Getting ready for release

README

+INTBuilder MANUAL
+
+In order to compile INTBuilder, place yourself in its directory and execute the command 
+make
+
+An help can then be printed with the following command :
+./INTBuilder -h
+Any option followed by '%' awaits an argument
+
+
+Here is an example to run INTBuilder:
+
+./INTBuilder -ZDOCK -dockingFile example/1E6E.out -pdbDir example/ -rec 1E6E_r_u_m -lig 1E6E_l_u_m
+
+This will output 2 interface file 1E6E_r_u_m-1E6E_l_u_m_lig_42_dockinter.txt and 1E6E_r_u_m-1E6E_l_u_m_rec_42_dockinter.txt.
+
+Each line of these files corresponds to one interface.
+The first number (ID) of the line corresponds to the ID of the conformation. It is then followed for each residue belonging to the interface by :
+'ID_res' 'chain'
+
+where ID_res corresponds to the ID of the residue in the given PDB and chain the chain where the residue belongs to.
+
+Should you run INTBuilder with an atomic resolution, the output will then be
+'ID_res' 'chain' 'Atom_name'
+
+for each atom belonging to the interface.
+
+

src/param.c

@@ -11,28 +11,28 @@ void print_usage() {
     printf("Usage:\n"
     "Mandatory\n"
     "=========\n\n"
-    "<-dockingFile>     docking file that needs to be analysed\n"
+    "<-dockingFile>%%    docking file that needs to be analysed\n"
     "OR\n"
     "<-complex>         This option means that we look at two PDBs instead of looking\n"
     "                   at the dockingFile. Both PBDs for '-rec' and '-lig' must be in\n"
     "                   '-pdbDir'\n"
     "--\n"
-    "<-pdbDir>          PDB directory containing the name of the receptor/ligand .pdb\n"
-    "<-rec>             name of the receptor\n"
-    "<-lig>             name of the ligand\n"
+    "<-pdbDir>%%         PDB directory containing the name of the receptor/ligand .pdb\n"
+    "<-rec>%%            name of the receptor\n"
+    "<-lig>%%            name of the ligand\n"
     "OPTIONAL\n"
     "=========\n\n"
-    "<-outputPDB>.......Output directory for the constructed PDB (ligand)\n"
+    "<-outputPDB>%%......Output directory for the constructed PDB (ligand)\n"
     "                   If nothing is specified, there will be no PDB output\n"
-    "<-o>...............Output directory for the docking interface\n"
+    "<-o>%%..............Output directory for the docking interface\n"
     "                   If nothing is specified, the current directory is used\n"
-    "<-pose>............Desired conformation. Default will compute all conformations\n"
+    "<-pose>%%...........Desired conformation. Default will compute all conformations\n"
     "<--atom-res>.......If specified, will computed the interface at atom level\n"
     "<-noOutput>........Will prevent the program to output the docking interface\n"
     "                   Useful if you only want to use the '-outputPDB' option\n"
     "<--force/-f>.......Will force the computation of the pause even in case of\n"
     "                   huge number of clashes (threshold defined in struct.h)\n"
-    "<-distTH>..........Distance for contact\n"
+    "<-distTH>%%.........Distance for contact\n"
     "--\n"
     "Leaving this option blank means that the default format for the docking file\n"
     "will be used.\n"