writeArchive.pl

Usage

usage:    writeArchive.pl archivefile [file]
options:  [-inx index]
          [-pdb]
          [-append]

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Description

This utility can be used to manually create or add entries to archive files. Archive files are used mainly for storing data from replica exchange simulations. They can be read with readArchive.pl.

The name of the archive file is required as command line parameter. The input data is either read from a file name given as a parameter or read from standard input otherwise. By default the data is added at the end of the archive file. The archive format expects that all entries have the same length. An error message is printed out if the user attempts to write data records of variable length.

A specific record can be replaced if the index is given -inx. PDB files can be saved more economically with the -pdb option. In this case only the coordinates are written to the archive file. However, in this case a PDB template is needed for retrieving data entries later with readArchive.pl.

Options

-help 

usage information

-inx index 

write a structure to the position in the archive file specified in the index value

-pdb 

write a PDB structure into the archive file

-append 

append an archive to a pre-existing archive file

Examples

writeArchive.pl chain.archive 1vii.exp.chain
adds the contents of 1vii.exp.chain to the archive file chain.archive

writeArchive.pl -inx 4 -pdb pdb.archive 1vii.sample.4.pdb
replaces the fourth PDB coordinate entry in the archive file pdb.archive

writeArchive.pl -inx 4 -append original.archive extra.archive
appends coordinates from extra.archive to original.archive starting at the fourth coordinate entry. This option may be useful for aarex.pl (see arcmode).