Chemical file formats

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. 

XYZ is a chemical file format that describes the geometry of the molecule [56], This format is utilized in importing and exporting coordinates for chemical stme-tures computationally. The imits itsed in XYZ format ate ustrally angstroms. ... 

As many different file formats have been developed since the early 1970s, the need for a standard chemical structure format has been increasingly felt. Various attempts have been made by different groups of the chemical commimity to define and push such a format, but none has achieved unanimous acceptance. 

The different internal and external file formats make it necessary to have programs which convert one format into another. One of the first conversion programs for chemical structure information was Babel (around 1992). It supports almost 50 data formats for input and output of chemical structure information [61]. CLIFF is another file format converter based on the CACTVS technology and which supports nearly the same number of file formats [29]. In contrast to Babel, the program is more comprehensive it is able to convert chemical reaction information, and can calculate missing atom coordinates [29]. 

Table 2-5. The most important File formats for exchange of chemical structure information.

Tabic 2-6 gives an overview on the most common file formats for chemical structure information and their respective possibilities of representing or coding the constitution, the configuration, i.c., the stereochemistry, and the 3D structure or conformation (see also Sections 2..3 and 2.4). Except for the Z-matrix, all the other file formats in Table 2-6 which are able to code 3D structure information arc using Cartesian coordinates to represent a compound in 3D space. 

The most important feature of editing software is the option to save the structure in standard file formats which contain information about the structure (e,g., Mol-filc. PDB-filc). Most of these file formats arc ASCII text files (which can be viewed in simple text editors) and cover international standardized and normalized specifications of the molecule, such as atom and bond types or connectivities (CT) (see Section 2,4). Thus, with these files, the structure can be exchanged between different programs. Furthermore, they can seiwe as input files to other chemical software, e.g, to calculate 3D structures or molecular properties. 

This format was developed in our group and is used fruitfully in SONNIA, software for producing Kohonen Self Organizing Maps (KSOM) and Coimter-Propaga-tion (CPG) neural networks for chemical application [6]. This file format is ASCII-based, contains the entire information about patterns and usually comes with the extension "dat . 

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. 

Molden now has the capacity to export a series of GIF files, creating an additional file with each screen update. Third-party utilities can be used to combine these images in animations with various file formats, including fii and animated GIF files. This is one of the easiest ways to create animations of chemical systems. 

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. 

M D Lmolfile Standardized file format for chemical structures including substructure query features (initially defined by Molecular Design Ltd)... 

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. 

One of the most widely used chemical structure-encoding schemas in the pharmaceutical industry is the MDL Connection Table (CT) File Format. Both Molfile and SD File are based on MDL CT File Format to represent chemical structures. A Molfile represents a single chemical structure. An SD File contains one to many records, each of which has a chemical structure and other data that are associated with the structure. MDL Connection Table File Format also supports RG File to describe a single Rgroup query, rxnfile, which contains structural information of a single reaction, RD File, which has one to many records, each of which has a reaction and data associated with the reaction, and lastly, MDL s newly developed XML representation of the above—XD File. The CT File Format definition can be downloaded from the MDL website http //www.mdl.com/downloads/public/ctfile/ctfile.jsp. 

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. 

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. 

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