# PHD2000 PARA
# --------------------------------------------------------------------------------
# Profile-based neural network prediction (PHD2)
# --------------------------------------------------------------------------------
# Copyright: 	Burkhard Rost, LION Biosciences AG, Heidelberg, Germany
# Contact:   	rost@columbia.edu
# Date:  	Dec 27, 1999
# 
# --------------------------------------------------------------------------------
# 
# directories
# 
#dir_home	/nfs/home1/yachdav/work/SNAP/prof/
#dir_net 	net/0012/

# --------------------------------------------------
# first level (sequence-to-structure)
# format: 	'kwd TAB name'
# 
#                         solvent accessibility
file_1	ACChssp1_13uall.jct
file_1	ACChssp1_13usumh.jct
file_1	ACChssp1_13ball.jct
file_1	ACChssp1_13bsumh.jct
#                         secondary structure
file_1	SEChssp1_17uall.jct
file_1	SEChssp1_17ball.jct
file_1	SEChssp1_21uall.jct
file_1	SEChssp1_21ball.jct

# --------------------------------------------------
# second level (structure-to-structure)
# format:  	'kwd TAB name TAB ptr2fst'
# ptr2fst:	which first level used as input to snd
# 
#                         secondary structure
file_2	SEChssp2_17uuall.jct	5
file_2	SEChssp2_17uball.jct	5
file_2	SEChssp2_17buall.jct	6
file_2	SEChssp2_17bball.jct	6
file_2	SEChssp2_21uuall.jct	7
file_2	SEChssp2_21uball.jct	7
file_2	SEChssp2_21buall.jct	8
file_2	SEChssp2_21bball.jct	8

# --------------------------------------------------
# third level (seq_str-to-structure)
# format:  	'kwd TAB name'
# 
file_3	ACChssp3_13usumh.jct	seq=1:2,sec=2:1-8,acc=1:1-4
file_3	ACChssp3_13bsumh.jct	seq=1:2,sec=2:1-8,acc=1:1-4
file_3	ACChssp3_13uall.jct	seq=1:1,sec=2:1-8,acc=1:1-4
file_3	ACChssp3_13uall.jct	seq=1:1,sec=2:1-8,acc=1:1-4

# --------------------------------------------------
# format:       'kwd TAB mode TAB ptr2file'
# kwd:          fin
# mode:         <sec|acc|htm|sec_hcap|sec_ecap>: 
# ptr2file:	which file to take
finfin	acc	3:4

# --------------------------------------------------
# note used at moment!
#mode_sec:HEL	JURYhel8.par
#mode_acc:10	JURY10_8.par
#mode_sec:Hcap	CapHsec.jct
#mode_sec:Ecap	CapEsec.jct


