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17.1.6 Table Input and Output

In order to allow users to input their own data into a table and to save the output from a particularly long property calculation (such as an accessible surface), the BUILD command allows properties to be read and written from files. The organization for such files is as follows:

     title             (up to 10 lines)
     *                 (line must be blank after asterisk)
     short header      (80A1)
     long header       (80A1)
     number of items   (I5)
     format            (80A1)
     data              (using format given above. One per line)

The title is short description of the file. The text is printed when the file is read. The short header is the header used over columns in a column printout (see Printing Tables). The long header is the title for printout when the table is pretty printed (see below). The number of items must be the same as the number of entities in the structure for the particular class. For example, for a table of class, ANGLE, the number of items must be equal to NTHETA, the number of angles in the PSF. The data uses an F15.0 format to allow 8 digits of accuracy plus exponents.

The order of the data is determined by the order in which CONGEN keeps its list of internal coordinates, hydrogen bonds, or atoms. For example, the bond list will contain the list of bonds for the chain of a protein followed by the bonds for any disulphide bridges which may been patched in later. If one is preparing a property input, it must follow this ordering exactly. If a bond is deleted, as is the case for the first bond in an extended atom protein, one must have an entry for it anyway in the property input. The NUMBER static property, which is defined for all classes, gives the correct position for each item in the table. In addition, when a property is written out, identifying information is written as well. Therefore, a property file may also serve as a guide for the order of the data.

The syntax for a property to be read from a file is as follows:

     property ::= READ unit-number

The WRITE option, which may be specified with any property, causes that property to be written to the given unit. The title used in writing that property is the one given by the TITLE option in the BUILD command. Only one title may be specified per BUILD command, so two different properties written out will have the same title. As a result, it is advantageous to write only one property at a time with the BUILD command. It is permissible to specify the WRITE option for a property which is being read in. The title is processed the same way title in the analysis command, WRITE, are processed.

The use of difference tables necessitates some different processing for the READ properties and the WRITE option. Since a difference table requires the calculation of two sets of properties, the READ property must use two units. Therefore, the property for the main calculation is read from the given unit, and property for the comparison calculation is read from unit plus 1. For example, if we are comparing hemoglobin to myoglobin, and hemoglobin is the main structure, then READ 24 will read the hemoglobin property from unit 24 and the property data for myoglobin will come from unit 25.

The WRITE option is not permitted with a difference table.