage of the ROSDAL string is that it allows for incoming communication from the customer location as an ASCII set of characters. This is precisely the kind of communication that is handled best by telecommunications networks worldwide and is subject to very high speed transmission with low error rates. 

QS QS The basic structure/substructure search command. It is entered before the ROSDAL string (linear representation of the structure) is entered or uploaded from MOLKICK. The system uses the ROSDAL string to identify the created set. 

QS FULL QS F QS FULL QSF Use to extend a TEST search to the entire database without having to upload or reenter the ROSDAL string. Must be used before other QS commands. 

QS < > ID=< > QS ID=amines QS T ID=search1 QS F ID searchl QS R 1500 ID=Smith2 Any QS command can be identified in the system response by adding a name after the ID. The QS command with its options and set identifier can have a maximum of 240 characters. If the ID= feature is not used, the system uses the ROSDAL string as the set Identifier. 

The ROSDAL string is maintained by the Beilstein Institute and is essentially in the pubhc domain, thus it is available for use by software developers and information speciahsts to formulate queries for the Dialog Information Retrieval Service. The advantage of the ROSDAL string is that it contains an ASCII set of characters and can be easily communicated using standard telecommunications networks. In addition, the string is easily generated manually and can be interpreted manually to provide structural display. 

Structural display of ROSDAL code after conversion using MOLKICK (or other chemical drawing software) ... 

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