updated param file format

Author: Truman-Xu

hyper.param

@@ -8,6 +8,8 @@ ligand_file = /home/ziqiaoxu/SampleDock/targets/CDK2_5IEV/Roniciclib.sd
                                                    # must be sd format
 ncycle = 1600                                      # number of cycles to be run
 ndesign = 20                                       # number of designs to be generated per cycle
+ensemble = 1                                       # top of number of design to generate the average structure 
+                                                   # (1 being just the top scoring structure)
 seed_smi = C1(C(NC2=CC=CC=C2)=NC=N3)=C3C=CC=C1     
                                                    # initial seeding SMILES for the first cycle, default to benzene
 

setup.py

@@ -9,11 +9,15 @@
 
 setup(
     name='sampledock',
-    version='0.3.4',
+    version='0.4',
     description='Molecular design framework the merges generative AI and molecular docking',
     author='Ziqiao Xu and Aaron Frank',
     author_email='[email protected]',
     url='https://github.com/atfrank/SampleDock',
     license=license,
     packages=find_packages()
+    package_data={
+        # Include hyper.param as default parameter file:
+        "hyperparameter": ["hyper.param"],
+    }
 )

test_hyper.param

@@ -6,6 +6,8 @@ receptor_file = ./targets/CDK2_5IEV/5IEV.mol2      # must be mol2 format
 ligand_file = ./targets/CDK2_5IEV/Roniciclib.sd    # must be sd format
 ncycle = 2                                         # number of cycles to be run
 ndesign = 10                                       # number of designs to be generated per cycle
+ensemble = 5                                       # top of number of design to generate the average structure 
+                                                   # (1 being just the top scoring structure)
 seed_smi = C1=CC=CC=C1                             # initial seeding SMILES for the first cycle, default to benzene
 
 ############### Parameters for rDock ###################