added receptor preprocessing

src/main.py

@@ -15,10 +15,6 @@ class DockeyApplication(QApplication):
 
 	def __init__(self, argv):
 		super().__init__(argv)
-		self.setOrganizationName("BIG")
-		self.setOrganizationDomain("dockey.readthedocs.io")
-		self.setApplicationName("Dockey")
-		self.setApplicationVersion(DOCKEY_VERSION)
 
 	def event(self, event):
 		if sys.platform == 'darwin':
@@ -33,14 +29,18 @@ def event(self, event):
 	#fix incorrect icon display in taskbar on Windows
 	if os.name == 'nt':
 		import ctypes
-		myappid = "BIG.Dockey.Dockey.{}".format(DOCKEY_VERSION)
+		myappid = "Dulab.Dockey.Dockey.{}".format(DOCKEY_VERSION)
 		ctypes.windll.shell32.SetCurrentProcessExplicitAppUserModelID(myappid)
 
+	QCoreApplication.setOrganizationName("Dulab")
+	QCoreApplication.setOrganizationDomain("big.cdu.edu.cn")
+	QCoreApplication.setApplicationName("Dockey")
+	QCoreApplication.setApplicationVersion(DOCKEY_VERSION)
+	QSettings.setDefaultFormat(QSettings.Format.IniFormat)
+
 	app = DockeyApplication(sys.argv)
 	win = DockeyMainWindow()
 
-	QSettings.setDefaultFormat(QSettings.Format.IniFormat)
-
 	#support for macos open with when associated with dock file
 	app.osx_open_with.connect(win.create_db_connect)
 

src/prepare.py

@@ -3,7 +3,10 @@
 import MolKit.molecule
 import MolKit.protein
 
-#from pdbfixer import PDBFixer
+from pdbfixer import PDBFixer
+from openmm.app import PDBFile
+
+from pdb2pqr.main import build_main_parser, main_driver
 
 from MolKit import Read
 from MolKit.molecule import BondSet
@@ -21,21 +24,64 @@
 from utils import load_molecule_from_file
 
 __all__ = ['prepare_autodock_ligand', 'prepare_autodock_receptor',
-	'prepare_meeko_ligand', 'prepare_ligand', 'prepare_flex_receptor'
+	'prepare_meeko_ligand', 'prepare_ligand', 'prepare_flex_receptor',
+	'fix_receptor_pdb', 'convert_pdb_to_pqr'
 ]
 
 
-def fix_receptor_pdb(receptor_file):
-	fixer = PDBFixer(receptor_file)
+def fix_receptor_pdb(pdbfile, outfile, params):
+	fixer = PDBFixer(filename = pdbfile)
 	fixer.findMissingResidues()
-	fixer.findNonstandardResidues()
-	fixer.replaceNonstandardResidues()
-	fixer.removeHeterogens(True)
-	fixer.findMissingAtoms()
-	fixer.addMissingAtoms()
-	fixer.addMissingHydrogens(7.0)
-	fixer.addSolvent(fixer.topology.getUnitCellDimensions())
 
+	if params['replace_nonres']:
+		fixer.findNonstandardResidues()
+		fixer.replaceNonstandardResidues()
+
+	if params['remove_heterogen']:
+		fixer.removeHeterogens(True)
+	else:
+		fixer.removeHeterogens(False)
+
+	if params['add_misheavy']:
+		fixer.findMissingAtoms()
+		fixer.addMissingAtoms()
+
+	if params['add_mishydrogen']:
+		fixer.addMissingHydrogens(params['mishydrogen_ph'])
+
+	with open(outfile, 'w') as fw:
+		PDBFile.writeFile(fixer.topology, fixer.positions, fw)
+
+def convert_pdb_to_pqr(pdbfile, pqrfile, params):
+	args_list = ["--ff", params['force_field']]
+
+	if params['force_field'] == 'PARSE':
+		if params['neutraln']:
+			args_list.append('--neutraln')
+
+		if params['neutralc']:
+			args_list.append('--neutralc')
+
+	if params['use_propka']:
+		args_list.extend(['--titration-state-method', 'propka'])
+		args_list.extend(['--with-ph', params['propka_ph']])
+
+	if params['node_bump']:
+		args_list.append('--nodebump')
+
+	if params['no_hopt']:
+		args_list.append('--noopt')
+
+	if params['remove_water']:
+		args_list.append('--drop-water')
+
+	args_list.append(pdbfile)
+	args_list.append(pqrfile)
+	args_list.extend(['--log-level', 'ERROR'])
+
+	parser = build_main_parser()
+	args = parser.parse_args(args_list)
+	main_driver(args)
 
 def prepare_autodock_ligand(ligand_file, ligand_pdbqt, params):
 	repairs = params['repairs']

src/process.py

@@ -211,6 +211,7 @@ def __init__(self, job, params, cmds, work_dir, producer):
 		self.dock_params = params[0]
 		self.ligp_params = params[1]
 		self.repp_params = params[2]
+		self.prep_params = params[3]
 		#self.grid_spacing = params[3]
 
 		if os.name == 'nt':
@@ -269,7 +270,7 @@ def update_success(self):
 	def prepare_receptor(self):
 		rpdbqt = os.path.join(self.work_dir, "{}.pdbqt".format(self.job.rn))
 
-		if self.job.rf in ['pdb', 'mol2']:
+		if self.job.rf == 'pdb':
 			content = self.job.rc
 			rfile = os.path.join(self.work_dir, "{}.{}".format(self.job.rn, self.job.rf))
 
@@ -280,6 +281,16 @@ def prepare_receptor(self):
 		with open(rfile, 'w', encoding='utf-8') as fw:
 			fw.write(content)
 
+		if self.prep_params['use_pdbfix']:
+			pfile = rfile
+			rfile = os.path.join(self.work_dir, "{}.fix.pdb".format(self.job.rn))
+			fix_receptor_pdb(pfile, rfile, self.prep_params)
+
+		if self.prep_params['use_pdbpqr']:
+			pfile = rfile
+			rfile = os.path.join(self.work_dir, "{}.pqr".format(self.job.rn))
+			convert_pdb_to_pqr(pfile, rfile, self.prep_params)
+
 		prepare_autodock_receptor(rfile, rpdbqt, self.repp_params)
 
 		#prepare flexible residues