Renaming:
CollapseToAtomTypes.pl = CondenseVol.pl
ExpandFromAtomTypes.pl = ExpandVol.pl
GetAAValFrom173file.pl = get-res-frvols.pl

Original Names
=====================
CondenseVol.pl	- takes output *.a-res file and condenses to atom type volumes
ExpandVol.pl	- takes atomtype volumes and expands to 173 types
get-res-frvols.pl - utility to get residue volume totals from 173 output files

get-res-frvols.pl < foo.a-vols > foo.a-vols-res
CondenseVol.pl [resfile(optional)] < foo.a-vols > foo.a-vols-cond
ExpandVol.pl < foo.a-vols-cond > foo.a-vols-exp
get-res-frvols.pl < foo.a-vols-exp > foo.a-vols-exp-res


Original README:
#!/bin/sh 

bin/nVradii.exe \
     -weed_level c \
     -surf_thresh 0.0001 \
     -types_file data/TS5H.ad \
     -res_file data/TS5H.rd \
     -outname best  \
     -pdb_dir ../pdbs/ \
     < data/pdblist-only-5 > best.err 2>&1

exit 


# .. _ .. _ .. .. _ .. _ .. .. _ .. _ .. .. _ .. _ .. .. _ .. _ .. .. _ ..


bin/nVradii.exe \
     -weed_level c \
     -surf_thresh 0.0001 \
     -types_file data/Chothia.ad \
     -res_file data/Chothia.rd \
     -outname best-vols2  \
     -pdb_dir ../pdbs/ \
     < data/pdblist-only-5 > a.err 2>&1

exit 


# .. _ .. _ .. .. _ .. _ .. .. _ .. _ .. .. _ .. _ .. .. _ .. _ .. .. _ ..


bin/nVradii.exe \
     -weed_level c \
     -surf_thresh 0.0001 \
     -types_file data/Chothia.ad \
     -res_file data/Chothia.rd \
     -outname foo  \
     -pdb_dir ../pdbs/ \
     < data/pdblist-only-5 \
     > debug.out 

exit

This directory contains the programs, parameters, and output files
to run and analyse voronoi polyhedra.

programs -

nVradii  	- current compiled version is for DEC alpha
	   	  code and makefile included
CondenseVol.pl	- takes output *.a-res file and condenses to atom type volumes
ExpandVol.pl	- takes atomtype volumes and expands to 173 types
get-res-frvols.pl - utility to get residue volume totals from 173 output files

for example:

(nVradii -weed_level [csAt] -surf_thresh [#] -types_file [name.ad] \
-res_file [name.rd] -outname [foo] -pdb_dir [dir] < input-pdbfile-list \
> output) >& log

the above command creates following files:

output		- for debugging output
foo.a-surf 	- 173 atom surfaces
foo.a-vols	- 173 atom volumes
log		- log
foo.res-surf	- surface stats for 21 residues if whole residue buired
foo.res-vols	- volume stats for 21 residues if whole residue buired

use to condense and expand:

get-res-frvols.pl < foo.a-vols > foo.a-vols-res
CondenseVol.pl [resfile(optional)] < foo.a-vols > foo.a-vols-cond
ExpandVol.pl < foo.a-vols-cond > foo.a-vols-exp
get-res-frvols.pl < foo.a-vols-exp > foo.a-vols-exp-res
-----------

pdb files in pdbs and pdbs-o (pdbs-o contains pdbs for use with pdblist-op.
all other structures in pdbs, nmr files in directory in pdbs)

-----------

output files in outputs. see output logs for specific parameters.

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