; Information on binaries
;
; gbfssp progarm to calculate Secondary Structur
; Firm 
; gzip Compess/decompress
; hbplus Calculation of H-Bonds
; CallLoopPred Script to calculate possible Loops
; x-povray Ray-Tracer
; surface our own Program to calculate surfaces
; surf Freeware to calculate nice surfaces, adopted for our needs
; brk2clustal Create alignment
; ffmpeg convert pictures to movie
; convert convert pictures to pictures, see ImageMagick
;
; Missing Links
;

[Linux]
BRAGI_LINEWIDTH=2.0

BRAGI_CALC_SSP=$BRAGI_HOME/Tools/Linux/Call_calc_SSp
BRAGI_GBFSSP=$BRAGI_HOME/Tools/Linux/gbfssp
BRAGI_DEAD_END=$BRAGI_HOME/Tools/Linux/run_dead_end
BRAGI_FIRM=$BRAGI_HOME/Tools/Linux/Firm
BRAGI_GZIP=/usr/bin/gzip
# BRAGI_HBPLUS=$BRAGI_HOME/Tools/Linux/hbplus
BRAGI_HBPLUS_EXE=/usr/local/bin/hbplus
# BRAGI_HBPLUS_EXT=hb2
BRAGI_HELP_DIR=$BRAGI_HOME/help/
# BRAGI_LOOP=$BRAGI_HOME/Tools/Linux/CallLoopPred
BRAGI_LOOP_DCANN=$BRAGI_HOME/Tools/Linux/builder4bragi
BRAGI_LOOP_HCAPD=$BRAGI_HOME/Tools/Linux/predictor4bragi
BRAGI_LOOP_DATABASE=$BRAGI_HOME/Tools/loops/
BRAGI_LOOP_NEWDATA=$BRAGI_HOME/Data/loop2/
BRAGI_POVRAY=$BRAGI_HOME/Tools/Linux/povray
BRAGI_POVRAY_LIB=$BRAGI_HOME/Tools/Linux/povray.script/
BRAGI_SURF_BAT=$BRAGI_HOME/Tools/Linux/surface
BRAGI_SURF_DIR=$BRAGI_HOME/Tools/Linux/surf
BRAGI_TO_CLUST=$BRAGI_HOME/Tools/Linux/brk2clustal
BRAGI_FFMPEG=$BRAGI_HOME/Tools/Linux/ffmpeg
BRAGI_CONVERT_STATUS=$BRAGI_HOME/Tools/Linux/convertStatus
BRAGI_CONVERT=/usr/bin/convert
BRAGI_ACROBAT=/usr/bin/X11/acroread
BRAGI_APBS=$BRAGI_HOME/Tools/Linux/apbs
BRAGI_APBS2surf=$BRAGI_HOME/Tools/Linux/merge_sur
BRAGI_APBS_CONTROL=$BRAGI_HOME/Tools/apbs/apbs.in

BRAGI_BROOKHAVEN=/tmp/

[WINDOWS]
BRAGI_LINEWIDTH=2.0

BRAGI_GBFSSP=$BRAGI_HOME\Tools\Windows\exe\gbfssp.exe
BRAGI_DEAD_END=$BRAGI_HOME\Tools\Windows\exe\deep.exe
BRAGI_FIRM=$BRAGI_HOME\\Tools\Windows\Firm
BRAGI_GZIP=$BRAGI_HOME\Tools\Windows\exe\gzip
## BRAGI_HBPLUS=$BRAGI_HOME\\Tools\Windows\hbplus.bat
## BRAGI_HBPLUS_EXE=\usr\local\bin\hbplus
## BRAGI_HBPLUS_EXT=hb2
BRAGI_HELP_DIR=$BRAGI_HOME\\help\
BRAGI_LOOP=$BRAGI_HOME\Tools\Windows\CallLoopPred.bat
BRAGI_LOOP_DCANN=$BRAGI_HOME\Tools\Windows\exe\builder4bragi.exe
BRAGI_LOOP_HCAPD=$BRAGI_HOME\Tools\Windows\exe\predictor4bragi.exe
BRAGI_LOOP_DATABASE=$BRAGI_HOME\Data\loops\
BRAGI_LOOP_NEWDATA=$BRAGI_HOME\Data\loop2\
BRAGI_POVRAY=C:\Programme\POV-Ray for Windows v3.5\bin\pvengine.exe
BRAGI_POVRAY_LIB=$BRAGI_HOME\Tools\Linux\povray.script\
BRAGI_SURF_BAT=$BRAGI_HOME\Tools\Windows\exe\surface.exe
BRAGI_SURF_DIR=$BRAGI_HOME\Tools\Windows\exe\surf.exe
BRAGI_TO_CLUST=$BRAGI_HOME\Tools\Windows\brk2clustal.bat
BRAGI_FFMPEG=$BRAGI_HOME\Tools\Windows\exe\ffmpeg.exe
BRAGI_CONVERT_STATUS=$BRAGI_HOME\Tools\Linux\convertStatus.exe
BRAGI_CONVERT=$BRAGI_HOME\Tools\Windows\exe\convert.exe
BRAGI_ACROBAT=AcroRd32.exe

BRAGI_AMB_LINK=\users\amber\com\link.com
BRAGI_AMB_EDIT=\users\amber\com\edit.com
BRAGI_AMB_PARM=\users\amber\com\parm_1.com
BRAGI_AMB_MIN=\users\amber\com\min.com
BRAGI_AMB_MD=\users\amber\com\md.com
BRAGI_AMB_DB_DAT=\users\amber\dat\db3.dat
BRAGI_AMB_PARAMS=\users\amber\dat\parmunihb.dat
BRAGI_AMB_PARM_IN=\users\amber\parm\parm.dat

BRAGI_BROOKHAVEN=$TEMP

BRAGI_RCSB_FTP=ftp://ftp.rcsb.org/pub/pdb/data/structures/all/pdb/

[IRIX]
BRAGI_LINEWIDTH=2.0

BRAGI_GBFSSP=$BRAGI_HOME/Tools/IRIX/gbfssp
BRAGI_CALC_SEC=$BRAGI_HOME/Tools/IRIX/Call_calc_sec
BRAGI_CALC_SSP=$BRAGI_HOME/Tools/IRIX/Call_calc_SSp
# BRAGI_DEAD_END=$BRAGI_HOME/Tools/IRIX/deep
BRAGI_DEAD_END=$BRAGI_HOME/Tools/IRIX/run_dead_end
BRAGI_FIRM=$BRAGI_HOME/Tools/IRIX/Firm
BRAGI_HBPLUS=$BRAGI_HOME/Tools/IRIX/hbplus
BRAGI_HBPLUS_EXE=/usr/local/bin/hbplus
BRAGI_HBPLUS_EXT=hb2
BRAGI_HELP_DIR=$BRAGI_HOME/help/
BRAGI_LOOP=$BRAGI_HOME/Tools/IRIX/CallLoopPred
BRAGI_LOOP_DATABASE=$BRAGI_HOME/Tools/loops/
BRAGI_LOOP_NEWDATA=$BRAGI_HOME/Data/loop2/
BRAGI_POVRAY=/usr/local/bin/x-povray
BRAGI_SURF_BAT=$BRAGI_HOME/Tools/IRIX/surface
BRAGI_SURF_DIR=$BRAGI_HOME/Tools/IRIX/surf
BRAGI_TO_CLUST=$BRAGI_HOME/Tools/IRIX/brk2clustal
BRAGI_FFMPEG=$BRAGI_HOME/Tools/IRIX/ffmpeg
BRAGI_CONVERT_STATUS=$BRAGI_HOME/Tools/IRIX/convertStatus
BRAGI_CONVERT=/usr/local/bin/convert
BRAGI_ACROBAT=/usr/bin/acroread

BRAGI_BROOKHAVEN=/tmp/

[ALL]
BRAGI_DAT=$BRAGI_HOME/Data/dead_end/
BRAGI_TOPOLOGIE=$BRAGI_HOME/topologie/
BRAGI_SWISSPROT_DATA=$BRAGI_HOME/Data/
BRAGI_STRUC_DIR=$BRAGI_HOME/demodata/
BRAGI_LOOP_NEWDATA=$BRAGI_HOME/Data/loop2/
BRAGI_LOOP_DATABASE=$BRAGI_HOME/Data/loops/
XPLOR_BRAGI_TOPOLOGIE=$BRAGI_HOME/xplor_top/
BRAGI_BWG_PIXMAP=$BRAGI_HOME/images/BlauWeissRot.png

BRAGI_BlastProDom=http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=
BRAGI_FPrintScan=http://bioinf.man.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false&prints_accn=
BRAGI_GO=http://www.informatics.jax.org/searches/GO.cgi?id=
BRAGI_HMMPfam=http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?
BRAGI_HMMSmart=http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&ACC=
BRAGI_HMMTigr=http://www.tigr.org/tigr-scripts/CMR2/hmm_report.spl?user=access&password=access&acc=
BRAGI_INTERPRO_URL=http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=
BRAGI_INTERPRO_HOST_XML=http://www.ebi.ac.uk
BRAGI_INTERPRO_URL_XML=/cgi-bin/iprscan/iprscan?tool=iprscan&crc=1&appl=BlastProDom&appl=FPrintScan&appl=HMMPIR&appl=HMMPfam&appl=HMMSmart&appl=HMMTigr&appl=ProfileScan&appl=ScanRegExp&appl=SuperFamily&trlen=100&stype=protein&sequence=
BRAGI_OCA=http://bioinfo.weizmann.ac.il:8500/oca-bin/ocaids?id=
BRAGI_PPsearch=http://www.expasy.ch/cgi-bin/prosite-search-ac?
BRAGI_ProfileScan=http://www.isrec.isb-sib.ch/cgi-bin/get_pstprf?
BRAGI_RCSB_FTP=ftp://ftp.rcsb.org/pub/pdb/data/structures/all/pdb/
BRAGI_SWISSPROT_URL=http://www.expasy.org/cgi-bin/niceprot.pl
BRAGI_ScanRegExp=http://www.expasy.ch/cgi-bin/prosite-search-ac?
BRAGI_XPLOREPDB=http://sb289/cgi-bin/getPdb.pl?pdb=
BRAGI_PROSITE=http://www.expasy.ch/cgi-bin/prosite-search-ac?
BRAGI_PRINTS=http://www.bioinf.man.ac.uk/cgi-bin/dbbrowser/PRINTS/DoPRINTS.pl?fun_a=Text&qst_a=
BRAGI_PFAM=http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?
BRAGI_PFAM1=http://www.cgr.ki.se/cgi-bin/Pfam/getacc?
BRAGI_PFAM2=http://pfam.wustl.edu/cgi-bin/getdesc?
BRAGI_SMART=http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=&ACC=
BRAGI_PROFILE=http://www.expasy.org/cgi-bin/nicesite.pl?
BRAGI_OMIM_URL=http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=
BRAGI_DALI_MAILTO=dali@ebi.ac.uk
BRAGI_FAQ=http://bragi.gbf.de/faq.html

# Uebersetzte Links fuer Blast, SwissProt etc.
BRAGI_DB_PRINTS_URL=$BRAGI_PRINTS
BRAGI_DB_SMART_URL=$BRAGI_SMART
BRAGI_DB_PROSITE_URL=$BRAGI_PROSITE
BRAGI_DB_InterPro_URL=$BRAGI_INTERPRO_URL
BRAGI_DB_Pfam_URL=$BRAGI_PFAM
BRAGI_DB_MEROPS_URL=http://merops.sanger.ac.uk/cgi-bin/merops.cgi?id=***;action=SUMMARY

BRAGI_COLORS_BACKGROUND=#222222
BRAGI_COLORS_BACKBONE=#b2b2b2
BRAGI_COLORS_NONPOLAR=#00d8d8
BRAGI_COLORS_POLAR=#d800d8
BRAGI_COLORS_AROMATIC=#e5cc00
BRAGI_COLORS_POSITIVE=#ff0000
BRAGI_COLORS_NEGATIVE=#0000ff
BRAGI_COLORS_CONNECTS=#3399cc
BRAGI_COLORS_DISULFIDE=#cce500
BRAGI_COLORS_SURFACE=#99cccc
BRAGI_COLORS_TEXT=#00ff00
BRAGI_COLORS_RIBON=#00b24c
BRAGI_COLORS_HELIX=#b20033
BRAGI_COLORS_TRACE=#b200ff
BRAGI_COLORS_TURN=#00b2ff
BRAGI_STEREO_DIST=0.6

# Bei Hardopy das Menu oben NICHT mitnehmen
BRAGI_HIDE_MENU=29

BRAGI_BLAST_SYNTAX=$BRAGI_HOME/Data/blast_syntax
BRAGI_BLAST_DB=pdb