Feature/analyse pose

.gitignore

@@ -15,7 +15,7 @@ unidock/example/screening_test/unidock
 unidock/example/screening_test/fail_result
 unidock/example/screening_test/receptor_grids
 unidock/example/screening_test/unidock_root
-unidock/example/screening_test/test_dock
+unidock/example/screening_test/astex
 unidock_tools/dist
 unidock_tools/dist/*
 *.egg-info

unidock/example/index.py

@@ -0,0 +1,23 @@
+import glob
+import os
+from pathlib import Path
+def find_sdf_files_recursively(folder_path):
+    # 将字符串路径转换为Path对象
+    folder_path = Path(folder_path)
+
+    # 使用rglob查找所有以.sdf结尾的文件
+    sdf_files = list(folder_path.rglob('*.sdf'))
+
+    # 将Path对象列表转换为字符串路径列表
+    sdf_files_str = [str(file) for file in sdf_files]
+
+    return sdf_files_str
+
+# 假设我们要搜索的文件夹路径为'/path/to/your/folder'
+folder_path = '/home/yxyy/Documents/code/Uni-Dock/unidock/example/screening_test/astex'
+
+# 调用函数并打印结果
+sdf_files = find_sdf_files_recursively(folder_path)
+print(sdf_files)
+for sdf in sdf_files:
+    print(sdf)

unidock/example/screening_test/run_analysis.py

@@ -0,0 +1,55 @@
+import csv
+import subprocess
+import glob
+import os
+from pathlib import Path
+def find_sdf_files_recursively(folder_path):
+    # 将字符串路径转换为Path对象
+    folder_path = Path(folder_path)
+
+    # 使用rglob查找所有以.sdf结尾的文件
+    sdf_files = list(folder_path.rglob('*.sdf'))
+
+    # 将Path对象列表转换为字符串路径列表
+    sdf_files_str = [str(file) for file in sdf_files]
+
+    return sdf_files_str
+
+# 假设我们要搜索的文件夹路径为'/path/to/your/folder'
+folder_path = '/home/yxyy/Documents/code/Uni-Dock/unidock/example/screening_test/astex'
+
+# 调用函数并打印结果
+sdf_files = find_sdf_files_recursively(folder_path)
+sdf_files.sort()
+for sdf in sdf_files:
+    print(sdf)
+def build_commands_from_csv(csv_file):
+    commands = []
+    with open(csv_file, newline='') as csvfile:
+        reader = csv.DictReader(csvfile)
+        i=0
+        file_path = "/home/yxyy/Documents/code/Uni-Dock/unidock/example/screening_test/def_ligands.txt"
+
+        for row in reader:
+            with open(file_path, "w") as file:
+                file.write(sdf_files[i])
+            pdb_id = row['PDB_ID']
+            x = row['X']
+            y = row['Y']
+            z = row['Z']
+            command = f"../../build/unidock  --receptor ./receptor_grids/{pdb_id}/unidock/receptor_grids/protein_conf_0/protein.pdbqt --ligand_index def_ligands.txt --center_x {x} --center_y {y} --center_z {z} --size_x 27 --size_y 27 --size_z 27 --dir ./result/def --exhaustiveness 1024 --max_step 1 --num_modes 1024 --scoring vina --refine_step 5 --seed 5 --verbosity 1"
+            commands.append(command)
+            try:
+                # 使用shell=True来执行字符串形式的命令
+                subprocess.run(command, shell=True, check=True)
+                print(f"命令执行成功: {command}")
+            except subprocess.CalledProcessError as e:
+                print(f"命令执行失败: {command}\n错误信息: {e}")
+            i+=1
+    return commands
+
+# 调用函数并打印结果
+csv_file = '/home/yxyy/Documents/code/Uni-Dock/unidock/example/screening_test/astex/pdb_center.csv'
+commands = build_commands_from_csv(csv_file)
+# for command in commands:
+#     print(command)

unidock/src/lib/vina.cpp

@@ -949,8 +949,10 @@ std::string Vina::get_sdf_poses_gpu(int ligand_id, int how_many, double energy_r
                     - If there is no conf to write
                     - The energy of the current conf is superior than best_energy + energy_range
             */
-            if (n >= how_many || !not_max(m_poses_gpu[ligand_id][i].e)
-                || m_poses_gpu[ligand_id][i].e > best_energy + energy_range)
+        //    std::cout<<i<<std::endl;
+            // if (n >= how_many || !not_max(m_poses_gpu[ligand_id][i].e)
+            //     || m_poses_gpu[ligand_id][i].e > best_energy + energy_range)
+            if (n >= how_many)
                 break;  // check energy_range sanity FIXME
 
             // Push the current pose to model

unidock/src/main/main.cpp

@@ -345,7 +345,7 @@ bug reporting, license agreements, and more information.      \n";
         int max_step = 0;
         int max_gpu_memory = 0;
         int refine_step = 5;
-
+        bool safe_mode = false;
         // autodock4.2 weights
         double weight_ad4_vdw = 0.1662;
         double weight_ad4_hb = 0.1209;
@@ -412,7 +412,8 @@ bug reporting, license agreements, and more information.      \n";
             // >(&gpu_batch_ligand_names_sdf)->multitoken(), "gpu batch ligand (SDF)")
 
             ("scoring", value<std::string>(&sf_name)->default_value(sf_name),
-             "scoring function (ad4, vina or vinardo)");
+             "scoring function (ad4, vina or vinardo)")
+            ("safe_mode",bool_switch(&safe_mode));
         // options_description search_area("Search area (required, except with --score_only)");
         options_description search_area("Search space (required)");
         search_area.add_options()(
@@ -1018,6 +1019,7 @@ bug reporting, license agreements, and more information.      \n";
                 }
                 std::sort(ligands.begin(), ligands.end(), compareLigands);
                 int groupSize = ligands.size() / 4;
+                if (safe_mode==false){
                 std::vector<Ligand> smallGroup(ligands.begin(), ligands.begin() + groupSize);
                 std::vector<Ligand> mediumGroup(ligands.begin() + groupSize, ligands.begin() + 2 * groupSize);
                 std::vector<Ligand> largeGroup(ligands.begin() + 2 * groupSize, ligands.begin() + 3 * groupSize);
@@ -1052,7 +1054,13 @@ bug reporting, license agreements, and more information.      \n";
                         min_rmsd,max_evals,max_step,seed, refine_step, local_only, energy_range);
                 template_batch_docking<ExtraLargeConfig>(v,all_ligands,extraLargeGroup,"Extra Large",exhaustiveness, multi_bias,max_memory,
                         receptor_atom_numbers, out_dir,bias_file, num_modes,
-                        min_rmsd,max_evals,max_step,seed, refine_step, local_only, energy_range);
+                        min_rmsd,max_evals,max_step,seed, refine_step, local_only, energy_range);}
+                else{
+                   std::vector<Ligand> extraLargeGroup(ligands.begin(), ligands.end()); 
+                   template_batch_docking<ExtraLargeConfig>(v,all_ligands,extraLargeGroup,"Extra Large in safe mode",exhaustiveness, multi_bias,max_memory,
+                        receptor_atom_numbers, out_dir,bias_file, num_modes,
+                        min_rmsd,max_evals,max_step,seed, refine_step, local_only, energy_range); 
+                }
             }
         }
     }