PeriodicTable: Atomic elements widgets

Periodic table widgets

Classes

Widgets:

• PeriodicTable
• PeriodicList
• PeriodicCombo

Data model:

• PeriodicTableItem
• ColoredPeriodicTableItem

Example of usage

This example uses the widgets with the standard builtin elements list.

from silx.gui import qt
from silx.gui.widgets.PeriodicTable import PeriodicTable,         PeriodicCombo, PeriodicList

a = qt.QApplication([])

w = qt.QTabWidget()

ptable = PeriodicTable(w, selectable=True)
pcombo = PeriodicCombo(w)
plist = PeriodicList(w)

w.addTab(ptable, "PeriodicTable")
w.addTab(plist, "PeriodicList")
w.addTab(pcombo, "PeriodicCombo")

ptable.setSelection(['H', 'Fe', 'Si'])
plist.setSelectedElements(['H', 'Be', 'F'])
pcombo.setSelection("Li")

def change_list(items):
    print("New list selection:", [item.symbol for item in items])

def change_combo(item):
    print("New combo selection:", item.symbol)

def click_table(item):
    print("New table click:", item.symbol)

def change_table(items):
    print("New table selection:", [item.symbol for item in items])

ptable.sigElementClicked.connect(click_table)
ptable.sigSelectionChanged.connect(change_table)
plist.sigSelectionChanged.connect(change_list)
pcombo.sigSelectionChanged.connect(change_combo)

w.show()
a.exec_()

The second example explains how to define custom elements.

from silx.gui import qt
from silx.gui.widgets.PeriodicTable import PeriodicTable,         PeriodicCombo, PeriodicList
from silx.gui.widgets.PeriodicTable import PeriodicTableItem

# subclass PeriodicTableItem
class MyPeriodicTableItem(PeriodicTableItem):
    "New item with added mass number and number of protons"
    def __init__(self, symbol, Z, A, col, row, name, mass,
                 subcategory=""):
        PeriodicTableItem.__init__(
                self, symbol, Z, col, row, name, mass,
                subcategory)

        self.A = A
        "Mass number (neutrons + protons)"

        self.num_neutrons = A - Z
        "Number of neutrons"

# build your list of elements
my_elements = [MyPeriodicTableItem("H", 1, 1, 1, 1, "hydrogen",
                                   1.00800, "diatomic nonmetal"),
               MyPeriodicTableItem("He", 2, 4, 18, 1, "helium",
                                    4.0030, "noble gas"),
               # etc ...
               ]

app = qt.QApplication([])

ptable = PeriodicTable(elements=my_elements, selectable=True)
ptable.show()

def click_table(item):
    "Callback function printing the mass number of clicked element"
    print("New table click, mass number:", item.A)

ptable.sigElementClicked.connect(click_table)
app.exec_()

Widgets

class PeriodicTable(parent=None, name='PeriodicTable', elements=None, selectable=False)

Bases: PyQt5.QtWidgets.QWidget

Periodic Table widget

The following example shows how to connect clicking to selection:

from silx.gui import qt
from silx.gui.widgets.PeriodicTable import PeriodicTable
app = qt.QApplication([])
pt = PeriodicTable()
pt.sigElementClicked.connect(pt.elementToggle)
pt.show()
app.exec_()

To print all selected elements each time a new element is selected:

def my_slot(item):
    pt.elementToggle(item)
    selected_elements = pt.getSelection()
    for e in selected_elements:
        print(e.symbol)

pt.sigElementClicked.connect(my_slot)

sigElementClicked

When any element is clicked in the table, the widget emits this signal and sends a PeriodicTableItem object.

sigSelectionChanged

When any element is selected/unselected in the table, the widget emits this signal and sends a list of PeriodicTableItem objects.

Note

To enable selection of elements, you must set selectable=True when you instantiate the widget. Alternatively, you can also connect sigElementClicked to elementToggle() manually:

pt = PeriodicTable()
pt.sigElementClicked.connect(pt.elementToggle)

Parameters:

• parent – parent QWidget
• name (str) – Widget window title
• elements – List of items (PeriodicTableItem objects) to be represented in the table. By default, take elements from a predefined list with minimal information (symbol, atomic number, name, mass).
• selectable (bool) – If True, multiple elements can be selected by clicking with the mouse. If False (default), selection is only possible with method setSelection().

getSelection()

Return a list of selected elements, as a list of PeriodicTableItem objects.

Returns:Selected items Return type:List[PeriodicTableItem]

setSelection(symbols)

Set selected elements.

This causes the sigSelectionChanged signal to be emitted, even if the selection didn’t actually change.

Parameters:symbols (List[str]) – List of symbols of elements to be selected (e.g. [“Fe”, “Hg”, “Li”])

setElementSelected(symbol, state)

Modify selected status of a single element (select or unselect)

Parameters:

• symbol (str) – PeriodicTableItem symbol to be selected
• state (bool) – True to select, False to unselect

isElementSelected(symbol)

Return True if element is selected, else False

Parameters:symbol (str) – PeriodicTableItem symbol Returns:True if element is selected, else False

class PeriodicList(parent=None, detailed=True, single=False, elements=None)

Bases: PyQt5.QtWidgets.QTreeWidget

List of atomic elements in a QTreeView

Parameters:

• parent (QWidget) – Parent widget
• detailed (bool) – True (default) display element symbol, Z and name. False display only element symbol and Z.
• single – True for single element selection with mouse click, False for multiple element selection mode.

sigSelectionChanged

When any element is selected/unselected in the widget, it emits this signal and sends a list of currently selected PeriodicTableItem objects.

getSelection()

Get a list of selected elements, as a list of PeriodicTableItem objects.

Returns:Selected elements Return type:List[PeriodicTableItem]

setSelectedElements(symbolList)

Parameters:symbolList – List of atomic symbols [“H”, “He”, “Li”…] to be selected in the widget

class PeriodicCombo(parent=None, detailed=True, elements=None)

Bases: PyQt5.QtWidgets.QComboBox

Combo list with all atomic elements of the periodic table

Parameters:

• detailed (bool) – True (default) display element symbol, Z and name. False display only element symbol and Z.
• elements – List of items (PeriodicTableItem objects) to be represented in the table. By default, take elements from a predefined list with minimal information (symbol, atomic number, name, mass).

sigSelectionChanged

Signal emitted when the selection changes. Send PeriodicTableItem object representing selected element

getSelection()

Get selected element

Returns:Selected element Return type:PeriodicTableItem

setSelection(symbol)

Set selected item in combobox by giving the atomic symbol

Parameters:symbol – Symbol of element to be selected

Data model

class PeriodicTableItem(symbol, Z, col, row, name, mass, subcategory='')

Periodic table item, used as generic item in PeriodicTable, PeriodicCombo and PeriodicList.

This implementation stores the minimal amount of information needed by the widgets:

• atomic symbol
• atomic number
• element name
• atomic mass
• column of element in periodic table
• row of element in periodic table

You can subclass this class to add additional information.

Parameters:

• symbol (str) – Atomic symbol (e.g. H, He, Li…)
• Z (int) – Proton number
• col (int) – 1-based column index of element in periodic table
• row (int) – 1-based row index of element in periodic table
• name (str) – PeriodicTableItem name (“hydrogen”, …)
• mass (float) – Atomic mass (gram per mol)
• subcategory (str) – Subcategory, based on physical properties (e.g. “alkali metal”, “noble gas”…)

symbol = None

Atomic symbol (e.g. H, He, Li…)

Z = None

Atomic number (Proton number)

col = None

1-based column index of element in periodic table

row = None

1-based row index of element in periodic table

name = None

PeriodicTableItem name (“hydrogen”, …)

mass = None

Atomic mass (gram per mol)

subcategory = None

Subcategory, based on physical properties (e.g. “alkali metal”, “noble gas”…)

class ColoredPeriodicTableItem(symbol, Z, col, row, name, mass, subcategory='', bgcolor=None)

Bases: silx.gui.widgets.PeriodicTable.PeriodicTableItem

PeriodicTableItem with an added bgcolor. The background color can be passed as a parameter to the constructor. If it is not specified, it will be defined based on subcategory.

Parameters:bgcolor (str) – Custom background color for element in periodic table, as a RGB string #RRGGBB

COLORS = {'': '#FFFFFF', 'actinide': '#F08080', 'alkali metal': '#FFE4B5', 'alkaline earth metal': '#FFA500', 'diatomic nonmetal': '#7FFF00', 'lanthanide': '#FFB6C1', 'metalloid': '#8FBC8F', 'noble gas': '#00FFFF', 'polyatomic nonmetal': '#7FFFD4', 'post transition metal': '#D3D3D3', 'transition metal': '#FFA07A'}

Dictionary defining RGB colors for each subcategory.

bgcolor = None

Background color of element in the periodic table, based on its subcategory. This should be a string of a hexadecimal RGB code, with the format #RRGGBB. If the subcategory is unknown, use white (#FFFFFF)