# $CVSHeader: pal8e/etc/pal8e.conf,v 1.2 2005/02/20 00:50:53 indraneel Rel $

# Input processing directives
[Input]

## Where are the PDB input files located? (only for multiple file runs)
pdbdir = ../../dat/tmp/

# Directory where listfiles (see below) are located. This needs to be defined
# if listfiles are used.
#listfiledir = ../../dat/lists/

# Filename containing list of files to run on (only for multiple file
# runs). Each line may be a complete path. If pdbdir (above) is defined
# path pointed to by pdbdir will be prepended to all lines in the listfile.
# If listfiledir (above) is defined and listfile is not, listfile will
# default to the hostname of the machine (for use on a cluster). listfile
# may be a filepath and will be appended to listfiledir (defined above).
# Special name "break" (without quotes) can be used to terminate processing
# lines of a listfile.
#listfile = unq_fold_B_AB_chains

# filenames must start with this. This part of the filename is
# stripped from output fileID for multiple file runs
#filename_prefilter = pdb

# Same as above except for filename endings.
#filename_postfilter = .ent
filename_postfilter = .pdb

# for weekly updates of new PDB files (broken: do not use)
# status directory distributed by rcsb.org
PDBstatusdir = /mnt/e13/data/pdb/data/status/
# weekly previous update info file used by pal8e
WeeklyInfoFile = /mnt/e13/data/pal8e.info

################

# Output processing directives
[Output]

# do output files need to be compressed? All output, debug, postscript
# plots and pymol script files will be gzipped.
compression = 0

# filename extension to use for output files. Output is in PDB format.
# Compression is bzip2 if defined.
secfilename_posttag = .ssd

# secondary structure definition outputs go here
secoutdir = ../../pal8e-test-out/

# overwrite previous secondary structure output files?
overwrite = 1

# are postscript plots of beta-sheets required as ps and eps files?
psfilereqd = 0

# postscript output files go here
psoutdir = ../../pal8e-test-out/

# are insight script (.log) files required?
insfilereqd = 0

# insight script files go here
insoutdir = ../../pal8e-test-out/

# are pymol script (.pml) files required?
pmlfilereqd = 0

# pymol script files go here
pmloutdir = ../../pal8e-test-out/

#################

# Debug processing directives
[Debug]

# global logfile will be created in the debug directory specified below
logfile = pssdlog

## All debug files (global + individual) are located here
dbgdir = ../../pal8e-test-out/

# Available debug items for each input file. 'all' overrides
# 'none'. Either 'all' or 'none' override all others.
#dbgitems = critical info element peptides quad quadtrace debug compare none all
# Please use "all" when submitting bug reports for non (rcsb.org) PDB files
dbgitems = critical

##################

# How many files to process simultaneously
[Process]

# children works for both fork() and pvm. Set this 0 or 2 for pvm on
# uni or dual processor nodes. (not fully tested with pvm. fork()
# works great on an openmosix cluster.)
children = 0
#use_pvm = 1

##################

# External display program script file directives
[Display]

# relative path from display program to pdbdir in display script file

# for insightII
inspdbdir = wrk/dat/tmp/

# for pymol
pmlpdbdir = ../../../wrk/dat/tmp/

#############################################################
# Changes below this are normally not required

# cutoffs and other data (as flatfiles)
[Data]
datdir = ../dat/

# prerun files for comparisons with different programs
[Compare]
use_dssp = 0
dsspdir = ../../pssd-compare/dsspout/
dssptail = .dssp

use_stride = 0
stridedir = ../../pssd-compare/strideout/
stridetail = .str

use_sstruc = 0
sstrucdir = ../../pssd-compare/sstrucout/
sstructail = .sst

use_pross = 0
prossdir = ../../pssd-compare/prossout/
prosstail = .pross

use_molauto = 0
molautodir = ../../pssd-compare/molautout/
molautotail = .mauto
