DockingPie now compatible with Vina > 1.2

DockingPie1/lib/docking_program_main/Functions/vina_functions.py

@@ -0,0 +1,268 @@
+# Copyright 2022 by Serena Rosignoli. All rights reserved.
+# This code is part of the DockingPie package and governed by its license. Please
+# see the LICENSE file.
+
+
+import os
+import sys
+import shutil
+import re
+import json
+import datetime
+
+# PyMOL.
+from pymol import cmd
+from pymol import cmd
+from pymol.cgo import *
+from pymol.vfont import plain
+from pymol import stored
+
+from pymol.Qt import QtWidgets, QtCore, QtGui
+
+import os
+import shutil
+import warnings
+import math
+import subprocess
+from subprocess import check_output
+import statistics
+import re
+
+from pathlib import Path
+
+from lib.docking_program_main.Functions.threads import Protocol_exec_dialog
+from lib.docking_program_main.Functions.handle_widgets import HandleWidgets
+
+from Bio.PDB import PDBParser, PDBIO
+from Bio.PDB.PDBIO import Select
+
+
+class Vina_docking():
+
+
+    """
+    A class to represent the Vina docking process
+
+    """
+
+
+    def __init__(self, tab, ligand, receptor, cavity = None):
+
+        self.tab = tab.tab
+        self.thread = tab
+
+        self.path_to_vina = self.tab.docking_programs_child_tabs.docking_programs.path_to_vina
+
+        ### CHECK VINA VERSION ###
+        check_vina = check_output([self.path_to_vina, "--version"])
+        self.vina_version = re.search("([\d.]+)", str(check_vina)).group(0)
+
+        self.docking_completed = False
+        self.interrupt = False
+        self.use_flex_protocol = False
+
+        # Initialize Standard Docking parameters
+        self.receptor_to_dock = receptor
+        self.poses = str(self.tab.poses_box.value())
+        self.ligand_to_dock = ligand
+
+        self.exhaustiveness = self.tab.exhaustiveness_box.value()
+        self.energy = self.tab.energy_box.value()
+
+        if cavity is not None:
+
+            name_cav = cavity
+            self.cavity_to_dock = self.tab.docking_programs_child_tabs.docking_programs.ready_grid_centers[name_cav]
+            self.cavity_name = name_cav
+
+        else:
+
+            name_cav = self.tab.loaded_cavities.currentText()
+            self.cavity_to_dock = self.tab.docking_programs_child_tabs.docking_programs.ready_grid_centers[name_cav]
+            self.cavity_name = name_cav
+
+        # Initialize Flexible Docking
+        if self.tab.use_flex_vina_cb.isChecked():
+            self.use_flex_protocol = True
+
+            self.flex_residues = self.tab.flex_arg_edit.text()
+            self.check_valid_flex_input()
+
+        # Initialize names and paths
+        self.results_file_name = str("Run_" + str(self.tab.docking_programs_child_tabs.docking_programs.vina_runs) + "_Vina")
+        self.results_file_name_ext = str(self.results_file_name + ".pdbqt")
+
+        if float(self.vina_version[:3]) > 1.1:
+            self.log_file_name = None
+        else:
+            self.log_file_name = str(self.results_file_name + "_log.txt")
+
+        # Change directory --> Vina tmp dir
+        os.chdir(self.tab.docking_programs_child_tabs.docking_programs.vina_tmp_dir)
+
+        self.show_resume_window()
+
+
+    def check_valid_flex_input(self):
+        pass
+
+
+    def show_resume_window(self):
+
+        self.run_docking_vina()
+
+
+    def run_docking_vina(self):
+
+        x_val = float(self.cavity_to_dock[3])*float(self.cavity_to_dock[6])
+        y_val = float(self.cavity_to_dock[4])*float(self.cavity_to_dock[6])
+        z_val = float(self.cavity_to_dock[5])*float(self.cavity_to_dock[6])
+
+        self.run_docking_vina_settings = [self.path_to_vina,
+        "--receptor", str(self.receptor_to_dock + ".pdbqt"),
+        "--ligand", str(self.ligand_to_dock  + ".pdbqt"),
+        "--center_x", self.cavity_to_dock[0],
+        "--center_y", self.cavity_to_dock[1],
+        "--center_z", self.cavity_to_dock[2],
+        "--size_x", str(x_val),
+        "--size_y", str(y_val),
+        "--size_z", str(z_val),
+        "--out", self.results_file_name_ext,
+        "--exhaustiveness", str(self.exhaustiveness),
+        "--num_modes", str(self.poses),
+        "--energy_range", str(self.energy)]
+
+        if float(self.vina_version[:3]) > 1.1:
+            pass
+        else:
+            self.run_docking_vina_settings.extend(["--log", self.log_file_name])
+
+        if self.use_flex_protocol:
+
+            # Generate pdbqt file with flexible side chains
+            self.prepare_flex_receptor_path = os.path.join(self.tab.docking_programs_child_tabs.docking_programs.config_path, "prepare_flexreceptor4.py")
+            self.preapre_flex_receptors_settings = ["python",
+            self.prepare_flex_receptor_path,
+            "-r", str(self.receptor_to_dock + ".pdbqt"),
+            "-s", self.receptor_to_dock + ":" + self.flex_residues, "-v"]
+
+            try:
+                subprocess.run(self.preapre_flex_receptors_settings,
+                check = True)
+
+            except subprocess.CalledProcessError as error:
+                print(error)
+                self.docking_completed = False
+
+            flexible_receptor_name = str(self.receptor_to_dock + "_flex.pdbqt")
+
+            # Extend options for docking
+            self.run_docking_vina_settings.extend(["--flex", flexible_receptor_name])
+
+        self.tab.docking_programs_child_tabs.docking_programs.vina_runs += 1
+
+
+    def check_if_docking_completed(self):
+
+        file_path = os.path.join(self.tab.docking_programs_child_tabs.docking_programs.vina_tmp_dir, self.results_file_name_ext)
+
+        if Path(file_path).is_file():
+
+            if os.path.getsize(file_path):
+                self.docking_completed = True
+                self.tab.docking_programs_child_tabs.docking_programs.vina_runs += 1
+
+            else:
+                self.docking_completed = False
+
+                if len(self.tab.ligands_to_dock) > 1 or len(self.tab.receptors_to_dock) > 1:
+
+                    os.remove(file_path)
+                    self.tab.docking_programs_child_tabs.docking_programs.vina_runs += 1
+
+                else:
+                    os.remove(file_path)
+                    self.tab.docking_programs_child_tabs.docking_programs.vina_runs += 1
+                    QtWidgets.QMessageBox.warning(self.tab, "", str("Something went wrong during Docking. \nPlease check LOG files."))
+
+        else:
+            self.docking_completed = False
+            QtWidgets.QMessageBox.warning(self.tab, "", str("Something went wrong during Docking. \nPlease check LOG files."))
+            self.tab.docking_programs_child_tabs.docking_programs.vina_runs += 1
+
+
+class Vina_Parse_Results:
+
+
+    """
+    A class to parse the Smina results file
+    """
+
+
+    def __init__(self, tab, results_file_name, results_dict, poses, results_data = [[]]):
+
+
+        self.tab = tab.tab
+        self.last_docking = self.tab.last_docking
+
+        self.results_file_name = results_file_name
+
+        self.results_dict = results_dict
+
+        self.results_data = results_data
+
+        self.SCORE = float(00.00)
+
+        self.docked_ligands_list = []
+
+        input = open(str(self.results_file_name + ".pdbqt"), "rt")
+
+        list_of_list = []
+        list_of_all_scores = []
+        self.poses_list = []
+
+        n = 0
+
+        for line in input:
+
+            if line.startswith("REMARK VINA RESULT: "):
+
+                values_line = str(line.strip())
+
+                self.SCORE = values_line.split()[3]
+                self.RMSD_lb = values_line.split()[4]
+                self.RMSD_ub = values_line.split()[5]
+
+            elif line.startswith("MODEL "):
+
+                # name_line = str(line.strip())
+                # name = name_line.split("/")[-1]
+
+                name = self.last_docking.ligand_to_dock
+                self.poses_list.append(name)
+                self.NAME = name
+                self.POSE = str(len(self.poses_list))
+
+            elif line.startswith("ENDMDL"):
+                new_list = [self.NAME, self.POSE, self.SCORE, self.RMSD_lb, self.RMSD_ub]
+                list_of_list.append(new_list)
+                list_of_all_scores.append(self.SCORE)
+
+
+        self.results_data = list_of_list
+        self.TOT_SCORE = list_of_all_scores
+
+        input.close()
+
+
+    def check_name(self, name):
+
+        if self.poses_list:
+
+            for i in self.poses_list:
+                if str(i) == name:
+                    return True
+                else:
+                     return False
+        else:
+            return True