Add new selectors and change layout in AtomSelectionWidget

MDANSE/Src/MDANSE/Framework/AtomSelector/group_selection.py

@@ -41,7 +41,7 @@ def select_labels(trajectory: Trajectory, **function_parameters: Dict[str, Any])
     atom_labels = function_parameters.get("atom_labels", None)
     for label in atom_labels:
         if label in system._labels:
-            selection = selection.union(reduce(list.__add__, system._labels[label]))
+            selection = selection.union(system._labels[label])
     return selection
 
 

MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/AtomSelectionWidget.py

@@ -30,6 +30,8 @@
     QPlainTextEdit,
     QWidget,
     QListView,
+    QAbstractItemView,
+    QScrollArea,
 )
 from MDANSE_GUI.InputWidgets.WidgetBase import WidgetBase
 from MDANSE_GUI.Tabs.Visualisers.View3D import View3D
@@ -40,6 +42,9 @@
     AllAtomSelection,
     AtomSelection,
     IndexSelection,
+    MoleculeSelection,
+    PatternSelection,
+    LabelSelection,
 )
 
 
@@ -110,29 +115,9 @@ class SelectionHelper(QDialog):
     ----------
     _helper_title : str
         The title of the helper dialog window.
-    _cbox_text : dict
-        The dictionary that maps the selector settings to text used in
-        the helper dialog.
     """
 
     _helper_title = "Atom selection helper"
-    _cbox_text = {
-        "all": "All atoms (excl. dummy atoms):",
-        "dummy": "All dummy atoms:",
-        "hs_on_heteroatom": "Hs on heteroatoms:",
-        "primary_amine": "Primary amine groups:",
-        "hydroxy": "Hydroxy groups:",
-        "methyl": "Methyl groups:",
-        "phosphate": "Phosphate groups:",
-        "sulphate": "Sulphate groups:",
-        "thiol": "Thiol groups:",
-        "water": "Water molecules:",
-        "hs_on_element": "Hs on elements:",
-        "element": "Elements:",
-        "name": "Atom name:",
-        "fullname": "Atom fullname:",
-        "index": "Indexes:",
-    }
 
     def __init__(
         self,
@@ -176,16 +161,19 @@ def __init__(
         for button in self.create_buttons():
             bottom.addWidget(button)
 
-        layouts[-1].addLayout(bottom)
-
         helper_layout = QHBoxLayout()
-        for layout in layouts:
-            helper_layout.addLayout(layout)
+        sub_layout = QVBoxLayout()
+        helper_layout.addLayout(layouts[0])
+        helper_layout.addLayout(sub_layout)
+        for layout in layouts[1:]:
+            sub_layout.addLayout(layout)
+        sub_layout.addLayout(bottom)
 
         self.setLayout(helper_layout)
 
         self.all_selection = True
         self.selected = set([])
+        self.reset()
 
     def closeEvent(self, a0):
         """Hide the window instead of closing. Some issues occur in the
@@ -224,7 +212,7 @@ def create_layouts(self) -> list[QVBoxLayout]:
         for widget in self.left_widgets():
             left.addWidget(widget)
 
-        right = QVBoxLayout()
+        right = QHBoxLayout()
         for widget in self.right_widgets():
             right.addWidget(widget)
 
@@ -238,7 +226,7 @@ def right_widgets(self) -> list[QWidget]:
             List of QWidgets to add to the right layout from
             create_layouts.
         """
-        return [self.selection_textbox]
+        return [self.selection_operations_view, self.selection_textbox]
 
     def left_widgets(self) -> list[QWidget]:
         """
@@ -251,11 +239,16 @@ def left_widgets(self) -> list[QWidget]:
 
         select = QGroupBox("selection")
         select_layout = QVBoxLayout()
+        scroll_area = QScrollArea()
+        scroll_area.setLayout(select_layout)
 
         self.selection_widgets = [
             AllAtomSelection(self),
             AtomSelection(self, self.trajectory),
             IndexSelection(self),
+            MoleculeSelection(self, self.trajectory),
+            PatternSelection(self),
+            LabelSelection(self, self.trajectory),
         ]
 
         for widget in self.selection_widgets:
@@ -274,15 +267,15 @@ def left_widgets(self) -> list[QWidget]:
 
         select.setLayout(select_layout)
 
-        preview = QGroupBox("Selection operations")
-        preview_layout = QVBoxLayout()
-        preview.setLayout(preview_layout)
-        self.selection_operations_view = QListView(preview)
+        self.selection_operations_view = QListView(self)
         self.selection_operations_view.setDragEnabled(True)
+        self.selection_operations_view.setAcceptDrops(True)
+        self.selection_operations_view.setDragDropMode(
+            QAbstractItemView.DragDropMode.InternalMove
+        )
         self.selection_operations_view.setModel(self.selection_model)
         self.selection_model.selection_changed.connect(self.recalculate_selection)
-        preview_layout.addWidget(self.selection_operations_view)
-        return [select, preview]
+        return [select]
 
     @Slot()
     def recalculate_selection(self):

MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/CheckableComboBox.py

@@ -44,6 +44,10 @@ def __init__(self, *args, **kwargs):
 
     def clear(self):
         result = super().clear()
+        self.items = []
+        self.checked = []
+        self.text = []
+        self.select_all_item = None
         self.addItem("select all", underline=True)
         self.lineEdit().setText("")
         return result

MDANSE_GUI/Src/MDANSE_GUI/Widgets/SelectionWidgets.py

@@ -30,11 +30,6 @@
 
 from MDANSE_GUI.InputWidgets.CheckableComboBox import CheckableComboBox
 from MDANSE.MolecularDynamics.Trajectory import Trajectory
-from MDANSE.Framework.AtomSelector.general_selection import (
-    select_all,
-    select_none,
-    invert_selection,
-)
 
 
 class BasicSelectionWidget(QGroupBox):
@@ -143,7 +138,7 @@ def parameter_dictionary(self):
 
 
 class IndexSelection(BasicSelectionWidget):
-    def __init__(self, parent=None, widget_label="Select atoms"):
+    def __init__(self, parent=None, widget_label="Index selection"):
         super().__init__(parent, widget_label)
         self.selection_keyword = "index_list"
 
@@ -170,18 +165,112 @@ def switch_mode(self, new_mode: str):
         if new_mode == "list":
             self.selection_field.setPlaceholderText("0,1,2")
             self.selection_keyword = "index_list"
-            self.selection_separator = ','
+            self.selection_separator = ","
         if new_mode == "range":
             self.selection_field.setPlaceholderText("0-20")
             self.selection_keyword = "index_range"
-            self.selection_separator = '-'
+            self.selection_separator = "-"
         if new_mode == "slice":
             self.selection_field.setPlaceholderText("first:last:step")
             self.selection_keyword = "index_slice"
-            self.selection_separator = ':'
+            self.selection_separator = ":"
 
     def parameter_dictionary(self):
         function_parameters = {"function_name": "select_atoms"}
         selection = self.selection_field.text()
-        function_parameters[self.selection_keyword] = [int(x) for x in selection.split(self.selection_separator)]
+        function_parameters[self.selection_keyword] = [
+            int(x) for x in selection.split(self.selection_separator)
+        ]
+        return function_parameters
+
+
+class MoleculeSelection(BasicSelectionWidget):
+    def __init__(
+        self,
+        parent=None,
+        trajectory: Trajectory = None,
+        widget_label="Select molecules",
+    ):
+        self.molecule_names = []
+        if trajectory:
+            self.molecule_names = list(trajectory.chemical_system._clusters.keys())
+        super().__init__(parent, widget_label)
+
+    def add_specific_widgets(self):
+        layout = self.layout()
+        layout.addWidget(QLabel("Select molecules named: "))
+        self.selection_field = CheckableComboBox(self)
+        layout.addWidget(self.selection_field)
+        self.selection_field.addItems(self.molecule_names)
+
+    def parameter_dictionary(self):
+        function_parameters = {"function_name": "select_molecules"}
+        selection = self.selection_field.checked_values()
+        function_parameters["molecule_names"] = selection
+        return function_parameters
+
+
+class LabelSelection(BasicSelectionWidget):
+    def __init__(
+        self,
+        parent=None,
+        trajectory: Trajectory = None,
+        widget_label="Select by label",
+    ):
+        self.labels = []
+        if trajectory:
+            self.labels = list(trajectory.chemical_system._labels.keys())
+        super().__init__(parent, widget_label)
+
+    def add_specific_widgets(self):
+        layout = self.layout()
+        layout.addWidget(QLabel("Select atoms with label: "))
+        self.selection_field = CheckableComboBox(self)
+        layout.addWidget(self.selection_field)
+        self.selection_field.addItems(self.labels)
+
+    def parameter_dictionary(self):
+        function_parameters = {"function_name": "select_labels"}
+        selection = self.selection_field.checked_values()
+        function_parameters["atom_labels"] = selection
+        return function_parameters
+
+
+class PatternSelection(BasicSelectionWidget):
+    def __init__(
+        self,
+        parent=None,
+        widget_label="SMARTS pattern matching",
+    ):
+        self.pattern_dictionary = {
+            "primary amine": "[#7X3;H2;!$([#7][#6X3][!#6]);!$([#7][#6X2][!#6])](~[H])~[H]",
+            "hydroxy": "[#8;H1,H2]~[H]",
+            "methyl": "[#6;H3](~[H])(~[H])~[H]",
+            "phosphate": "[#15X4](~[#8])(~[#8])(~[#8])~[#8]",
+            "sulphate": "[#16X4](~[#8])(~[#8])(~[#8])~[#8]",
+            "thiol": "[#16X2;H1]~[H]",
+        }
+        super().__init__(parent, widget_label)
+
+    def add_specific_widgets(self):
+        layout = self.layout()
+        layout.addWidget(QLabel("Pick a group"))
+        self.selection_field = QComboBox(self)
+        layout.addWidget(self.selection_field)
+        self.selection_field.addItems(self.pattern_dictionary.keys())
+        layout.addWidget(QLabel("pattern:"))
+        self.input_field = QLineEdit("", self)
+        self.input_field.setPlaceholderText("can be edited")
+        layout.addWidget(self.input_field)
+        self.selection_field.currentTextChanged.connect(self.update_string)
+
+    @Slot(str)
+    def update_string(self, key_string: str):
+        if key_string in self.pattern_dictionary:
+            self.input_field.setText(self.pattern_dictionary[key_string])
+
+    def parameter_dictionary(self):
+        function_parameters = {"function_name": "select_pattern"}
+        selection = self.input_field.text()
+        function_parameters["rdkit_pattern"] = selection
         return function_parameters