Feature/imc

PyAttract/attract.py

@@ -231,7 +231,7 @@ def checkFile(name, comment):
 def check_ffversion(reduced):
     header = open(reduced, 'r').readline()
     if not 'HEADER' in header:
-         sys.stderr.write("ERROR: reduced PDB file must contain a HEADER line specifying the chosen forcefield (scorpion, attract1, attract2)\n")
+         sys.stderr.write("ERROR: reduced PDB file must contain a HEADER line specifying the chosen forcefield (scorpion, attract1, attract2, imc)\n")
          sys.exit(1)
 
     #read cg format:
@@ -260,7 +260,11 @@ def check_ffversion(reduced):
                           'ff_class': AttractForceField2,
                           'minimizer_class': Lbfgs
                           },
-
+
+             'IMC': {'ff_file': 'imc.par', 
+                          'ff_class': ImcForceField,
+                          'minimizer_class': ImcLbfgs
+                          },
            }
 
 
@@ -418,9 +422,9 @@ def check_ffversion(reduced):
 
         #calculates true energy, and rmsd if possible
         #with the new ligand position
-        forcefield=ff_specs['ff_class'](ff_specs['ff_file'],  surreal(500))
+        forcefield=ff_specs['ff_class'](ff_specs['ff_file'],  surreal(15))
         print "%4s %6s %6s %13s %13s"  %(" ","Trans", "Rot", "Ener", "RmsdCA_ref")
-        pl = AttractPairList(rec, ligand,surreal(500))
+        pl = AttractPairList(rec, ligand,surreal(15))
         print "%-4s %6d %6d %13.7f %13s" %("==", transnb, rotnb, forcefield.nonbon8(rec,ligand,pl), str(rms))
         output.PrintMatrix()
 

PyAttract/reduce.py

@@ -11,7 +11,7 @@
 parser = OptionParser(usage)
 
 # --ff option: choice of forcefield
-parser.add_option("--ff",type="str",dest="ffversion",help="choice of CG force field: attract1, attract2 or scorpion")
+parser.add_option("--ff",type="str",dest="ffversion",help="choice of CG force field: attract1, attract2, scorpion, or imc")
 
 # --cgopt option: choice of charge optimization with SCORPION
 parser.add_option("--cgopt", dest="optimizecharges", action="store_true", default=False,
@@ -39,8 +39,8 @@
 
 # define other parameter files
 cmd_options=[]
-if options.ffversion not in ["attract1","attract2","scorpion"]:
-    sys.stderr.write ("Error: please choose one of the following CG force field: attract1, attract2 or scorpion\n")
+if options.ffversion not in ["attract1","attract2","scorpion","imc"]:
+    sys.stderr.write ("Error: please choose one of the following CG force field: attract1, attract2, scorpion, or imc\n")
     sys.exit(1)
 if options.warning:
     if options.ffversion!="scorpion":
@@ -72,3 +72,9 @@
     prgname = os.path.join(thispath, "reduce_attract2.py")
 
     os.system(prgname +  " %s"%" ".join(cmd_options))
+
+if options.ffversion=="imc":
+    cmd_options.append(args[0])
+    prgname = os.path.join(thispath, "reduce_imc.py")
+
+    os.system(prgname +  " %s"%" ".join(cmd_options))