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Difference between revisions of "writeArchive.pl"
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This utility can be used to manually create or add entries to archive files. Archive files are used mainly for | 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]].<BR> | storing data from replica exchange simulations. They can be read with [[readArchive.pl]].<BR> | ||
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The name of the archive file is required as command line parameter. The input data is either read from a file name | 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 | 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 | 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.<BR> | out if the user attempts to write data records of variable length.<BR> | ||
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A specific record can be replaced if the index is given <B>-inx</B>. PDB files can be saved more economically | A specific record can be replaced if the index is given <B>-inx</B>. PDB files can be saved more economically | ||
with the <B>-pdb</B> option. In this case only the coordinates are written to the archive file. However, in | with the <B>-pdb</B> option. In this case only the coordinates are written to the archive file. However, in | ||
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; -help : usage information | ; -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 == | == Examples == | ||
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<mmtsbToolExample cmd="writeArchive.pl" set="/apps/mmtsb/bench/writeArchive.pl-test/test2"></mmtsbToolExample> | <mmtsbToolExample cmd="writeArchive.pl" set="/apps/mmtsb/bench/writeArchive.pl-test/test2"></mmtsbToolExample> | ||
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| + | <mmtsbToolExample cmd="writeArchive.pl" set="/apps/mmtsb/bench/writeArchive.pl-test/test3"></mmtsbToolExample> | ||
Latest revision as of 21:14, 30 July 2009
Usage
usage: writeArchive.pl archivefile [file]
options: [-inx index]
[-pdb]
[-append]
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).