fixed ad4 parameter file

src/config.py

@@ -18,7 +18,7 @@
 
 DOCKEY_VERSION = "0.9.0"
 
-DOCKEY_BUILD = "230830"
+DOCKEY_BUILD = "230915"
 
 DOCKEY_ABOUT = """
 <p>Dockey - Molecular Docking and Virtual Screening</p>

src/param.py

@@ -157,7 +157,7 @@ def __init__(self):
 			type = str,
 			default = '',
 			value = '',
-			comment = 'Parameter library filename',
+			comment = 'Parameter library file',
 			scope = 'global',
 			required = False,
 			user = True
@@ -788,6 +788,14 @@ def make_dpf_file(self, receptor_file, ligand_file, flex=False):
 				for m in v.value:
 					rows.append("map {}".format(m))
 
+			if k == 'parameter_file':
+				if os.path.isfile(v):
+					plf = os.path.join(os.path.dirname(receptor_file), "param_library.dat")
+					with open(v) as fh, open(plf, 'w') as fw:
+						fw.write(fh.read())
+
+					rows.append("parameter_file param_library.dat")
+
 			elif v.type in (int, str):
 				rows.append("{} {}".format(k, v.value))
 

src/widget.py

@@ -1864,20 +1864,35 @@ def sizeHint(self):
 	@Slot()
 	def update_resource_usage(self):
 		process_count = 1
-		cpu_percent = self.proc.cpu_percent(interval=0.1)
-		memory_size = self.proc.memory_info().rss
-		memory_percent = self.proc.memory_percent()
-
-		for child in self.proc.children(recursive=True):
-			process_count += 1
-			cpu_percent += child.cpu_percent(interval=0.1)
-			memory_size += child.memory_info().rss
-			memory_percent += child.memory_percent()
-
-		self.cpu_usage.setValue(int(cpu_percent/psutil.cpu_count(False)))
+		cpu_percent = 0
+		memory_size = 0
+		memory_percent = 0
+
+		try:
+			with self.proc.oneshot():
+				cpu_percent = self.proc.cpu_percent(interval=0.1)
+				memory_size = self.proc.memory_info().rss
+				memory_percent = self.proc.memory_percent()
+		except psutil.NoSuchProcess:
+			pass
+
+		try:
+			children = self.proc.children(recursive=True)
+		except psutil.NoSuchProcess:
+			children = []
+
+		for child in children:
+			try:
+				with child.oneshot():
+					process_count += 1
+					cpu_percent += child.cpu_percent(interval=0.1)
+					memory_size += child.memory_info().rss
+					memory_percent += child.memory_percent()
+			except psutil.NoSuchProcess:
+				pass
+
+		self.cpu_usage.setValue(int(cpu_percent/psutil.cpu_count()))
 		self.memory_usage.setValue(int(memory_percent))
 		self.memory_text.setText("Memory: {} \t Running processes: {}".format(
 			memory_format(memory_size), process_count
 		))
-
-

src/window.py

@@ -554,7 +554,7 @@ def create_actions(self):
 		self.pymol_cmd_act.setChecked(False)
 		self.pymol_cmd_act.setIconVisibleInMenu(False)
 
-		self.check_cpu_act = QAction(QIcon(':/icons/cpu.svg'), "View CPU Consumption", self)
+		self.check_cpu_act = QAction(QIcon(':/icons/cpu.svg'), "CPU and Memory Usage", self)
 		self.check_cpu_act.setIconVisibleInMenu(False)
 		self.check_cpu_act.triggered.connect(self.view_cpu_consumption)
 
@@ -701,6 +701,7 @@ def create_menus(self):
 
 		self.task_menu = self.menuBar().addMenu("&Task")
 		self.task_menu.addAction(self.task_act)
+		self.task_menu.addAction(self.check_cpu_act)
 
 		self.pymol_menu = self.menuBar().addMenu("&PyMOL")