Formats computer files

SMD format " is a computer file format which is being proposed as a standard for the exchange of chemical structure information between different organisations and computer programs. 

Dalby A, J G Nourse, W D Hounshell, A K I Gushurst, D L Grier, B A Leland and J Laufer 1991 Description of Several Chemical Structure File Formats Used by Computer Programs Developei at Molecular Design Limited, journal of Chemical Information and Computer Science 32 244-255. 

Chem3D can read a wide variety of popular chemical structure files, including Gaussian, MacroModel, MDL, MOPAC, PDB, and SYBYL. Two-dimensional structures imported from ChemDraw or ISIS/Draw are automatically converted to three-dimensional structures. The Chem3D native file format contains both the molecular structure and results of computations. Data can be exported in a variety of chemical-structure formats and graphics files. 

Image Files. Only the physical problem of moving or storing files has been discussed herein. The format in which the data is actually stored or transmitted is another part of the process. There are a number of file formats, many of which are proprietary, developed to suit the needs of a particular computer platform or software appHcation. There has been some effort to standardize to a few file types, but many others are in use. A thorough discussion of graphics file formats is available (20). 

Figure 7.3-1 outlines steps in the scoping process. However, if this information is to be gathered, it should be in a convenient form such as collecting the data as a computer file in a notebook personal computer. The file may be a word processor, a spreadsheet, or a database. If the input is into a word processor such as WordPerfect or Word, it may be in table format. Very similar but Process Scoping Steps... 

B. A., Laufer, J. Description of several chemical structure file formats used by computer programs developed at Molecular Design Limited. J. Chem. Inf. Comput. Sci. 1992, 32, 244-255. 

PDF is a file format that represents a document in a manner independent of the hardware, operating system, and the application software used to create the document. PDF was developed to allow documents to be transferred and shared across computer platforms. This capability allows one to construct a single document under one common format from many different applications. 

The Neutral File format is conqirised of a computer file, records, groips, and fields of data A sanqile file fmmat is shown below. 

The naming convention for the computer file is established directly between the trading partners. However, the preferred file format is as follows ... 

The first task of chemoinformatics is to transform chemical knowledge, such as molecular structures and chemical reactions, into computer-legible digital information. The digital representations of chemical information are the foundation for all chemoin-formatic manipulations in computer. There are many file formats for molecular information to be imported into and exported from computer. Some formats contain more information than others. Usually, intended applications will dictate which format is more suitable. For example, in a quantum chemistry calculation the molecular input file usually includes atomic symbols with three-dimensional (3D) atomic coordinates as the atomic positions, while a molecular dynamics simulation needs, in addition, atom types, bond status, and other relevant information for defining a force field. 

Chemical representation can be rule-based or descriptive. Here we will give a short description of two popular file formats for molecular structures, MOLfiles (9) and SMILES (10-13), to illustrate how molecules are represented in computer. SMILES is a rule-based format while MOLfile is a more descriptive one. 

Another way to get a structure into the computer is to import (read) a molecule file containing the atomic co-ordinates (and perhaps other atomic and molecular information) into your program. Unfortunately, there is no single standard file format that all programs use. However, some of the commonly encountered formats include those of SYBYL MOL2 files and Protein Data Bank (PDB) files. There are also free programs available for download from the World Wide Web that can interconvert the numerous file formats still in use. 

The next type of standard output is the spreadsheet. These file formats use comma-separated ASCII code, but also add calculation information and addressing information for the columns and rows they occupy. The simplest of these are. DIF files, which originated to allow information transfer between VisiCalc worksheets in the Apple II computer and have been retained as a standard format.. WK files are Lotus-1,2,3 formats and. XLS are Microsoft Excel formats that have become spreadsheet standards, allowing transfer of data, calculations, addresses, and macro programs. 

The first part of this section describes how this interpretation is done and which assumptions have been made to retrieve plausible results. The second part will then describe the algorithms used to compute bond characteristics from geometric information, because the PDB file format and its successors include no means to specify hybridization states or bond orders, which are essential for the characterization of properties of small organic ligands. Ligand bond characteristics interpretation is a prerequisite for the step to follow the detailed description of protein-ligand interactions by pharmacophore models. 

Both authors would like to thank Professor J.H.S. Blaxter for the original invitation to write this review and Professor A. J. Southward for his assistance through many revisions. Mr C. Silver generously helped in conversion of the early computer files to IBM format, and redrafted many of the diagrams. Dr Eve Southward helped correct the references and taxonomic details. Last but not least, both authors thank their wives, Svetlana and Muriel, for their support during this arduous undertaking. 

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.

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