NAME

des - interconvert descriptor files between internal (binary) and external (text) formats

SYNOPSIS

des [ -check level ] -i inputfile -o outputfile

DESCRIPTION

The descriptor inputfile is read, converted and written to outputfile. The conversion is between internal (binary) and external (text) format. If inputfile is a binary descriptor then outputfile will be a text format descriptor and vice versa. The format can be easily determined by the program provided inputfile is a legitimate descriptor file.

The binary format version is used in all yammp programs. The text format version can be read and modified; the revision can then be converted to binary format.

The descripter can be checked by specifying -check and a level which is one of four numbers 0, 1, 2 or 3. At level 0, no checks will be made. If -check is not specified a level of 1 is assumed. The errors that a level 1 check would reveal are those that can cause serious program execution errors such as illegal memory access and illegal mathematical operations and errors that would invalidate a simulation such as an illegal exclusion list. Level 2 checks look for errors that would cause the system to be non-physical (such as negative force constants) but which would not cause any problem with program execution. Level 3 checks are time consuming, typically involving checking one component of a force term against another component or one force term against another.

EXAMPLES

des -i protein.dx -o protein.ds

Convert the descriptor file protein.dx to another descriptor protein.ds. The conversion depends on whether protein.dx is a text or binary descriptor. An informal convention is to use the file name extension .dx for text format descriptors and the extension .ds for binary descriptors. Since -check is not specified a checking level of 1 is implied.

des -example

Write out a descriptor template to the standard output. The output can be redirected to a file and the template can then be used as a starting point for the creation of a descriptor. Such low level manipulation of descriptors is tedious and error prone. Descriptors should be created using one of the descriptor creation programs.

FILES

SEE ALSO

The descriptor file format, the des diagnostics.

DIAGNOSTICS

The -check option potentially produces extensive diagnostics which are documented on a separate page.

BUGS

NOTES