Source code for aiidalab_widgets_base.structures

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

import datetime
import functools
import io
import pathlib
import tempfile
from collections import OrderedDict

import ase
import ipywidgets as ipw
import numpy as np

# spglib for cell converting
import spglib

# AiiDA imports
from aiida.engine import calcfunction
from aiida.orm import (
from aiida.plugins import DataFactory
from ase import Atom, Atoms
from import chemical_symbols, covalent_radii
from traitlets import Instance, Int, List, Unicode, Union, default, dlink, link, observe

# Local imports
from .data import LigandSelectorWidget
from .utils import StatusHTML, exceptions, get_ase_from_file, get_formula
from .viewers import StructureDataViewer

CifData = DataFactory("core.cif")
StructureData = DataFactory("core.structure")
TrajectoryData = DataFactory("core.array.trajectory")

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

[docs]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": "core.cif", "StructureData": "core.structure"}
[docs] 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(**kwargs) dlink((self, "structure_node"), (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._structure_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)
[docs] def _structure_importers(self, importers): """Preparing structure importers.""" if not isinstance(importers, (list, tuple)): raise exceptions.ListOrTuppleError(importers) # 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 = list(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
[docs] def _structure_editors(self, editors): """Preparing structure editors.""" if editors and len(editors) == 1: link((editors[0], "structure"), (self, "structure")) if editors[0].has_trait("input_selection"): dlink((editors[0], "input_selection"), (self.viewer, "input_selection")) if editors[0].has_trait("selection"): dlink((self.viewer, "selection"), (editors[0], "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 = tuple(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
[docs] 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.output.value = f"Stored in AiiDA [{structure_node}]"
[docs] 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()
[docs] 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)
[docs] def _convert_to_structure_node(self, structure): """Convert structure of any type to the StructureNode object.""" if structure is None: return None structure_node_type = 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): # If the Atoms object was created by SmilesWidget, # attach its SMILES code as an extra. structure_node = structure_node_type(ase=structure) if "smiles" in structure_node.base.extras.set("smiles",["smiles"]) return structure_node # If the input_structure trait is set to AiiDA node, check what type if isinstance(structure, Data): # Transform the structure to the structure_node_type if needed. if isinstance(structure, structure_node_type): return structure # Using self.structure, as it was already converted to the ASE Atoms object. return structure_node_type(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 = 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()
[docs]class StructureUploadWidget(ipw.VBox): """Class that allows to upload structures from user's computer.""" structure = Union([Instance(Atoms), Instance(Data)], allow_none=True)
[docs] def __init__( self, title="", description="Upload Structure", allow_trajectories=False ): self.title = title self.file_upload = ipw.FileUpload( description=description, multiple=False, layout={"width": "initial"} ) # Whether to allow uploading multiple structures from a single file. # In this case, we create TrajectoryData node. self.allow_trajectories = allow_trajectories supported_formats = ipw.HTML( """<a href="" target="_blank"> Supported structure formats </a>""" ) self._status_message = StatusHTML(clear_after=5) self.file_upload.observe(self._on_file_upload, names="value") super().__init__( children=[self.file_upload, supported_formats, self._status_message] )
[docs] 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 """ if not ase_structure: return None cell = ase_structure.cell # TODO: Since AiiDA 2.0, zero cell is possible if PBC=false # so we should honor that here and do not put artificial cell # around gas phase molecules. 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
[docs] def _on_file_upload(self, change=None): """When file upload button is pressed.""" for fname, item in change["new"].items(): self.structure = self._read_structure(fname, item["content"]) self.file_upload.value.clear() break
[docs] def _read_structure(self, fname, content): suffix = "".join(pathlib.Path(fname).suffixes) if suffix == ".cif": try: return CifData(file=io.BytesIO(content)) except Exception as e: self._status_message.message = f""" <div class="alert alert-warning">Could not parse CIF file {fname}: {e} Trying ASE reader...</div> """ with tempfile.NamedTemporaryFile(suffix=suffix) as temp_file: temp_file.write(content) temp_file.flush() try: if suffix == ".cif": structures = get_ase_from_file(, format="cif") else: structures = get_ase_from_file( except ValueError as e: self._status_message.message = f""" <div class="alert alert-danger">ERROR: {e}</div> """ return None except KeyError: self._status_message.message = f""" <div class="alert alert-danger">ERROR: Could not parse file {fname}</div> """ return None if len(structures) > 1: if self.allow_trajectories: return TrajectoryData( structurelist=[ StructureData( ase=self._validate_and_fix_ase_cell(ase_struct) ) for ase_struct in structures ] ) else: self._status_message.message = f""" <div class="alert alert-danger">ERROR: More than one structure found in file {fname}</div> """ return None return self._validate_and_fix_ase_cell(structures[0])
[docs]class StructureExamplesWidget(ipw.VBox): """Class to provide example structures for selection.""" structure = Instance(Atoms, allow_none=True)
[docs] 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)
[docs] @staticmethod def get_example_structures(examples): """Get the list of example structures.""" if not isinstance(examples, list): raise TypeError( f"parameter examples should be of type list, {type(examples)} given" ) return [("Select structure", False)] + examples
[docs] def _on_select_structure(self, change): # pylint: disable=unused-argument """When structure is selected.""" self.structure = ( get_ase_from_file(self._select_structure.value)[0] if self._select_structure.value else None )
@default("structure") def _default_structure(self): return None
[docs]class StructureBrowserWidget(ipw.VBox): """Class to query for structures stored in the AiiDA database. :param title: Title of the widget displayed on a tab in StructureManagerWidget :type title: string :param query_types: A tuple of Data node types that are searched (default: StructureData, CifData) :type query_types: tuple """ structure = Union([Instance(Atoms), Instance(Data)], allow_none=True)
[docs] def __init__(self, title="", query_types=None): self.title = title # Structure objects we want to query for. if query_types: self.query_structure_type = query_types else: self.query_structure_type = (StructureData, CifData) # 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(, 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(, 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: # 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( 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, names="value") super().__init__([box, h_line, self.results])
[docs] 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 base.extras.set() try: formula = get_formula(item[0]) item[0].base.extras.set("formula", formula) except ValueError: pass
[docs] 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.timedelta(days=7) end_date = + 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[f"Select a Structure ({len(matches)} found)"] = False for mch in matches: label = f"PK: {}" label += " | " + mch.ctime.strftime("%Y-%m-%d %H:%M") label += " | " + mch.base.extras.get("formula", "") label += " | " + mch.node_type.split(".")[-2] label += " | " + mch.label label += " | " + mch.description options[label] = mch self.results.options = options
[docs] def _on_select_structure(self, _=None): self.structure = self.results.value or None
[docs]class SmilesWidget(ipw.VBox): """Convert SMILES into 3D structure.""" structure = Instance(Atoms, allow_none=True) SPINNER = """<i class="fa fa-spinner fa-pulse" style="color:red;" ></i>"""
[docs] def __init__(self, title=""): # pylint: disable=unused-import self.title = title try: from openbabel import openbabel # noqa: F401 from openbabel import pybel # noqa: F401 except ImportError: self.disable_openbabel = True try: # noqa: TC101 from rdkit import Chem # noqa: F401 from rdkit.Chem import AllChem # noqa: F401 except ImportError: super().__init__( [ ipw.HTML( "The SmilesWidget requires the rdkit library, " "but the library was not found." ) ] ) return self.smiles = ipw.Text(placeholder="C=C") self.create_structure_btn = ipw.Button( description="Generate molecule", button_style="primary", tooltip="Generate molecule from SMILES string", ) self.create_structure_btn.on_click(self._on_button_pressed) self.output = ipw.HTML("") super().__init__( [ipw.HBox([self.smiles, self.create_structure_btn]), self.output] )
[docs] def _make_ase(self, species, positions, smiles): """Create ase Atoms object.""" from sklearn.decomposition import PCA # Get the principal axes and realign the molecule along z-axis. positions = PCA(n_components=3).fit_transform(positions) atoms = Atoms(species, positions=positions, pbc=False) atoms.cell = np.ptp(atoms.positions, axis=0) + 10 # We're attaching this info so that it # can be later stored as an extra on AiiDA Structure node.["smiles"] = smiles return atoms
[docs] def _pybel_opt(self, smiles, steps): """Optimize a molecule using force field and pybel (needed for complex SMILES).""" from openbabel import openbabel as ob from openbabel import pybel as pb obconversion = ob.OBConversion() obconversion.SetInFormat("smi") obmol = ob.OBMol() obconversion.ReadString(obmol, smiles) pbmol = pb.Molecule(obmol) pbmol.make3D(forcefield="uff", steps=50) pbmol.localopt(forcefield="gaff", steps=200) pbmol.localopt(forcefield="mmff94", steps=100) f_f = pb._forcefields["uff"] # pylint: disable=protected-access f_f.Setup(pbmol.OBMol) f_f.ConjugateGradients(steps, 1.0e-9) f_f.GetCoordinates(pbmol.OBMol) species = [chemical_symbols[atm.atomicnum] for atm in pbmol.atoms] positions = np.asarray([atm.coords for atm in pbmol.atoms]) return self._make_ase(species, positions, smiles)
[docs] def _rdkit_opt(self, smiles, steps): """Optimize a molecule using force field and rdkit (needed for complex SMILES).""" from rdkit import Chem from rdkit.Chem import AllChem mol = Chem.MolFromSmiles(smiles) if mol is None: # Something is seriously wrong with the SMILES code, # just return None and don't attempt anything else. self.output.value = "RDKit ERROR: Invalid SMILES string" return None mol = Chem.AddHs(mol) AllChem.EmbedMolecule(mol, maxAttempts=20, randomSeed=42) if AllChem.UFFHasAllMoleculeParams(mol): AllChem.UFFOptimizeMolecule(mol, maxIters=steps) else: self.output.value = "RDKit WARNING: Missing UFF parameters" positions = mol.GetConformer().GetPositions() natoms = mol.GetNumAtoms() species = [mol.GetAtomWithIdx(j).GetSymbol() for j in range(natoms)] return self._make_ase(species, positions, smiles)
[docs] def _mol_from_smiles(self, smiles, steps=1000): """Convert SMILES to ase structure try rdkit then pybel""" try: return self._rdkit_opt(smiles, steps) except ValueError as e: self.output.value = str(e) if self.disable_openbabel: return None self.output.value += " Trying OpenBabel..." return self._pybel_opt(smiles, steps)
[docs] def _on_button_pressed(self, change): # pylint: disable=unused-argument """Convert SMILES to ase structure when button is pressed.""" self.output.value = "" if not self.smiles.value: return spinner = f"Screening possible conformers {self.SPINNER}" # font-size:20em; self.output.value = spinner self.structure = self._mol_from_smiles(self.smiles.value) # Don't overwrite possible error/warning messages if self.output.value == spinner: self.output.value = ""
@default("structure") def _default_structure(self): return None
[docs]def _register_structure(operator): """ Decorator for methods that manipulate (operate on) the selected structure. Checks whether a structure and selection is set and ensures that the arguments for structure and selection are passed by copy rather than reference. A pop-up warning message is shown in case that neither a structure or selection are set. """ @functools.wraps(operator) def inner(ref, *args, **kwargs): if not ref.structure: ref._status_message.message = """ <div class="alert alert-info"> <strong>Please choose a structure first.</strong> </div> """ else: operator( ref, *args, **kwargs, atoms=ref.structure.copy(), ) return inner
[docs]def _register_selection(operator): """ Decorator for methods that manipulate (operate on) the selected structure. Checks whether a structure and selection is set and ensures that the arguments for structure and selection are passed by copy rather than reference. A pop-up warning message is shown in case that neither a structure or selection are set. """ @functools.wraps(operator) def inner(ref, *args, **kwargs): if not ref.selection: ref._status_message.message = """ <div class="alert alert-info"> <strong>Please select atoms first.</strong> </div> """ else: operator( ref, *args, **kwargs, selection=ref.selection.copy(), ) return inner
[docs]class BasicCellEditor(ipw.VBox): """Widget that allows for the basic cell editing.""" structure = Instance(Atoms, allow_none=True)
[docs] def __init__(self, title="Cell transform"): self.title = title self._status_message = StatusHTML() # cell transfor opration widget primitive_cell = ipw.Button( description="Convert to primitive cell", layout={"width": "initial"}, ) primitive_cell.on_click(self.def_primitive_cell) conventional_cell = ipw.Button( description="Convert to conventional cell", layout={"width": "initial"}, ) conventional_cell.on_click(self.def_conventional_cell) super().__init__( children=[ ipw.HBox( [ primitive_cell, conventional_cell, ], ), self._status_message, ], )
[docs] @_register_structure def def_primitive_cell(self, _=None, atoms=None): atoms = self._to_standard_cell(atoms, to_primitive=True) self.structure = atoms
[docs] @_register_structure def def_conventional_cell(self, _=None, atoms=None): atoms = self._to_standard_cell(atoms, to_primitive=False) self.structure = atoms
[docs] @staticmethod def _to_standard_cell( structure: Atoms, to_primitive=False, no_idealize=False, symprec=1e-5 ): """The `standardize_cell` method from spglib and apply to ase.Atoms""" lattice = structure.get_cell() positions = structure.get_scaled_positions() numbers = structure.get_atomic_numbers() cell = (lattice, positions, numbers) # operation lattice, positions, numbers = spglib.standardize_cell( cell, to_primitive=to_primitive, no_idealize=no_idealize, symprec=symprec ) return Atoms( cell=lattice, scaled_positions=positions, numbers=numbers, pbc=[True, True, True], )
[docs]class BasicStructureEditor(ipw.VBox): # pylint: disable=too-many-instance-attributes """ Widget that allows for the basic structure (molecule and position of periodic structure in cell) editing.""" structure = Instance(Atoms, allow_none=True) input_selection = List(Int, allow_none=True) selection = List(Int) camera_orientation = List()
[docs] 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"}, ) # Mirror atoms. btn_mirror_perp = ipw.Button(description="Mirror", layout={"width": "10%"}) btn_mirror_perp.on_click(self.mirror) btn_mirror_3p = ipw.Button(description="Mirror", layout={"width": "10%"}) btn_mirror_3p.on_click(self.mirror_3p) # Rotate atoms while aligning action vector with XYZ vector. btn_align = ipw.Button(description="Align", layout={"width": "10%"}) btn_align.on_click(self.align) # 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")) # Copy atoms. btn_copy_sel = ipw.Button( description="Copy selected", layout={"width": "initial"} ) btn_copy_sel.on_click(self.copy_sel) # 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"}, ) self._status_message = StatusHTML() 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.HBox( [ ipw.HTML( "Mirror on the plane perpendicular to the action vector", layout={"margin": "0px 0px 0px 0px"}, ), btn_mirror_perp, ], layout={"margin": "0px 0px 0px 20px"}, ), ipw.HBox( [ ipw.HTML( "Mirror on the plane containing action vector and action point", layout={"margin": "0px 0px 0px 0px"}, ), btn_mirror_3p, ], layout={"margin": "0px 0px 0px 20px"}, ), ipw.HBox( [ ipw.HTML( "Rotate atoms while aligning the action vector with the XYZ vector", layout={"margin": "0px 0px 0px 0px"}, ), btn_align, ], layout={"margin": "0px 0px 0px 20px"}, ), ipw.HTML( "<b>Modify atom(s):</v>", layout={"margin": "20px 0px 10px 0px"} ), ipw.HBox([btn_copy_sel], layout={"margin": "0px 0px 0px 20px"}), 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"}), self._status_message, ] )
[docs] def str2vec(self, string): return np.array(list(map(float, string.split())))
[docs] def vec2str(self, vector): return ( str(round(vector[0], 2)) + " " + str(round(vector[1], 2)) + " " + str(round(vector[2], 2)) )
[docs] 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)
[docs] def def_point(self, _=None): """Define the action point.""" self.point.value = self.vec2str(self.sel2com()) if self.autoclear_selection.value: self.input_selection = None self.input_selection = []
[docs] 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.input_selection = None self.input_selection = []
[docs] def def_axis_p2(self, _=None): """Define the second point of axis.""" if not self.selection: self._status_message.message = """ <div class="alert alert-info"> <strong>Please select atoms first.</strong> </div> """ else: 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.input_selection = None self.input_selection = []
[docs] 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())
[docs] @_register_structure @_register_selection def translate_dr(self, _=None, atoms=None, selection=None): """Translate by dr along the selected vector.""" atoms.positions[self.selection] += np.array( self.action_vector * self.displacement.value ) self.structure, self.input_selection = atoms, selection
[docs] @_register_structure @_register_selection def translate_dxdydz(self, _=None, atoms=None, selection=None): """Translate by the selected XYZ delta.""" # The action. atoms.positions[self.selection] += np.array(self.str2vec(self.dxyz.value)) self.structure, self.input_selection = atoms, selection
[docs] @_register_structure @_register_selection def translate_to_xyz(self, _=None, atoms=None, selection=None): """Translate to the selected XYZ position.""" # 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, self.input_selection = atoms, selection
[docs] @_register_structure @_register_selection def rotate(self, _=None, atoms=None, selection=None): """Rotate atoms around selected point in space and vector.""" # 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[self.selection] = rotated_subset.positions self.structure, self.input_selection = atoms, selection
[docs] @_register_structure @_register_selection def mirror(self, _=None, norm=None, point=None, atoms=None, selection=None): """Mirror atoms on the plane perpendicular to the action vector.""" # The action. # Vector and point define the mirrorring surface. p_normal = norm if norm is not None else self.action_vector p_point = point if point is not None else self.str2vec(self.point.value) # Check if norm vector makes sense. if np.isnan(p_normal).any() or np.linalg.norm(p_normal) < 1e-4: self._status_message.message = """ <div class="alert alert-info"> <strong>Norm vector not makes sense.</strong> </div> """ return # Define vectors from p_point that point to the atoms which are to be moved. mirror_subset = atoms.positions[selection] - p_point # Project vectors onto the plane normal. projections = ( p_normal *, p_normal)[:, np.newaxis] /, p_normal) ) # Mirror atoms. atoms.positions[selection] -= 2 * projections self.structure, self.input_selection = atoms, selection
[docs] def mirror_3p(self, _=None): """Mirror atoms on the plane containing action vector and action point.""" pt1 = self.str2vec(self.axis_p2.value) pt2 = self.str2vec(self.axis_p1.value) pt3 = self.str2vec(self.point.value) normal = np.cross(pt1 - pt2, pt3 - pt2) normal = normal / np.linalg.norm(normal) self.mirror(norm=normal, point=pt3)
[docs] @_register_structure @_register_selection def align(self, _=None, atoms=None, selection=None): """Rotate atoms to align action vector with XYZ vector.""" if not self.selection: return # The action. center = self.str2vec(self.point.value) subset = atoms[selection] subset.rotate(self.action_vector, self.str2vec(self.dxyz.value), center=center) atoms.positions[selection] = subset.positions self.structure, self.input_selection = atoms, selection
[docs] @_register_structure @_register_selection def mod_element(self, _=None, atoms=None, selection=None): """Modify selected atoms into the given element.""" last_atom = atoms.get_global_number_of_atoms() 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 new_selection = selection 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 new_selection = list( range(last_atom, last_atom + len(selection) * len(lgnd)) ) self.structure, self.input_selection = atoms, new_selection
[docs] @_register_structure @_register_selection def copy_sel(self, _=None, atoms=None, selection=None): """Copy selected atoms and shift by 1.0 A along X-axis.""" last_atom = atoms.get_global_number_of_atoms() # The action add_atoms = atoms[self.selection].copy() add_atoms.translate([1.0, 0, 0]) atoms += add_atoms new_selection = list(range(last_atom, last_atom + len(selection))) self.structure, self.input_selection = atoms, new_selection
[docs] @_register_structure @_register_selection def add(self, _=None, atoms=None, selection=None): """Add atoms.""" last_atom = atoms.get_global_number_of_atoms() 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 new_selection = list(range(last_atom, last_atom + len(selection) * len(lgnd))) self.structure, self.input_selection = atoms, new_selection
[docs] @_register_structure @_register_selection def remove(self, _, atoms=None, selection=None): """Remove selected atoms.""" del [atoms[selection]] self.structure = atoms self.input_selection = None self.input_selection = []