structures.py

"""Module to provide functionality to import structures."""
# pylint: disable=no-self-use

import io
import datetime
from collections import OrderedDict
import numpy as np
import ipywidgets as ipw
from traitlets import Instance, Int, List, Unicode, Union, dlink, link, default, observe

from sklearn.decomposition import PCA

# ASE imports
import ase
from ase import Atom, Atoms
from ase.data import chemical_symbols, covalent_radii

# AiiDA and AiiDAlab imports
from aiida.engine import calcfunction
from aiida.orm import CalcFunctionNode, CalcJobNode, Data, QueryBuilder, Node, WorkChainNode
from aiida.plugins import DataFactory
from .utils import get_ase_from_file
from .viewers import StructureDataViewer
from .data import LigandSelectorWidget

CifData = DataFactory('cif')  # pylint: disable=invalid-name
StructureData = DataFactory('structure')  # pylint: disable=invalid-name

SYMBOL_RADIUS = {key: covalent_radii[i] for i, key in enumerate(chemical_symbols)}


class StructureManagerWidget(ipw.VBox):
    '''Upload a structure and store it in AiiDA database.

    Attributes:
        structure(Atoms): trait that contains the selected structure. 'None' if no structure is selected.
        structure_node(StructureData, CifData): trait that contains AiiDA structure object
        node_class(str): trait that contains structure_node type (as string).
    '''

    input_structure = Union([Instance(Atoms), Instance(Data)], allow_none=True)
    structure = Union([Instance(Atoms), Instance(Data)], allow_none=True)
    structure_node = Instance(Data, allow_none=True, read_only=True)
    node_class = Unicode()

    SUPPORTED_DATA_FORMATS = {'CifData': 'cif', 'StructureData': 'structure'}

    def __init__(self, importers, viewer=None, editors=None, storable=True, node_class=None, **kwargs):
        """
        Arguments:
            importers(list): list of tuples each containing the displayed name of importer and the
                importer object. Each object should contain 'structure' trait pointing to the imported
                structure. The trait will be linked to 'structure' trait of this class.

            storable(bool): Whether to provide Store button (together with Store format)

            node_class(str): AiiDA node class for storing the structure.
                Possible values: 'StructureData', 'CifData' or None (let the user decide).
                Note: If your workflows require a specific node class, better fix it here.
        """

        # History of modifications
        self.history = []

        # Undo functionality.
        btn_undo = ipw.Button(description='Undo', button_style='success')
        btn_undo.on_click(self.undo)
        self.structure_set_by_undo = False

        # To keep track of last inserted structure object
        self._inserted_structure = None

        # Structure viewer.
        if viewer:
            self.viewer = viewer
        else:
            self.viewer = StructureDataViewer(downloadable=False)
        dlink((self, 'structure'), (self.viewer, 'structure'))

        # Store button.
        self.btn_store = ipw.Button(description='Store in AiiDA', disabled=True)
        self.btn_store.on_click(self.store_structure)

        # Label and description that are stored along with the new structure.
        self.structure_label = ipw.Text(description='Label')
        self.structure_description = ipw.Text(description='Description')

        # Store format selector.
        data_format = ipw.RadioButtons(options=self.SUPPORTED_DATA_FORMATS, description='Data type:')
        link((data_format, 'label'), (self, 'node_class'))

        # Store button, store class selector, description.
        store_and_description = [self.btn_store] if storable else []

        if node_class is None:
            store_and_description.append(data_format)
        elif node_class in self.SUPPORTED_DATA_FORMATS:
            self.node_class = node_class
        else:
            raise ValueError("Unknown data format '{}'. Options: {}".format(node_class,
                                                                            list(self.SUPPORTED_DATA_FORMATS.keys())))
        self.output = ipw.HTML('')

        children = [
            self._structure_importers(importers), self.viewer,
            ipw.HBox(store_and_description + [self.structure_label, self.structure_description])
        ]

        structure_editors = self._struture_editors(editors)
        if structure_editors:
            structure_editors = ipw.VBox([btn_undo, structure_editors])
            accordion = ipw.Accordion([structure_editors])
            accordion.selected_index = None
            accordion.set_title(0, 'Edit Structure')
            children += [accordion]

        super().__init__(children=children + [self.output], **kwargs)

    def _structure_importers(self, importers):
        """Preparing structure importers."""
        if not importers:
            raise ValueError("The parameter importers should contain a list (or tuple) of "
                             "importers, got a falsy object.")

        # If there is only one importer - no need to make tabs.
        if len(importers) == 1:
            # Assigning a function which will be called when importer provides a structure.
            dlink((importers[0], 'structure'), (self, 'input_structure'))
            return importers[0]

        # Otherwise making one tab per importer.
        importers_tab = ipw.Tab()
        importers_tab.children = [i for i in importers]  # One importer per tab.
        for i, importer in enumerate(importers):
            # Labeling tabs.
            importers_tab.set_title(i, importer.title)
            dlink((importer, 'structure'), (self, 'input_structure'))
        return importers_tab

    def _struture_editors(self, editors):
        """Preparing structure editors."""
        if editors and len(editors) == 1:
            link((editors[0], 'structure'), (self, 'structure'))
            if editors[0].has_trait('selection'):
                link((editors[0], 'selection'), (self.viewer, 'selection'))
            if editors[0].has_trait('camera_orientation'):
                dlink((self.viewer._viewer, '_camera_orientation'), (editors[0], 'camera_orientation'))  # pylint: disable=protected-access
            return editors[0]

        # If more than one editor was defined.
        if editors:
            editors_tab = ipw.Tab()
            editors_tab.children = [i for i in editors]
            for i, editor in enumerate(editors):
                editors_tab.set_title(i, editor.title)
                link((editor, 'structure'), (self, 'structure'))
                if editor.has_trait('selection'):
                    link((editor, 'selection'), (self.viewer, 'selection'))
                if editor.has_trait('camera_orientation'):
                    dlink((self.viewer._viewer, '_camera_orientation'), (editor, 'camera_orientation'))  # pylint: disable=protected-access
            return editors_tab
        return None

    def store_structure(self, _=None):
        """Stores the structure in AiiDA database."""

        if self.structure_node is None:
            return
        if self.structure_node.is_stored:
            self.output.value = "Already stored in AiiDA [{}], skipping...".format(self.structure_node)
            return
        self.btn_store.disabled = True
        self.structure_node.label = self.structure_label.value
        self.structure_label.disabled = True
        self.structure_node.description = self.structure_description.value
        self.structure_description.disabled = True

        if isinstance(self.input_structure, Data) and self.input_structure.is_stored:

            # Make a link between self.input_structure and self.structure_node
            @calcfunction
            def user_modifications(source_structure):  # pylint: disable=unused-argument
                return self.structure_node

            structure_node = user_modifications(self.input_structure)

        else:
            structure_node = self.structure_node.store()
        self.output.value = "Stored in AiiDA [{}]".format(structure_node)

    def undo(self, _):
        """Undo modifications."""
        self.structure_set_by_undo = True
        if self.history:
            self.history = self.history[:-1]
            if self.history:
                self.structure = self.history[-1]
            else:
                self.input_structure = None
        self.structure_set_by_undo = False

    @staticmethod
    @default('node_class')
    def _default_node_class():
        return 'StructureData'

    @observe('node_class')
    def _change_structure_node(self, _=None):
        with self.hold_trait_notifications():
            self._sync_structure_node()

    def _sync_structure_node(self):
        """Synchronize the structure_node trait using the currently provided info."""
        if len(self.history) > 1:
            # There are some modifications, so converting from ASE.
            structure_node = self._convert_to_structure_node(self.structure)
        else:
            structure_node = self._convert_to_structure_node(self.input_structure)
        self.set_trait('structure_node', structure_node)

    def _convert_to_structure_node(self, structure):
        """Convert structure of any type to the StructureNode object."""
        if structure is None:
            return None
        StructureNode = DataFactory(self.SUPPORTED_DATA_FORMATS[self.node_class])  # pylint: disable=invalid-name

        # If the input_structure trait is set to Atoms object, structure node must be created from it.
        if isinstance(structure, Atoms):
            return StructureNode(ase=structure)

        # If the input_structure trait is set to AiiDA node, check what type
        if isinstance(structure, Data):
            # Transform the structure to the StructureNode if needed.
            if isinstance(structure, StructureNode):
                return structure

        # Using self.structure, as it was already converted to the ASE Atoms object.
        return StructureNode(ase=self.structure)

    @observe('structure_node')
    def _observe_structure_node(self, change):
        """Modify structure label and description when a new structure is provided."""
        struct = change['new']
        if struct is None:
            self.btn_store.disabled = True
            self.structure_label.value = ''
            self.structure_label.disabled = True
            self.structure_description.value = ''
            self.structure_description.disabled = True
            return
        if struct.is_stored:
            self.btn_store.disabled = True
            self.structure_label.value = struct.label
            self.structure_label.disabled = True
            self.structure_description.value = struct.description
            self.structure_description.disabled = True
        else:
            self.btn_store.disabled = False
            self.structure_label.value = self.structure.get_chemical_formula()
            self.structure_label.disabled = False
            self.structure_description.value = ''
            self.structure_description.disabled = False

    @observe('input_structure')
    def _observe_input_structure(self, change):
        """Returns ASE atoms object and sets structure_node trait."""
        # If the `input_structure` trait is set to Atoms object, then the `structure` trait should be set to it as well.
        self.history = []

        if isinstance(change['new'], Atoms):
            self.structure = change['new']

        # If the `input_structure` trait is set to AiiDA node, then the `structure` trait should
        # be converted to an ASE Atoms object.
        elif isinstance(change['new'], CifData):  # Special treatement of the CifData object
            str_io = io.StringIO(change['new'].get_content())
            self.structure = ase.io.read(str_io, format='cif', reader='ase', store_tags=True)
        elif isinstance(change['new'], StructureData):
            self.structure = change['new'].get_ase()

        else:
            self.structure = None

    @observe('structure')
    def _structure_changed(self, change=None):
        """Perform some operations that depend on the value of `structure` trait.

        This function enables/disables `btn_store` widget if structure is provided/set to None.
        Also, the function sets `structure_node` trait to the selected node type.
        """
        if not self.structure_set_by_undo:
            self.history.append(change['new'])

        # If structure trait was set to None, structure_node should become None as well.
        if self.structure is None:
            self.set_trait('structure_node', None)
            self.btn_store.disabled = True
            return

        self.btn_store.disabled = False
        with self.hold_trait_notifications():
            self._sync_structure_node()


class StructureUploadWidget(ipw.VBox):
    """Class that allows to upload structures from user's computer."""
    structure = Union([Instance(Atoms), Instance(Data)], allow_none=True)

    def __init__(self, title='', description="Upload Structure"):
        self.title = title
        self.file_upload = ipw.FileUpload(description=description, multiple=False, layout={'width': 'initial'})
        supported_formats = ipw.HTML(
            """<a href="https://wiki.fysik.dtu.dk/ase/_modules/ase/io/formats.html" target="_blank">
        Supported structure formats
        </a>""")
        self.file_upload.observe(self._on_file_upload, names='value')
        super().__init__(children=[self.file_upload, supported_formats])

    def _validate_and_fix_ase_cell(self, ase_structure, vacuum_ang=10.0):
        """
        Checks if the ase Atoms object has a cell set,
        otherwise sets it to bounding box plus specified "vacuum" space
        """
        cell = ase_structure.cell

        if (np.linalg.norm(cell[0]) < 0.1 or np.linalg.norm(cell[1]) < 0.1 or np.linalg.norm(cell[2]) < 0.1):
            # if any of the cell vectors is too short, consider it faulty
            # set cell as bounding box + vacuum_ang
            bbox = np.ptp(ase_structure.positions, axis=0)
            new_structure = ase_structure.copy()
            new_structure.cell = bbox + vacuum_ang
            return new_structure
        return ase_structure

    def _on_file_upload(self, change=None):
        """When file upload button is pressed."""
        for fname, item in change['new'].items():
            frmt = fname.split('.')[-1]
            if frmt == 'cif':
                self.structure = CifData(file=io.BytesIO(item['content']))
            else:
                self.structure = self._validate_and_fix_ase_cell(
                    get_ase_from_file(io.StringIO(item['content'].decode()), format=frmt))
            self.file_upload.value.clear()
            break


class StructureExamplesWidget(ipw.VBox):
    """Class to provide example structures for selection."""
    structure = Instance(Atoms, allow_none=True)

    def __init__(self, examples, title='', **kwargs):
        self.title = title
        self.on_structure_selection = lambda structure_ase, name: None
        self._select_structure = ipw.Dropdown(options=self.get_example_structures(examples))
        self._select_structure.observe(self._on_select_structure, names=['value'])
        super().__init__(children=[self._select_structure], **kwargs)

    @staticmethod
    def get_example_structures(examples):
        """Get the list of example structures."""
        if not isinstance(examples, list):
            raise ValueError("parameter examples should be of type list, {} given".format(type(examples)))
        return [("Select structure", False)] + examples

    def _on_select_structure(self, change):  # pylint: disable=unused-argument
        """When structure is selected."""

        self.structure = get_ase_from_file(self._select_structure.value) if self._select_structure.value else None

    @default('structure')
    def _default_structure(self):
        return None


class StructureBrowserWidget(ipw.VBox):
    """Class to query for structures stored in the AiiDA database."""
    structure = Union([Instance(Atoms), Instance(Data)], allow_none=True)

    def __init__(self, title=''):
        self.title = title

        # Structure objects we want to query for.
        self.query_structure_type = (DataFactory('structure'), DataFactory('cif'))

        # Extracting available process labels.
        qbuilder = QueryBuilder().append((CalcJobNode, WorkChainNode), project="label")
        self.drop_label = ipw.Dropdown(options=sorted({'All'}.union({i[0] for i in qbuilder.iterall() if i[0]})),
                                       value='All',
                                       description='Process Label',
                                       disabled=True,
                                       style={'description_width': '120px'},
                                       layout={'width': '50%'})
        self.drop_label.observe(self.search, names='value')

        # Disable process labels selection if we are not looking for the calculated structures.
        def disable_drop_label(change):
            self.drop_label.disabled = not change['new'] == 'calculated'

        # Select structures kind.
        self.mode = ipw.RadioButtons(options=['all', 'uploaded', 'edited', 'calculated'], layout={'width': '25%'})
        self.mode.observe(self.search, names='value')
        self.mode.observe(disable_drop_label, names='value')

        # Date range.
        # Note: there is Date picker widget, but it currently does not work in Safari:
        # https://ipywidgets.readthedocs.io/en/latest/examples/Widget%20List.html#Date-picker
        date_text = ipw.HTML(value='<p>Select the date range:</p>')
        self.start_date_widget = ipw.Text(value='', description='From: ', style={'description_width': '120px'})
        self.end_date_widget = ipw.Text(value='', description='To: ')

        # Search button.
        btn_search = ipw.Button(description='Search',
                                button_style='info',
                                layout={
                                    'width': 'initial',
                                    'margin': '2px 0 0 2em'
                                })
        btn_search.on_click(self.search)

        age_selection = ipw.VBox(
            [date_text, ipw.HBox([self.start_date_widget, self.end_date_widget, btn_search])],
            layout={
                'border': '1px solid #fafafa',
                'padding': '1em'
            })

        h_line = ipw.HTML('<hr>')
        box = ipw.VBox([age_selection, h_line, ipw.HBox([self.mode, self.drop_label])])

        self.results = ipw.Dropdown(layout={'width': '900px'})
        self.results.observe(self._on_select_structure)
        self.search()
        super().__init__([box, h_line, self.results])

    def preprocess(self):
        """Search structures in AiiDA database and add formula extra to them."""

        queryb = QueryBuilder()
        queryb.append(self.query_structure_type, filters={'extras': {'!has_key': 'formula'}})
        for item in queryb.all():  # iterall() would interfere with set_extra()
            try:
                formula = item[0].get_formula()
            except AttributeError:
                # Slow part.
                formula = item[0].get_ase().get_chemical_formula()
            item[0].set_extra("formula", formula)

    def search(self, _=None):
        """Launch the search of structures in AiiDA database."""
        self.preprocess()

        qbuild = QueryBuilder()

        # If the date range is valid, use it for the search
        try:
            start_date = datetime.datetime.strptime(self.start_date_widget.value, '%Y-%m-%d')
            end_date = datetime.datetime.strptime(self.end_date_widget.value, '%Y-%m-%d') + datetime.timedelta(hours=24)

        # Otherwise revert to the standard (i.e. last 7 days)
        except ValueError:
            start_date = datetime.datetime.now() - datetime.timedelta(days=7)
            end_date = datetime.datetime.now() + datetime.timedelta(hours=24)

            self.start_date_widget.value = start_date.strftime('%Y-%m-%d')
            self.end_date_widget.value = end_date.strftime('%Y-%m-%d')

        filters = {}
        filters['ctime'] = {'and': [{'>': start_date}, {'<=': end_date}]}

        if self.mode.value == "uploaded":
            qbuild2 = QueryBuilder().append(self.query_structure_type, project=["id"],
                                            tag='structures').append(Node, with_outgoing='structures')
            processed_nodes = [n[0] for n in qbuild2.all()]
            if processed_nodes:
                filters['id'] = {"!in": processed_nodes}
            qbuild.append(self.query_structure_type, filters=filters)

        elif self.mode.value == "calculated":
            if self.drop_label.value == 'All':
                qbuild.append((CalcJobNode, WorkChainNode), tag='calcjobworkchain')
            else:
                qbuild.append((CalcJobNode, WorkChainNode),
                              filters={'label': self.drop_label.value},
                              tag='calcjobworkchain')
            qbuild.append(self.query_structure_type, with_incoming='calcjobworkchain', filters=filters)

        elif self.mode.value == "edited":
            qbuild.append(CalcFunctionNode)
            qbuild.append(self.query_structure_type, with_incoming=CalcFunctionNode, filters=filters)

        elif self.mode.value == "all":
            qbuild.append(self.query_structure_type, filters=filters)

        qbuild.order_by({self.query_structure_type: {'ctime': 'desc'}})
        matches = {n[0] for n in qbuild.iterall()}
        matches = sorted(matches, reverse=True, key=lambda n: n.ctime)

        options = OrderedDict()
        options["Select a Structure ({} found)".format(len(matches))] = False

        for mch in matches:
            label = "PK: {}".format(mch.id)
            label += " | " + mch.ctime.strftime("%Y-%m-%d %H:%M")
            label += " | " + mch.get_extra("formula")
            label += " | " + mch.node_type.split('.')[-2]
            label += " | " + mch.label
            label += " | " + mch.description
            options[label] = mch

        self.results.options = options

    def _on_select_structure(self, _=None):
        self.structure = self.results.value or None


class SmilesWidget(ipw.VBox):
    """Conver SMILES into 3D structure."""
    structure = Instance(Atoms, allow_none=True)

    SPINNER = """<i class="fa fa-spinner fa-pulse" style="color:red;" ></i>"""

    def __init__(self, title=''):
        self.title = title
        try:
            import openbabel  # pylint: disable=unused-import
        except ImportError:
            super().__init__(
                [ipw.HTML("The SmilesWidget requires the OpenBabel library, "
                          "but the library was not found.")])
            return

        self.smiles = ipw.Text()
        self.create_structure_btn = ipw.Button(description="Generate molecule", button_style='info')
        self.create_structure_btn.on_click(self._on_button_pressed)
        self.output = ipw.HTML("")
        super().__init__([self.smiles, self.create_structure_btn, self.output])

    @staticmethod
    def pymol_2_ase(pymol):
        """Convert pymol object into ASE Atoms."""

        species = [chemical_symbols[atm.atomicnum] for atm in pymol.atoms]
        pos = np.asarray([atm.coords for atm in pymol.atoms])
        pca = PCA(n_components=3)
        posnew = pca.fit_transform(pos)
        atoms = Atoms(species, positions=posnew, pbc=True, cell=np.ptp(posnew, axis=0) + 10)
        atoms.center()
        return atoms

    def _optimize_mol(self, mol):
        """Optimize a molecule using force field (needed for complex SMILES)."""

        # Note, the pybel module imported below comes together with openbabel package. Do not confuse it with
        # pybel package available on PyPi: https://pypi.org/project/pybel/
        import pybel  # pylint:disable=import-error

        self.output.value = "Screening possible conformers {}".format(self.SPINNER)  #font-size:20em;

        f_f = pybel._forcefields["uff"]  # pylint: disable=protected-access
        if not f_f.Setup(mol.OBMol):
            f_f = pybel._forcefields["mmff94"]  # pylint: disable=protected-access
            if not f_f.Setup(mol.OBMol):
                self.output.value = "Cannot set up forcefield"
                return

        # Initial cleanup before the weighted search.
        f_f.Setup(mol.OBMol)
        f_f.SteepestDescent(5000, 1.0e-9)
        f_f.GetCoordinates(mol.OBMol)
        self.output.value = ""

    def _on_button_pressed(self, change):  # pylint: disable=unused-argument
        """Convert SMILES to ase structure when button is pressed."""
        self.output.value = ""

        # Note, the pybel module imported below comes together with openbabel package. Do not confuse it with
        # pybel package available on PyPi: https://pypi.org/project/pybel/
        import pybel  # pylint:disable=import-error

        if not self.smiles.value:
            return

        mol = pybel.readstring("smiles", self.smiles.value)
        self.output.value = """SMILES to 3D conversion {}""".format(self.SPINNER)
        mol.make3D()
        mol.addh()

        pybel._builder.Build(mol.OBMol)  # pylint: disable=protected-access

        self._optimize_mol(mol)
        self.structure = self.pymol_2_ase(mol)

    @default('structure')
    def _default_structure(self):
        return None


class BasicStructureEditor(ipw.VBox):  # pylint: disable=too-many-instance-attributes
    """Widget that allows for the basic structure editing."""

    structure = Instance(Atoms, allow_none=True)
    selection = List(Int)
    camera_orientation = List()

    def __init__(self, title=''):

        self.title = title
        # Define action vector.
        self.axis_p1 = ipw.Text(description='Starting point', value='0 0 0', layout={'width': 'initial'})
        self.axis_p2 = ipw.Text(description='Ending point', value='0 0 1', layout={'width': 'initial'})
        btn_def_atom1 = ipw.Button(description='From selection', layout={'width': 'initial'})
        btn_def_atom1.on_click(self.def_axis_p1)
        btn_def_atom2 = ipw.Button(description='From selection', layout={'width': 'initial'})
        btn_def_atom2.on_click(self.def_axis_p2)
        btn_get_from_camera = ipw.Button(description='Perp. to screen',
                                         button_style='warning',
                                         layout={'width': 'initial'})
        btn_get_from_camera.on_click(self.def_perpendicular_to_screen)

        # Define action point.
        self.point = ipw.Text(description='Action point', value='0 0 0', layout={'width': 'initial'})
        btn_def_pnt = ipw.Button(description='From selection', layout={'width': 'initial'})
        btn_def_pnt.on_click(self.def_point)

        # Move atoms.
        btn_move_dr = ipw.Button(description='Move', layout={'width': 'initial'})
        btn_move_dr.on_click(self.translate_dr)
        self.displacement = ipw.FloatText(description=r'Move along action vector by $\Delta=$ ',
                                          value=1,
                                          step=0.1,
                                          style={'description_width': 'initial'},
                                          layout={'width': 'initial'})

        btn_move_dxyz = ipw.Button(description='Move by XYZ', layout={'width': 'initial'})
        btn_move_dxyz.on_click(self.translate_dxdydz)
        btn_move_to_xyz = ipw.Button(description='Move to XYZ', layout={'width': 'initial'})
        btn_move_to_xyz.on_click(self.translate_to_xyz)
        self.dxyz = ipw.Text(description='XYZ move:',
                             value='0 0 0',
                             style={'description_width': 'initial'},
                             layout={
                                 'width': 'initial',
                                 'margin': '0px 0px 0px 20px'
                             })

        # Rotate atoms.
        btn_rotate = ipw.Button(description='Rotate', layout={'width': '10%'})
        btn_rotate.on_click(self.rotate)
        self.phi = ipw.FloatText(description='Rotate around the action vector which starts from the action point',
                                 value=0,
                                 step=5,
                                 style={'description_width': 'initial'},
                                 layout={'width': 'initial'})

        # Atoms selection.
        self.element = ipw.Dropdown(
            description="Select element",
            options=chemical_symbols[1:],
            value="H",
            style={'description_width': 'initial'},
            layout={'width': 'initial'},
        )

        def disable_element(_=None):
            if self.ligand.value == 0:
                self.element.disabled = False
            else:
                self.element.disabled = True

        # Ligand selection.
        self.ligand = LigandSelectorWidget()
        self.ligand.observe(disable_element, names='value')

        # Add atom.
        btn_add = ipw.Button(description='Add to selected', layout={'width': 'initial'})
        btn_add.on_click(self.add)
        self.bond_length = ipw.FloatText(description="Bond lenght.", value=1.0, layout={'width': '140px'})
        use_covalent_radius = ipw.Checkbox(
            value=True,
            description='Use covalent radius',
            style={'description_width': 'initial'},
        )
        link((use_covalent_radius, 'value'), (self.bond_length, 'disabled'))

        # Modify atom.
        btn_modify = ipw.Button(description='Modify selected', button_style='warning', layout={'width': 'initial'})
        btn_modify.on_click(self.mod_element)

        # Remove atom.
        btn_remove = ipw.Button(description='Remove selected', button_style='danger', layout={'width': 'initial'})
        btn_remove.on_click(self.remove)

        # Automatically clear selection after point definition
        self.autoclear_selection = ipw.Checkbox(description='Clear selection after pressing "From seletion"',
                                                value=True,
                                                style={'description_width': 'initial'})

        super().__init__(children=[
            ipw.HTML("<b>Action vector and point:</b>", layout={'margin': '20px 0px 10px 0px'}),
            ipw.HBox([self.axis_p1, btn_def_atom1, self.axis_p2, btn_def_atom2, btn_get_from_camera],
                     layout={'margin': '0px 0px 0px 20px'}),
            ipw.HBox([self.point, btn_def_pnt, self.autoclear_selection], layout={'margin': '0px 0px 0px 20px'}),
            ipw.HTML("<b>Move atom(s):</b>", layout={'margin': '20px 0px 10px 0px'}),
            ipw.HBox([self.displacement, btn_move_dr, self.dxyz, btn_move_dxyz, btn_move_to_xyz],
                     layout={'margin': '0px 0px 0px 20px'}),
            ipw.HBox([self.phi, btn_rotate], layout={'margin': '0px 0px 0px 20px'}),
            ipw.HTML("<b>Modify atom(s):</v>", layout={'margin': '20px 0px 10px 0px'}),
            ipw.HBox([self.element, self.ligand], layout={'margin': '0px 0px 0px 20px'}),
            ipw.HBox([
                btn_modify,
                btn_add,
                self.bond_length,
                use_covalent_radius,
            ],
                     layout={'margin': '0px 0px 0px 20px'}),
            ipw.HBox([btn_remove], layout={'margin': '0px 0px 0px 20px'}),
        ])

    def str2vec(self, string):
        return np.array(list(map(float, string.split())))

    def vec2str(self, vector):
        return str(round(vector[0], 2)) + ' ' + str(round(vector[1], 2)) + ' ' + str(round(vector[2], 2))

    def sel2com(self):
        """Get center of mass of the selection."""
        if self.selection:
            com = np.average(self.structure[self.selection].get_positions(), axis=0)
        else:
            com = [0, 0, 0]

        return com

    @property
    def action_vector(self):
        """Define the action vector."""
        normal = self.str2vec(self.axis_p2.value) - self.str2vec(self.axis_p1.value)
        return normal / np.linalg.norm(normal)

    def def_point(self, _=None):
        """Define the action point."""
        self.point.value = self.vec2str(self.sel2com())
        if self.autoclear_selection.value:
            self.selection = list()

    def def_axis_p1(self, _=None):
        """Define the first point of axis."""
        self.axis_p1.value = self.vec2str(self.sel2com())
        if self.autoclear_selection.value:
            self.selection = list()

    def def_axis_p2(self, _=None):
        """Define the second point of axis."""
        com = np.average(self.structure[self.selection].get_positions(), axis=0) if self.selection else [0, 0, 1]
        self.axis_p2.value = self.vec2str(com)
        if self.autoclear_selection.value:
            self.selection = list()

    def def_perpendicular_to_screen(self, _=None):
        """Define a normalized vector perpendicular to the screen."""
        cmr = self.camera_orientation
        if cmr:
            self.axis_p1.value = "0 0 0"
            versor = np.array([-cmr[2], -cmr[6], -cmr[10]]) / np.linalg.norm([-cmr[2], -cmr[6], -cmr[10]])
            self.axis_p2.value = self.vec2str(versor.tolist())

    def translate_dr(self, _=None):
        """Translate by dr along the selected vector."""
        atoms = self.structure.copy()

        selection = self.selection

        atoms.positions[self.selection] += np.array(self.action_vector * self.displacement.value)

        self.structure = atoms
        self.selection = selection

    def translate_dxdydz(self, _=None):
        """Translate by the selected XYZ delta."""
        selection = self.selection
        atoms = self.structure.copy()

        # The action.
        atoms.positions[self.selection] += np.array(self.str2vec(self.dxyz.value))

        self.structure = atoms
        self.selection = selection

    def translate_to_xyz(self, _=None):
        """Translate to the selected XYZ position."""
        selection = self.selection
        atoms = self.structure.copy()

        # The action.
        geo_center = np.average(self.structure[self.selection].get_positions(), axis=0)
        atoms.positions[self.selection] += self.str2vec(self.dxyz.value) - geo_center

        self.structure = atoms
        self.selection = selection

    def rotate(self, _=None):
        """Rotate atoms around selected point in space and vector."""

        selection = self.selection
        atoms = self.structure.copy()

        # The action.
        rotated_subset = atoms[self.selection]
        vec = self.str2vec(self.vec2str(self.action_vector))
        center = self.str2vec(self.point.value)
        rotated_subset.rotate(self.phi.value, v=vec, center=center, rotate_cell=False)
        atoms.positions[list(self.selection)] = rotated_subset.positions

        self.structure = atoms
        self.selection = selection

    def mod_element(self, _=None):
        """Modify selected atoms into the given element."""
        atoms = self.structure.copy()
        selection = self.selection

        if self.ligand.value == 0:
            for idx in self.selection:
                new = Atom(self.element.value)
                atoms[idx].mass = new.mass
                atoms[idx].magmom = new.magmom
                atoms[idx].momentum = new.momentum
                atoms[idx].symbol = new.symbol
                atoms[idx].tag = new.tag
                atoms[idx].charge = new.charge
        else:
            initial_ligand = self.ligand.rotate(align_to=self.action_vector, remove_anchor=True)
            for idx in self.selection:
                position = self.structure.positions[idx].copy()
                lgnd = initial_ligand.copy()
                lgnd.translate(position)
                atoms += lgnd

        self.structure = atoms
        self.selection = selection

    def add(self, _=None):
        """Add atoms."""
        atoms = self.structure.copy()
        selection = self.selection

        if self.ligand.value == 0:
            initial_ligand = Atoms([Atom(self.element.value, [0, 0, 0])])
            rad = SYMBOL_RADIUS[self.element.value]
        else:
            initial_ligand = self.ligand.rotate(align_to=self.action_vector)
            rad = SYMBOL_RADIUS[self.ligand.anchoring_atom]

        for idx in self.selection:
            # It is important to copy, otherwise the initial structure will be modified
            position = self.structure.positions[idx].copy()
            lgnd = initial_ligand.copy()

            if self.bond_length.disabled:
                lgnd.translate(position + self.action_vector * (SYMBOL_RADIUS[self.structure.symbols[idx]] + rad))
            else:
                lgnd.translate(position + self.action_vector * self.bond_length.value)

            atoms += lgnd

        self.structure = atoms
        self.selection = selection

    def remove(self, _):
        """Remove selected atoms."""
        atoms = self.structure.copy()
        del [atoms[self.selection]]
        self.structure = atoms