Scripts of the NMRPipe System
Adjust Data in Selected Table Lines, with Optional Sorting:

Flag	Argument	Default	Description
`-in`	`inName`	`test.tab`	Input Table or PDB File.
`-out`	`outName`	`None`	Output Table.

Options to Set Values in Table (Use Either -val or -expr, not both):

`-set`	`vName`	`None`	Table Variable to Adjust.
`-cond`	`cond`	`1`	Selection Condition.
`-val`	`tclVal`	`0`	TCL Expression for New Value;

Should be the Last Argument.

-expr tclExpr None TCL Numerical Expression for New Value;

Should be the Last Argument.

-keep Keep Table Data Unchanged.

Options for Changing the Variable:

`-rename`	`newName`	`None`	New Name for Variable.
`-refmt`	`newFmt`	`None`	New Format for Variable.

Options for Sorting Table Output:

`-sort`	`sVar`	`None`	Table Variable for Sort.
`-up`			Sort by Ascending Order (Default).
`-down`			Sort by Descending Order (Default).
`-before`			Sort Before Setting Values.
`-after`			Sort After Setting Values (Default).
`-numSort`			Sort Text Data Numerically.

PDB Options:

`-pdb`			Input is PDB Data (Default for .pdb).
`-nopdb`			Input is NMRPipe-Format Table.
`-hetatm`			Interpret HETATMs as ATOMs.

Other Options:

`-tcl`	`sName`	`None`	Name of TCL Initialize File to source.
`-del`			Delete All Non-Selected Entries from Table.
`-notext`			Delete Comment Text from Table.
`-verb`			Verbose Mode ON (Default).
`-noverb`			Verbose Mode OFF.

Notes:
1. Use table variable names as TCL variables for the -expr argument;
use ' (single quote) characters or \ (backslash) characters
to preserve $ (dollar-signs) in variable names.
characters in the command-line.
2. Addition variables are defined for use in expressions:
$n Number of entries in the table.
$m Number of entries in the selection.
$i Selection number of the entry, 0 to $m - 1.
$loc Entry number, in the range of 0 to $n - 1.
3. Use the -tcl option to define special functions for expressions,
set random number seeds, etc.
4. PDB data will only be saved in PDB format if the output
name ends in the .pdb extension.
Examples:
Set table variable SIGMA to 100.0:

-set SIGMA -val 100.0

Set table variable SIGMA to have the value of table variable DD:

-set SIGMA -val {'$DD'}

Set table variable RESNAME to text ALA:

-set RESNAME -val ALA

Set table variable SHIFT to sum of table variables RC_SHIFT and BASE:

-set SHIFT -expr {'$RC_SHIFT} + {$BASE`}

Renumber table variable INDEX:

-set INDEX -expr {'$loc} + 1`

Frank Delaglio, Ph.D.