psize(1) [debian man page]

PSIZE(1)							  PDB2PQR Manual							  PSIZE(1)

NAME

       psize - Get dimensions and other information from PQR files

SYNOPSIS

       psize [--cfact=value] [--fadd=value] [--space=value] [--gememfac=value] [--gememceil=value] [--ofrac=value] [--redfac=value] {pqrfile}

       psize {--help | -h}

DESCRIPTION

       psize derives information from PQR files to preprare the models of proteins and chemicals for electrostatics calculations. The tool
       calculates dimensions for coarse and fine grids, grid spacings, box size and estimates the memory required to perform an electrostatics
       calculation.

       The calculation of this information can be influenced by giving constraints to psize as parameters.

OPTIONS

       psize accepts the following options:

       --help, -h
	   Print a help message and exit.

       --cfact=value
	   Factor by which to expand the molecule dimensions to get the coarse grid dimensions

       --fadd=value
	   Amount to add to the molecule dimensions to get the fine grid dimensions.

       --space=value
	   Desired fine mesh resolution.

       --gememfac=value
	   Number of bytes per grid point required for sequential MG calculation.

       --gememceil=value
	   Maximum MB allowed for sequential MG calculation. Adjust this to force the script to perform faster calculations (which require more
	   parallelism).

       --ofrac=value
	   Overlap factor between mesh partitions.

       --redfac=value
	   Maximum factor by which a domain dimension can be reduced during focusing.

SEE ALSO

       apbs(1), pdb2pqr(1)

AUTHOR

       Manuel Prinz <debian@pinguinkiste.de>
	   Wrote this manpage for the Debian System.

COPYRIGHT

       Copyright (C) 2008 Manuel Prinz

psize								    2008-06-04								  PSIZE(1)

ImageND(3)						User Contributed Perl Documentation						ImageND(3)

NAME

       PDL::ImageND - useful image processing routines which work in N-dimensions

DESCRIPTION

       In some cases (though not as many as one would like) it is possible to write general routines that operate on N-dimensional objects.

       An example in this module is a N-Dim convolution algorithm I made up one day - it works but the boundary condtions are a bit funny.

SYNOPSIS

	use PDL::ImageND;

FUNCTIONS

       convolve

	 Signature: (a(m); b(n); int adims(p); int bdims(q); [o]c(m))

       N-dimensional convolution algorithm.

       $new = convolve $a, $kernel

       Convolve an array with a kernel, both of which are N-dimensional.

       Note because of the algorithm used (writing N-dim routines is not easy on the brain!) the boundary conditions are a bit strange. They wrap,
       but up to the NEXT row/column/cube-slice/etc. If this is a problem consider using zero-padding or something.

       ninterpol()

       N-dimensional interpolation routine

	Signature: ninterpol(point(),data(n),[o]value())

	     $value = ninterpol($point, $data);

       "ninterpol" uses "interpol" to find a linearly interpolated value in N dimensions, assuming the data is spread on a uniform grid.  To use
       an arbitrary grid distribution, need to find the grid-space point from the indexing scheme, then call "ninterpol" -- this is far from triv-
       ial (and ill-defined in general).

       rebin

	 Signature: (a(m); [o]b(n); int ns => n)

       N-dimensional rebinning algorithm

       $new = rebin $a, $dim1, $dim2,..;.  $new = rebin $a, $template; $new = rebin $a, $template, {Norm => 1};

       Rebin an N-dimensional array to newly specified dimensions.  Specifying `Norm' keeps the sum constant, otherwise the intensities are kept
       constant.  If more template dimensions are given than for the input pdl, these dimensions are created; if less, the final dimensions are
       maintained as they were.

       So if $a is a 10 x 10 pdl, then "rebin($a,15)" is a 15 x 10 pdl, while "rebin($a,15,16,17)" is a 15 x 16 x 17 pdl (where the values along
       the final dimension are all identical).

       circ_mean_p

       Calculates the circular mean of an n-dim image and returns the projection. Optionally takes the center to be used.

	  $cmean=circ_mean_p($im);
	  $cmean=circ_mean_p($im,{Center => [10,10]});

       circ_mean

       Smooths an image by applying circular mean.  Optionally takes the center to be used.

	  circ_mean($im);
	  circ_mean($im,{Center => [10,10]});

AUTHORS

       Copyright (C) Karl Glazebrook 1997.  All rights reserved. There is no warranty. You are allowed to redistribute this software / documenta-
       tion under certain conditions. For details, see the file COPYING in the PDL distribution. If this file is separated from the PDL distribu-
       tion, the copyright notice should be included in the file.

perl v5.8.0							    2003-01-29								ImageND(3)