Bug fix on tmap plotter

Author: Truman-Xu

hyper.param

@@ -1,15 +1,18 @@
 ## All relative path starts from the location of working directory not this file
 
 ############### Parameters for SnD #####################
-receptor_name = nCoV_6LU7                          # name the receptor to create dir
-receptor_file = ./targets/nCoV_6LU7/6LU7.mol2      # must be mol2 format
-ligand_file = ./targets/nCoV_6LU7/N3.sdf           # must be sd format
-ncycle = 1000                                      # number of cycles to be run
+receptor_name = CDK2_5IEV                          # name the receptor to create dir
+receptor_file = /home/ziqiaoxu/SampleDock/targets/CDK2_5IEV/5IEV.mol2      
+                                                   # must be mol2 format
+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
-seed_smi = C1=CC=CC=C1                             # initial seeding SMILES for the first cycle, default to benzene
+seed_smi = C1(C(NC2=CC=CC=C2)=NC=N3)=C3C=CC=C1     
+                                                   # initial seeding SMILES for the first cycle, default to benzene
 
 ############### Parameters for rDock ###################
-cavity_protocol = rbcavity -W -d -r                # cmd and option for creating pocket 
+cavity_protocol = rbcavity -was -d -r                # cmd and option for creating pocket 
                                                    # -W option for rxdock precompiled bin file, -was for locally compiled rdock installation
 docking_prm = dock.prm                             # docking protocol (-p), no solvation term by default 
 npose = 100                                        # number of poses generated (-n)
@@ -24,3 +27,7 @@ depthG = 3
 vocab_loc = ./models/moses-h450z56/vocab.txt
 model_loc = ./models/moses-h450z56/model.iter-400000
 
+########## Parameters for LSH Forest (tmap) #############
+node_size = 1/20                                   # Node size for tmap
+k = 20                                             # nearest neighbors
+mmm_repeats = 2

test_hyper.param

@@ -4,12 +4,12 @@
 receptor_name = CDK2-5IEV                          # name the receptor to create dir
 receptor_file = ./targets/CDK2_5IEV/5IEV.mol2      # must be mol2 format
 ligand_file = ./targets/CDK2_5IEV/Roniciclib.sd    # must be sd format
-ncycle = 5                                         # number of cycles to be run
+ncycle = 2                                         # number of cycles to be run
 ndesign = 10                                       # number of designs to be generated per cycle
 seed_smi = C1=CC=CC=C1                             # initial seeding SMILES for the first cycle, default to benzene
 
 ############### Parameters for rDock ###################
-cavity_protocol = rbcavity -W -d -r                # cmd and option for creating pocket
+cavity_protocol = rbcavity -was -d -r                # cmd and option for creating pocket
 docking_prm = dock.prm                             # docking protocol (-p), no solvation term by default 
 npose = 10                                         # number of poses generated (-n)
 prefix = pose_docked_                              # prefix of the output files from rDock
@@ -23,3 +23,7 @@ depthG = 3
 vocab_loc = ./models/moses-h450z56/vocab.txt
 model_loc = ./models/moses-h450z56/model.iter-400000
 
+########## Parameters for LSH Forest (tmap) #############
+node_size = 1/20                                   # Node size for tmap
+k = 20                                             # nearest neighbors
+mmm_repeats = 2