JPRED-2 Add sources of all binaries (except alscript) to Git

[jpred.git] / sources / multicoil / multicoil_config

diff --git a/sources/multicoil/multicoil_config b/sources/multicoil/multicoil_config
new file mode 100644 (file)
index 0000000..7ab7600
--- /dev/null
+++ b/sources/multicoil/multicoil_config
@@ -0,0 +1,93 @@
+###############################################################################
+#  NOTE:  Output options can be "turned off" by placing a "#" symbol in front #
+#         of the line declaring the location of the output file.              #
+#  Output locations are by default a directory.  However, you can ouptut to   #
+#         a file name by entering the name in this config file, i.e.:         #
+#      change       log dir = <DIRECTORY NAME>                               #
+#       to           log = <FILE NAME>                                        #
+#  Important:  DIRECTORY NAMES should end with the character "/".             #
+
+
+
+##############################################################################
+#      The scoring methods include:  MultiCoil, PairCoil, NEWCOILS, HMMCoil #
+#      For more advanced users (me) using pos mode, is also ActualCoil.     # 
+method = MultiCoil
+prn = .5       #The bound controls what is classified as a coiled coils.
+no GUI         #Including the "no GUI" option allows for the creation of 
+               #ouput files without going through the on screen interface.
+
+
+##############################################################################
+#      The window length determines how many residues contribute to each    #
+#       score computation.                                                  #
+#      If the window lengths are changed, then different conversion files   #
+#      will be used from the conversion directory (see below).              #
+#       Currently sizes 28 and 21 are allowed.  Size 28 is recommended.      # 
+window length = 28
+
+
+##############################################################################
+#      These values determine which distances are used as scoring           #
+#      dimensions by the programs.  MultiCoil only allows at most 6 scoring #
+#      dimensions total for the 2 scoring tables (1=dimer, 2=trimer).       #
+multi_lib dim 1 = 3 4 5  
+multi_lib dim 2 = 2 3 4 
+#pair_lib = 1 2 4 
+
+
+
+##############################################################################
+#      The printfile is the postscript file for a hard copy of the          #
+#       graphical display (obtained by pressing the "print" button.          #
+#       The default size of the printed display holds 300-350 residues per   #
+#       line, but the user can increase this by entering the number with the #
+#       residues per line command.  The "one print line" command can also be #
+#       used to fit the entire
+#       the display is around 300-350, but that can be changed with the      #
+#       "ps res per line" option or the "one print line" option to customize #
+#       your hard copy (the output picture will be fit to the page).         #
+
+
+##############################################################################
+#      Sequences scoring above the bound (set above) are output to the log  #
+#      file.  The "Show Seq" option causes the sequence and the predicted   #
+#      coiled coil registers to be printed out.  Otherwise, only the scores #
+#      and locations of the high scoring regions are output.                #
+Show Seq
+
+##############################################################################
+#      Sequence scores (seq scores) give a single dimeric and trimeric      #
+#      to the entire sequence (based on a weighted average or residue       #
+#      scores).  If the "Just Scores" option is enabled, then the scores    #
+#      will NOT be labelled by the identification tags (seq code and name). #
+
+
+#############################################################################
+#   Only one method for outputting "out" file can be done at a time.        #
+#   Using "out" method, gives a file of positions, scores, and registers.   #
+#   Using "sparse_out" gives a list of the dimer and trimer probabilities   #
+#         scoring above the bound without any labels (useful for plotting).#
+
+#out dir = ~/MULTICOIL/TEST_RUNS/
+#sparse_out dir = ~/MULTICOIL/TEST_RUNS/
+
+
+
+##############################################################################
+#      Gaussian files are precomputed data files used to convert the        #
+#      MultiCoil scores into prediction probabilities.                      #
+#       The likelihood files convert the PairCoil Scores into Probabilities. #
+
+
+##############################################################################
+#      Table 1 is the table of data to estimate the residues probabilities  #
+#      in DIMERIC coiled coils.  Table 2 is for TRIMERIC coiled coils.      #
+table1 = ../cgi-bin/lib/dimer28.txt
+table2 =  ../cgi-bin/lib/trimer28.txt
+genbnk = ../cgi-bin/lib/genbnk.txt       
+
+gauss_param combo = ../cgi-bin/lib/gauss_parameters_combo28
+
+log = data.log
+out = data.out