Molecular structure file format

There are many programs available to parse the various molecular structure file format. OpenBabel is an open-source program that can read many file formats and produce a SMILES representation of molecular structure. There are many other commercial products that can do this as well. In the following examples, the OpenBabel/plpythonu implementation of molfile parsing will be used. This was introduced in Chapter 10. The code to define the necessary functions is shown in the Appendix. 

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. 

In most programs, it is still possible to input a geometry manually in an ASCII input file. If the geometry is already in a file but of the wrong format, there are several utilities for converting molecular structure files. The most popular of these is the Babel program, which is described in Appendix A. 

CODESSA reads molecular structure files or output files created by other software packages as the starting point for QSAR analysis. It can import computational results from AMPAC, MOPAC, and Gaussian as well as structures in a number of common formats. 

VMD is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, and lipid bilayer assemblies. It may be used to view more general molecules, as VMD can read several different structural file formats and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. 

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. 

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... 

A traditional client program reads from a molecular structure file and performs some computation that depends on the molecular structural data. This read(file) function reads particular columns or fields from the file. A different function would be necessary for each type of file format. A traditional client program can be modified to read molecular structure data from... 

As a foundation for comparing the SRP RNAs in three dimensions, we used the human SRP RNA model, generated earlier with ERNA-3D (9). Next, we focused on the SRP RNA of M. jannaschii to take advantage of the large number base pairs compounded into helical sections 5bcd, 5gh, 5ij, and 6bc. A simple textual input file was generated to contain the M. Jannaschii SRP RNA sequence, information about the paired residues, and about positions of the helical sections. The positions of the helical sections were copied from the PDB-formatted (18) molecular structure file of the human SRP RNA model (9). 

A. Dalby, J. Nourse, W. D. Hounshell, A. Gushurst, D. Grier, B. Leland, and J. Laufer, /. Chetn. Inf. Comput. Set., 32, 244 (1992). Description of Several Chemical Structure File Formats Used by Computer Programs Developed at Molecular Design Limited. 

As this short example shows. PDB files use different syntax for different records and both writing and reading such files require much effort. Another problem is the extensibility of this format to handle new kinds of information, which further complicates the file structure. The Protein Data Bank has been faced with the consequences - the existing legacy data comply with several different PDB formats, so they are not uniform and they arc more difEcuh to handle (145, 155, 157]. As mentioned in Section 2,9.7.1, there is a much more flexible and general way of representing molecular structure codes and associated information - the STAR file format and the file formats based on it. 

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. 

Output data can be printed or exported to a spreadsheet. The rendering quality is very good. Structures can be rendered and labeled in several different ways. Molecular structures can be saved in several different formats or as image files. The presentation mode allows molecular structures to be combined with text. 

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. 

AMPAC can also be run from a shell or queue system using an ASCII input file. The input file format is easy to use. It consists of a molecular structure defined either with Cartesian coordinates or a Z-matrix and keywords for the type of calculation. The program has a very versatile set of options for including molecular geometry and symmetry constraints. 

The molecular structures were rendered with good-quality shading on a blue background. Isosurfaces produced from cube files or checkpoint files also looked nice. Molecular vibrations can be animated on screen and vibrational displacement vectors displayed. The vibrational line spectrum may be displayed too, but the user has no control over the axes. There is no way to set the background color. The display can be saved using several image file formats. 

---