"""Definition of the Batoms class in the batoms package.

# TODO: get evaluated positiosn
# TODO: add location for boundary, bond and all child objects
# TODO: add feature: cavity
"""
import bpy
from batoms.bspecies import Bspecies
from batoms.volumetric_data import VolumetricData
from batoms.cell import Bcell
from batoms.bselect import Selects
from batoms.base.collection import BaseCollection
from batoms.base.object import ObjectGN
from batoms.ribbon.ribbon import Ribbon
from batoms.utils.butils import (
    get_node_with_node_tree_by_name,
    show_index,
    get_node_by_name,
)
from batoms.utils import string2Number, read_from_others, deprecated
from batoms.plugins import plugin_info

import numpy as np
from time import time

import logging

# logger = logging.getLogger('batoms')
logger = logging.getLogger(__name__)

default_attributes = [
    {"name": "select", "data_type": "INT"},
    {"name": "species_index", "data_type": "INT"},
    {"name": "species", "data_type": "STRING"},
    {"name": "show", "data_type": "INT"},
    {"name": "scale", "data_type": "FLOAT"},
    {"name": "model_style", "data_type": "INT"},
]

default_GroupInput = [
    ["select", "NodeSocketInt"],
    ["species_index", "NodeSocketInt"],
    ["show", "NodeSocketBool"],
    ["scale", "NodeSocketFloat"],
]

subcollections = ["instancer", "surface", "ribbon", "plane"]


class Batoms(BaseCollection, ObjectGN):
    """Batoms Class
    The Batoms object is a interface to a batoms object in Blender. It is a subclass of BaseCollection and ObjectGN.
    """

    def __init__(
        self,
        label="batoms",
        species=None,
        positions=None,
        attributes=None,
        species_props=None,
        pbc=False,
        cell=np.array([0, 0, 0]),
        location=np.array([0, 0, 0]),
        volume=None,
        info=None,
        show_unit_cell=True,
        scale=1.0,
        model_style=0,
        radius_style="0",
        color_style="0",
        from_ase=None,
        from_pymatgen=None,
        from_pybel=None,
        load_trajectory=False,
        segments=None,
    ):
        """Batoms Class
        The Batoms object is a interface to a batoms object in Blender.

        Args:
            label (str, optional):
                Name for the object in Blender. Defaults to 'batoms'.
            species (list, optional):
                List of species, e.g. ['O', 'H', 'H'] or ['Fe_u', 'Fe_d', 'O'].
                Defaults to [].
            positions (list, optional):
                Positions of atoms. Defaults to [].
            attributes (dict, optional):
                Properties for each atoms. Defaults to {}.
            species_props (dict, optional):
                Properties for each species. Defaults to {}.
            info (dict, optional):
                Other properties, e.g. secondary structure of protein.
                Defaults to {}.
            pbc (bool or list of bool, optional):
                Periodic boundary conditions. Defaults to False.
            cell (3x3 matrix or length 3 or 6 vector, optional):
                Unit cell. Defaults to None.
            location (array, optional):
                The location of whole Batoms object, the same as
                the origin of cell.
                Defaults to np.array([0, 0, 0]).
            show_unit_cell (bool, optional):
                Show unit cell during rendering. Defaults to True.
            volume (_type_, optional):
                Volumetric data. e.g. electron density.
                Defaults to None.
            scale (float, optional):
                Scale factor for all atoms. Defaults to 1.0.
            model_style (int, optional):
                Enum in [0, 1, 2, 3]. Defaults to 0.
            from_ase (ASE Atoms, optional):
                Import structure from ASE. Defaults to None.
            from_pymatgen (Pymatgen structure, optional):
                Import structure from pymatgen. Defaults to None.
            metaball (bool, optional):
                Show atoms as metaball. Defaults to False.
            load_trajectory (bool, optional):
                Load all trajectory. Defaults to True.
            segments (_type_, optional):
                Resolution of the sphere. Defaults to None.

        Examples:

        >>> from batoms import Batoms
        >>> h2o = Batom('h2o', species = ['O', 'H', 'H'],
                    positions= [[0, 0, 0.40],
                                [0, -0.76, -0.2],
                                [0, 0.76, -0.2]])
        >>> h2o.pbc = True
        """
        #
        self.obj_name = label
        ObjectGN.__init__(self, label)
        BaseCollection.__init__(self, coll_name=label)
        self._render = None
        self._bond = None
        self._polyhedra = None
        self._boundary = None
        self._volumetric_data = None
        #
        if from_ase or from_pymatgen or from_pybel:
            species, positions, attributes, cell, pbc, info = read_from_others(
                from_ase, from_pymatgen, from_pybel
            )
        if species is None and self.check_batoms(label):
            self.from_batoms(label)
        else:
            if species is None:
                species = []
                positions = []
            self.set_collection(
                label, color_style=color_style, radius_style=radius_style
            )
            self._cell = Bcell(label, cell, batoms=self)
            positions = np.array(positions)
            if len(positions.shape) == 3:
                self._trajectory = {"positions": positions}
                positions = positions[0]
            else:
                self._trajectory = {"positions": []}
            # init attributes
            natom = len(positions)
            self.coll.batoms.scale = scale
            self.coll.batoms.model_style = str(model_style)
            arrays = {
                "species": species,
                "species_index": [string2Number(sp) for sp in species],
                "scale": np.ones(natom) * scale,
                "show": np.ones(natom, dtype=bool),
                "model_style": np.ones(natom, dtype=int) * model_style,
                "select": np.zeros(natom, dtype=int),
            }
            if attributes is not None:
                arrays.update(attributes)
            self.build_object(label, positions, arrays, location)
            self.selects = Selects(label, self)
            if species_props is None:
                species_props = species
            self._species = Bspecies(label, species_props, self, segments=segments)
            self.selects.add("all", np.arange(len(self)))
            self._volumetric_data = VolumetricData(label, volume, self)
            self.set_pbc(pbc)
            # self.label = label
            if load_trajectory:
                self.set_trajectory()
            self.show_unit_cell = show_unit_cell

        self.ribbon = Ribbon(self.label, batoms=self, datas=info, update=True)
        show_index()
        self.hideOneLevel()

    def set_collection(self, label, color_style="0", radius_style="0"):
        """Build main collection and its child collections.

        Args:
            label (str): name of Batoms object

        Raises:
            Exception: The label is already in use.
        """
        if bpy.data.collections.get(label):
            raise Exception("Failed, the name %s already in use!" % label)
        coll = bpy.data.collections.new(label)
        bpy.context.scene.collection.children.link(coll)
        for sub_name in subcollections:
            subcoll = bpy.data.collections.new("%s_%s" % (label, sub_name))
            coll.children.link(subcoll)
        coll.batoms.type = "BATOMS"
        coll.batoms.label = label
        # set internal data
        self.coll.batoms.color_style = str(color_style)
        self.coll.batoms.radius_style = str(radius_style)

    def hideOneLevel(self):
        """Hide one level of collecitons in the outline in Blender"""
        # from batoms.utils.butils import hideOneLevel

        # hideOneLevel()
        pass

    def build_object(self, label, positions, arrays, location=[0, 0, 0]):
        """Build the main Batoms object

        Args:
            label (str):
                Name of the object
            arrays (array):
                arrays of properties for each atoms
            location (list, optional):
                Location of the object. Defaults to [0, 0, 0].
        """
        from batoms.bond.bond import default_bond_attributes

        self.delete_obj(label)
        mesh = bpy.data.meshes.new(label)
        obj = bpy.data.objects.new(label, mesh)
        obj.data.from_pydata(positions, [], [])
        obj.location = location
        obj.batoms.type = "BATOMS"
        obj.batoms.label = label
        self.coll.objects.link(obj)
        # add cell object as its child
        self.cell.obj.parent = self.obj
        # add attributes
        for att in default_attributes:
            self.add_attribute(**att)
        for att in default_bond_attributes:
            self.add_attribute(**att)
        self.set_attributes(arrays)
        self.init_geometry_node_modifier(default_GroupInput)
        self.build_geometry_node()
        logger.info("Add object {}".format(self.label))

    def build_geometry_node(self):
        """Geometry node for instancing sphere on vertices!"""
        # first create the nodes for the top level
        parent = self.gn_node_group
        nodes = parent.nodes
        links = parent.links
        GroupInput = nodes[0]
        GroupOutput = nodes[1]
        JoinGeometry = get_node_by_name(
            parent.nodes, "%s_JoinGeometry" % self.label, "GeometryNodeJoinGeometry"
        )
        SeparateGeometry = get_node_by_name(
            parent.nodes,
            "%s_SeparateGeometry" % self.label,
            "GeometryNodeSeparateGeometry",
        )
        links.new(GroupInput.outputs["Geometry"], SeparateGeometry.inputs["Geometry"])
        links.new(GroupInput.outputs["select"], SeparateGeometry.inputs["Selection"])
        links.new(SeparateGeometry.outputs[0], JoinGeometry.inputs["Geometry"])
        links.new(JoinGeometry.outputs["Geometry"], GroupOutput.inputs["Geometry"])
        # then create the nodes for the Wrap level
        self.build_wrap_node_group()
        # then create the nodes for the atoms level
        self.build_atoms_node_group()

    def build_wrap_node_group(self):
        parent = self.gn_node_group
        default_interface = [
            ["Geometry", "NodeSocketGeometry", "INPUT"],
            ["Geometry", "NodeSocketGeometry", "OUTPUT"],
        ]
        name = f"Wrap_{self.label}"
        node = get_node_with_node_tree_by_name(
            parent.nodes, name=name, interface=default_interface
        )
        nodes = node.node_tree.nodes
        links = node.node_tree.links
        GroupInput = nodes[0]
        GroupOutput = nodes[1]
        # link the input to parent node
        parent.links.new(
            parent.nodes["Group Input"].outputs["Geometry"], node.inputs["Geometry"]
        )
        # -------------------------------------------------------------
        # set positions
        PositionBatoms = get_node_by_name(
            nodes, "%s_PositionBatoms" % (self.label), "GeometryNodeInputPosition"
        )
        SetPosition = get_node_by_name(
            nodes, "%s_SetPosition" % self.label, "GeometryNodeSetPosition"
        )
        links.new(GroupInput.outputs["Geometry"], SetPosition.inputs["Geometry"])
        # TODO: use cell object directly.
        cell = self.cell.array
        if np.isclose(np.linalg.det(self.cell.array), 0):
            cell = np.eye(3)
        icell = np.linalg.inv(cell)
        scaledPositionsNode = self.vectorDotMatrix(
            node.node_tree, PositionBatoms.outputs[0], icell, "scaled"
        )
        VectorWrap = get_node_by_name(
            nodes, "%s_VectorWrap" % (self.label), "ShaderNodeVectorMath"
        )
        VectorWrap.operation = "WRAP"
        VectorWrap.inputs[1].default_value = [1, 1, 1]
        VectorWrap.inputs[2].default_value = [0, 0, 0]
        links.new(scaledPositionsNode.outputs[0], VectorWrap.inputs["Vector"])
        PositionsNode = self.vectorDotMatrix(
            node.node_tree, VectorWrap.outputs[0], cell, ""
        )
        links.new(PositionsNode.outputs[0], SetPosition.inputs["Position"])
        links.new(SetPosition.outputs[0], GroupOutput.inputs["Geometry"])
        self.wrap = self.pbc

    def build_atoms_node_group(self):
        """Create node group for atoms"""
        # then create the nodes for the atoms level
        parent = self.gn_node_group
        JoinGeometry = get_node_by_name(
            parent.nodes, "%s_JoinGeometry" % self.label, "GeometryNodeJoinGeometry"
        )
        #
        default_interface = [
            ["Geometry", "NodeSocketGeometry", "INPUT"],
            ["Geometry", "NodeSocketGeometry", "OUTPUT"],
        ]
        name = f"Atoms_{self.label}"
        node = get_node_with_node_tree_by_name(
            self.gn_node_group.nodes, name=name, interface=default_interface
        )
        nodes = node.node_tree.nodes
        links = node.node_tree.links
        GroupOutput = nodes[1]
        # link the input to parent node
        parent.links.new(
            parent.nodes["Group Input"].outputs["Geometry"], node.inputs["Geometry"]
        )
        # link the outputs to parent node
        parent.links.new(node.outputs["Geometry"], JoinGeometry.inputs["Geometry"])
        # -------------------------------------------------------------
        JoinGeometry = get_node_by_name(
            nodes, "%s_JoinGeometry" % self.label, "GeometryNodeJoinGeometry"
        )
        links.new(JoinGeometry.outputs["Geometry"], GroupOutput.inputs["Geometry"])

    def add_species_node(self, spname, instancer):
        """Add geometry node for each species

        Args:
            spname (str):
                Name of the species
            instancer (bpy.data.object):
                Object to be instanced
        """
        from batoms.utils.butils import get_node_by_name

        # Create Node Group if not exit
        nt = bpy.data.node_groups[f"Atoms_{self.label}"]
        name = "Atoms_%s_%s" % (self.label, spname)
        node = get_node_by_name(nt.nodes, name, type="GeometryNodeGroup")
        node_tree = self.create_geometry_node_for_species(spname)
        node.node_tree = node_tree
        node.inputs["Instancer"].default_value = instancer
        node.inputs["Species"].default_value = int(string2Number(spname))
        node.inputs["Material"].default_value = instancer.data.materials[0]
        # link the input to parent node
        nt.links.new(nt.nodes[0].outputs["Geometry"], node.inputs["Geometry"])
        # link the outputs to parent node
        JoinGeometry = get_node_by_name(
            nt.nodes, "%s_JoinGeometry" % self.label, "GeometryNodeJoinGeometry"
        )
        nt.links.new(node.outputs["Geometry"], JoinGeometry.inputs["Geometry"])

    def create_geometry_node_for_species(self, spname):
        """Create geometry node for one species."""
        from batoms.utils.butils import get_socket_by_identifier, create_node_tree

        default_interface = [
            ["Geometry", "NodeSocketGeometry", "INPUT"],
            ["Species", "NodeSocketInt", "INPUT"],
            ["Instancer", "NodeSocketObject", "INPUT"],
            ["Material", "NodeSocketMaterial", "INPUT"],
            ["Geometry", "NodeSocketGeometry", "OUTPUT"],
        ]
        name = "Atoms_%s_%s" % (self.label, spname)
        node_tree = create_node_tree(name=name, interface=default_interface)
        nodes = node_tree.nodes
        links = node_tree.links
        GroupInput = nodes[0]
        GroupOutput = nodes[1]
        # compare to species,
        SpeciesIndexAttribute = get_node_by_name(
            nodes,
            "%s_Attribute_species_index" % (self.label),
            "GeometryNodeInputNamedAttribute",
        )
        SpeciesIndexAttribute.inputs["Name"].default_value = "species_index"
        SpeciesIndexAttribute.data_type = "INT"
        CompareSpecies = get_node_by_name(
            nodes, "CompareSpecies_%s_%s" % (self.label, spname), "FunctionNodeCompare"
        )
        CompareSpecies.operation = "EQUAL"
        CompareSpecies.data_type = "INT"
        output_socket = get_socket_by_identifier(
            SpeciesIndexAttribute, "Attribute_Int", type="outputs"
        )
        socket = get_socket_by_identifier(CompareSpecies, "B_INT")
        links.new(GroupInput.outputs["Species"], socket)
        compare_species_socket = get_socket_by_identifier(CompareSpecies, "A_INT")
        links.new(output_socket, compare_species_socket)
        # SetPosition = get_node_by_name(nodes,
        # '%s_SetPosition' % self.label)
        InstanceOnPoint = get_node_by_name(
            nodes,
            "InstanceOnPoint_%s_%s" % (self.label, spname),
            "GeometryNodeInstanceOnPoints",
        )
        ObjectInfo = get_node_by_name(
            nodes, "ObjectInfo_%s_%s" % (self.label, spname), "GeometryNodeObjectInfo"
        )
        links.new(GroupInput.outputs["Instancer"], ObjectInfo.inputs["Object"])
        BoolShow = get_node_by_name(
            nodes,
            "BooleanMath_%s_%s_1" % (self.label, spname),
            "FunctionNodeBooleanMath",
        )
        # set materials
        SetMaterial = get_node_by_name(
            nodes, "SetMaterial_%s_%s" % (self.label, spname), "GeometryNodeSetMaterial"
        )
        links.new(GroupInput.outputs["Material"], SetMaterial.inputs[2])
        # get attribute
        ScaleAttribute = get_node_by_name(
            nodes,
            "%s_NamedAttribute_scale" % (self.label),
            "GeometryNodeInputNamedAttribute",
        )
        ScaleAttribute.inputs["Name"].default_value = "scale"
        ScaleAttribute.data_type = "FLOAT"
        scale_socket = get_socket_by_identifier(
            ScaleAttribute, "Attribute_Float", type="outputs"
        )
        ShowAttribute = get_node_by_name(
            nodes,
            "%s_NamedAttribute_show" % (self.label),
            "GeometryNodeInputNamedAttribute",
        )
        ShowAttribute.inputs["Name"].default_value = "show"
        ShowAttribute.data_type = "INT"
        show_socket = get_socket_by_identifier(
            ShowAttribute, "Attribute_Int", type="outputs"
        )
        # TODO select attribute is not used
        SelectAttribute = get_node_by_name(
            nodes,
            "%s_NamedAttribute_select" % (self.label),
            "GeometryNodeInputNamedAttribute",
        )
        SelectAttribute.inputs["Name"].default_value = "select"
        SelectAttribute.data_type = "INT"
        get_socket_by_identifier(SelectAttribute, "Attribute_Int", type="outputs")
        #
        links.new(show_socket, BoolShow.inputs[0])
        links.new(GroupInput.outputs["Geometry"], InstanceOnPoint.inputs["Points"])
        links.new(scale_socket, InstanceOnPoint.inputs["Scale"])
        links.new(CompareSpecies.outputs[0], BoolShow.inputs[1])
        links.new(BoolShow.outputs["Boolean"], InstanceOnPoint.inputs["Selection"])
        links.new(ObjectInfo.outputs["Geometry"], InstanceOnPoint.inputs["Instance"])
        links.new(InstanceOnPoint.outputs["Instances"], SetMaterial.inputs["Geometry"])
        links.new(SetMaterial.outputs["Geometry"], GroupOutput.inputs["Geometry"])
        return node_tree

    def check_batoms(self, label):
        """Check batoms exist or not

        Args:
            label (str):
                Name of the Batoms

        Returns:
            bool: Batoms label exist or not
        """
        flag = True
        if label not in bpy.data.collections:
            flag = False
        elif bpy.data.collections[label].batoms.type == "OTHER":
            flag = False
        if label not in bpy.data.objects:
            flag = False
        elif bpy.data.objects[label].batoms.type == "OTHER":
            flag = False
        return flag

    def from_batoms(self, label):
        """Load a Batoms object

        Args:
            label (str):
                Name of the Batoms
        """
        from batoms.boundary import Boundary

        print("Load batoms {}".format(label))
        self.coll_name = label
        self.obj_name = label
        self._cell = Bcell(label=label, batoms=self)
        self._boundary = Boundary(label, batoms=self, load=True)
        self._species = Bspecies(label, {}, self)
        self._volumetric_data = VolumetricData(label, None, self)
        self.selects = Selects(label, self)

    @classmethod
    def from_dict(cls, data):
        """Build batoms object from a dictionary.

        Args:
            data (dict): _description_


        Returns:
            Batoms: _description_

        """
        pass

    def as_dict(self):
        """ """
        data = {
            "batoms": {"label": self.label},
            "cell": None,
            "bond": {},
            "polyhedra": {},
            "boundary": {},
        }
        data["batoms"]["array"] = dict(self.arrays)
        data["batoms"]["species"] = self.species.as_dict()
        data["batoms"].update(self.coll.batoms.as_dict())
        data["cell"] = self.cell.as_dict()
        data["bond"] = self.bond.as_dict()
        data["polyhedra"] = self.polyhedra.as_dict()
        data["boundary"] = self.boundary.as_dict()
        # plugins
        for key, info in plugin_info.items():
            if len(info) == 0:
                continue
            if getattr(getattr(self.coll, info[2]), "active"):
                plugin = getattr(self, key)
                data[key] = plugin.as_dict()
        return data

    def get_trajectory(self, local=True):
        """ """
        trajectory = {"positions": self.get_shape_key(self.obj, local=local)}
        return trajectory

    def set_trajectory(self, trajectory=None, frame_start=0):
        if trajectory is None:
            trajectory = self._trajectory
        nframe = len(trajectory["positions"])
        if nframe == 0:
            return
        name = self.label
        obj = self.obj
        self.set_shape_key(name, obj, trajectory["positions"], frame_start=frame_start)

    def set_arrays(self, arrays):
        """ """
        # if len(arrays['positions']) == 0:
        #     return
        attributes = self.attributes
        # same length
        dnvert = len(arrays["species_index"]) - len(attributes["species_index"])
        if dnvert > 0:
            # self.obj.data.vertices.add(dnvert)
            self.add_vertices_bmesh(dnvert)
            # self.udpate_mesh(self.obj)
        elif dnvert < 0:
            self.delete_vertices_bmesh(range(-dnvert))
        self.positions = arrays["positions"]
        print("positions", self.positions)
        for key, value in arrays.items():
            if key in ["positions", "position"]:
                continue
            self.set_attributes({key: value})
        self.update_mesh()

    @property
    def label(self):
        return self.get_label()

    @label.setter
    def label(self, label):
        self.set_label(label)

    def get_label(self):
        return self.coll.batoms.label

    def set_label(self, label):
        self.coll.batoms.label = label

    @property
    def scale(self):
        return self.get_scale()

    @scale.setter
    def scale(self, scale):
        self.set_scale(scale)

    def get_scale(self):
        # scale = self.attributes['scale']
        scale = self.coll.batoms.scale
        return scale

    def set_scale(self, scale):
        """ """
        self.coll.batoms.scale = scale
        scale_array = np.ones(len(self)) * scale
        self.set_scale_array(scale_array)

    def set_scale_array(self, scale_array):
        self.set_attributes({"scale": scale_array})

    @property
    def species(self):
        return self.get_species()

    def get_species(self):
        return self._species

    @species.setter
    def species(self, species):
        self.set_species(species)

    def set_species(self, species):
        for key, data in species.items():
            self._species[key] = data

    @property
    def volumetric_data(self):
        return self.get_volumetric_data()

    def get_volumetric_data(self):
        return self._volumetric_data

    @volumetric_data.setter
    def volumetric_data(self, value):
        self.set_volumetric_data(value)

    def set_volumetric_data(self, value):
        for key, data in value.items():
            self._volumetric_data[key] = data

    @property
    def elements(self):
        return self.get_elements()

    def get_elements(self):
        # main elements
        arrays = self.arrays
        main_elements = self.species.main_elements
        elements = [main_elements[sp] for sp in arrays["species"]]
        return elements

    @property
    def model_style(self):
        return self.get_model_style()

    @model_style.setter
    def model_style(self, model_style):
        self.set_model_style(model_style)

    def get_model_style(self):
        return int(self.coll.batoms.model_style)

    def set_model_style(self, model_style):
        if int(model_style) == 0:
            self.scale = 1
        elif int(model_style) == 1:
            self.scale = 0.4
        elif int(model_style) == 2:
            self.scale = 0.4
        elif int(model_style) == 3:
            self.scale = 0.0001
        scale = np.ones(len(self)) * self.scale
        self.set_attribute("scale", scale)
        self.coll.batoms.model_style = str(model_style)
        model_style_array = np.ones(len(self), dtype=int) * int(model_style)
        self.set_model_style_array(model_style_array)

    @property
    def model_style_array(self):
        return self.get_attribute("model_style")

    @model_style_array.setter
    def model_style_array(self, model_style_array):
        self.set_model_style_array(model_style_array)

    def set_model_style_array(self, model_style_array):
        model_style = {"model_style": model_style_array}
        self.set_attributes(model_style)
        self.draw()
        if self._boundary is not None:
            self.boundary.update()

    @property
    def polyhedra_style(self):
        return int(self.coll.batoms.polyhedra_style)

    @polyhedra_style.setter
    def polyhedra_style(self, polyhedra_style):
        self.coll.batoms.polyhedra_style = str(polyhedra_style)
        self.draw()

    @property
    def show_unit_cell(self):
        return self.coll.batoms.show_unit_cell

    @show_unit_cell.setter
    def show_unit_cell(self, show_unit_cell):
        if show_unit_cell:
            self.coll.batoms.show_unit_cell = show_unit_cell
            self.cell.hide = False
        else:
            self.cell.hide = True

    @property
    def radius(self):
        return self.get_radius()

    def get_radius(self):
        radius = {}
        instancers = self.species.instancers
        for sp in self.species:
            radius[sp.name] = instancers[sp.name].batoms.atom.radius
        return radius

    @property
    def radius_style(self):
        return self.coll.batoms.radius_style

    @radius_style.setter
    def radius_style(self, radius_style):
        from batoms.utils import get_default_species_data

        self.coll.batoms.radius_style = str(radius_style)
        for name, sp in self.species.items():
            data = sp.as_dict()
            props = get_default_species_data(
                data["elements"],
                radius_style=radius_style,
                color_style=self.color_style,
            )
            data.update(props)
            sp.update(data)

    @property
    def color_style(self):
        return self.coll.batoms.color_style

    @color_style.setter
    def color_style(self, color_style):
        from batoms.utils import get_default_species_data

        self.coll.batoms.color_style = str(color_style)
        for name, sp in self.species.items():
            data = sp.as_dict()
            props = get_default_species_data(
                data["elements"],
                radius_style=self.radius_style,
                color_style=color_style,
            )
            data.update(props)
            self.species.bpy_setting[name].color = props["elements"][sp.main_element][
                "color"
            ]
            sp.update(data)

    @property
    def radii_vdw(self):
        from ase.data import vdw_radii, chemical_symbols

        # object_mode()
        radii = []
        elements = self.arrays["elements"]
        for element in elements:
            if element == "X":
                continue
            number = chemical_symbols.index(element)
            radii.append(vdw_radii[number])
        return np.array(radii)

    @property
    def size(self):
        return self.get_size()

    @size.setter
    def size(self, size):
        self.set_size(size)

    def get_size(self):
        return self.arrays["size"]

    def set_size(self, size):
        scale = {}
        radius = self.radius
        for sp in self.species:
            scale[sp] = [size[sp] / radius[sp]] * 3
        self.scale = scale

    def get_scaled_positions(self, cell=None):
        """
        Get array of scaled_positions.
        """
        from ase.cell import Cell

        if not cell:
            cell = self.cell
        cell = Cell.new(cell)
        scaled_positions = cell.scaled_positions(self.positions)
        return scaled_positions

    def get_arrays(self, batoms=None, local=False, X=False, sort=True):
        """ """
        # object_mode()
        # tstart = time()
        arrays = self.attributes
        arrays.update({"positions": self.positions})
        # radius
        radius = self.radius
        arrays.update({"radius": np.zeros(len(self))})
        for sp, value in radius.items():
            mask = np.where(arrays["species"] == sp)
            arrays["radius"][mask] = value
        # size
        arrays["size"] = arrays["radius"] * arrays["scale"]
        main_elements = self.species.main_elements
        elements = [main_elements[sp] for sp in arrays["species"]]
        arrays.update({"elements": np.array(elements, dtype="U20")})
        # print('get_arrays: %s'%(time() - tstart))
        return arrays

    @property
    def cell(self):
        return self._cell

    @cell.setter
    def cell(self, cell):
        from ase.cell import Cell

        cell = Cell.ascell(cell)
        self._cell[:] = cell

    def set_cell(self, cell, scale_atoms=False):
        """Set unit cell vectors.

        Args:
            cell (array):
                New cell array
            scale_atoms (bool, optional):
                Scale all atoms or not. Defaults to False.
        """
        from ase.cell import Cell

        cell = Cell.new(cell)
        oldcell = Cell(self.cell)
        self.cell = cell
        if scale_atoms:
            M = np.linalg.solve(oldcell.complete(), cell.complete())
            self.positions = np.dot(self.positions, M)

    @property
    def pbc(self):
        return self.get_pbc()

    @pbc.setter
    def pbc(self, pbc):
        self.set_pbc(pbc)

    def get_pbc(self):
        return list(self.cell.obj.batoms.cell.pbc)

    def set_pbc(self, pbc):
        if isinstance(pbc, bool):
            pbc = [pbc] * 3
        self.cell.obj.batoms.cell.pbc = pbc

    @property
    def index(self):
        return self.get_index()

    def get_index(self):
        """
        using foreach_get and foreach_set to improve performance.
        """
        # index
        me = self.obj.data
        nvert = len(me.vertices)
        index = np.zeros(nvert, dtype=int)
        layer = me.vertex_layers_int.get("index")
        layer.data.foreach_get("value", index)
        return index

    @property
    def subdivisions(self):
        return self.get_subdivisions()

    @subdivisions.setter
    def subdivisions(self, subdivisions):
        self.set_subdivisions(subdivisions)

    def get_subdivisions(self):
        nverts = len(self.instancer.data.vertices)
        return nverts

    def set_subdivisions(self, subdivisions):
        if not isinstance(subdivisions, int):
            raise Exception("subdivisions should be int!")
        scale = self.scale
        radius = self.radius
        self.clean_batom_objects(self.instancer_name)
        instancer = self.build_instancer(
            radius=radius, scale=scale, subdivisions=subdivisions, shape="ICO_SPHERE"
        )
        instancer.parent = self.obj

    @property
    def shape(self):
        return self.get_shape()

    @shape.setter
    def shape(self, shape):
        self.set_shape(shape)

    def get_shape(self):
        """
        TODO
        """
        # nverts = len(self.instancer.data.vertices)
        return "to do"

    def set_shape(self, shape):
        """
        "UV_SPHERE", "ICO_SPHERE", "CUBE"
        """
        shapes = ["UV_SPHERE", "ICO_SPHERE", "CUBE", "METABALL"]
        scale = self.scale
        if shape not in [0, 1, 2]:
            raise Exception("Shape %s is not supported!" % shape)
        scale = self.scale
        radius = self.radius
        self.clean_batom_objects(self.instancer_name)
        instancer = self.build_instancer(
            radius=radius, scale=scale, shape=shapes[shape]
        )
        instancer.parent = self.obj

    def delete(self, index=[]):
        """Delete atoms by index.

        index: list
            index of atoms to be delete

        Example:

        >>> h2o.delete([1])

        Please note that index start from 0.

        """
        if isinstance(index[0], (bool, np.bool_)):
            index = np.where(index)[0]
        if isinstance(index, int):
            index = [index]
        self.delete_vertices_bmesh(index)

    def __delitem__(self, index):
        """ """
        self.delete(index)

    def draw_constraints(self):
        """Draw label for constraints
        # TODO
        """
        pass

    def __getitem__(self, indices):
        """Return a subset of the Batom.

        i -- int, describing which atom to return.

        #todo: this is slow for large system

        """
        from batoms.slicebatoms import SliceBatoms

        if isinstance(indices, str):
            bspecies = self.species[indices]
            return bspecies
        else:
            slicebatoms = SliceBatoms(self.label, indices, batoms=self)
            # bpy.ops.object.mode_set(mode=mode)
            return slicebatoms

    def __setitem__(self, indices, value):
        """Return a subset of the Batom.

        i -- int, describing which atom to return.

        #todo: this is slow for large system

        """
        positions = self.positions
        positions[indices] = value
        self.set_positions(positions)

    def repeat_positions(self, positions, cell, m):
        """Repeat positions by cell and m.
        cell: 3x3 matrix
        m: 3x1 vector
        """
        M = np.product(m)
        n = len(positions)
        positions = np.tile(positions, (M,) + (1,) * (len(positions.shape) - 1))
        i0 = 0
        for m0 in range(m[0]):
            for m1 in range(m[1]):
                for m2 in range(m[2]):
                    i1 = i0 + n
                    positions[i0:i1] += np.dot((m0, m1, m2), cell)
                    i0 = i1
        return positions

    def __imul__(self, m):
        """
        In-place repeat of atoms.

        >>> from batoms.batoms import Batoms
        >>> co = Batoms('co', ['C', 'O'], [[0, 0, 0], [1.2, 0, 0]])
        >>> co.cell = [3, 3, 3]
        >>> co *= [2, 2, 1]
        """
        cell = self.cell
        if isinstance(m, int):
            m = (m, m, m)
        for x, vec in zip(m, cell):
            if x != 1 and not vec.any():
                raise ValueError("Cannot repeat along undefined lattice " "vector")
        M = np.product(m)
        attributes = self.attributes
        for key, data in attributes.items():
            attributes[key] = np.tile(data, (M,) + (1,) * (len(data.shape) - 1))
        # repeat positions
        attributes["positions"] = self.repeat_positions(self.positions, cell, m)
        # repeat trajectory
        trajectory = self.get_trajectory()
        nframe = self.nframe
        trajectory_new = {"positions": []}
        for i in range(0, nframe):
            positions = self.repeat_positions(trajectory["positions"][i], cell, m)
            trajectory_new["positions"].append(positions)
        self.set_arrays(attributes)
        self.set_trajectory(trajectory_new)
        self.cell.repeat(m)
        self.update_gn_cell()
        if self.volumetric_data is not None:
            self._volumetric_data *= m
        self.species.update_geometry_node()
        if self._boundary is not None:
            self.boundary.update()
        self.draw()
        return self

    def repeat(self, m):
        """ """
        self *= m
        return self

    def __mul__(self, m):
        self.repeat(m)
        return self

    def copy(self, label, displacement=[2, 2, 2]):
        """
        Return a copy.

        label: str
            The label of the copy.

        For example, copy H species:

        >>> h_new = h.copy(label = 'h_new', species = 'H')
        # TODO Support copy of other prroperties: materials, info ...
        """
        # object_mode()
        # copy object first
        arrays = self.arrays
        batoms = self.__class__(
            label=label,
            location=self.location + np.array(displacement),
            species=arrays["species"],
            positions=self.positions,
            pbc=self.pbc,
            cell=self.cell.array,
        )
        return batoms

    def extend(self, other):
        """
        Extend batom object by appending batoms from *other*.

        >>> slab = au111 + co
        todo: merge bond setting
        """
        # could also use self.add_arrays(other.positions)
        # object_mode()
        # merge bondetting
        if self.nframe > 0 or other.nframe > 0:
            raise Exception("Extend is not supported for trajectory!")
        self.bond.settings.extend(other.bond.settings)
        # creat new selections
        n1 = len(self)
        n2 = len(other)
        indices1 = list(range(n1))
        indices2 = list(range(n1, n1 + n2))
        bpy.ops.object.select_all(action="DESELECT")
        self.obj.select_set(True)
        other.obj.select_set(True)
        bpy.context.view_layer.objects.active = self.obj
        bpy.ops.object.join()
        # update species and species_index
        self._species.extend(other._species)
        self.selects.add(self.label, indices1)
        self.selects.add(other.label, indices2)
        # remove old
        bpy.ops.batoms.delete(label=other.label)

    def __iadd__(self, other):
        """
        >>> h1 += h2
        """
        self.extend(other)
        return self

    def __add__(self, other):
        """
        >>> h1 = h1 + h2
        """
        self += other
        return self

    def separate(self):
        """
        Separate batoms object based on selects.

        >>> slab = au111 + co
        >>> slab.separate()
        >>> au111=Batoms('au111')
        >>> co=Batoms('co')
        """
        # could also use self.add_arrays(other.positions)
        # object_mode()
        arrays = self.arrays
        selects = self.selects.selects
        self_indices = []
        for name, sel in selects.items():
            if name == "all":
                continue
            if name == self.label:
                self_indices = sel.indices
                continue
            indices = sel.indices
            sel = self.__class__(
                name,
                species=arrays["species"][indices],
                positions=arrays["positions"][indices],
            )
            new_arrays = {}
            for key, array in arrays.items():
                if key in ["positions", "species"]:
                    continue
                new_arrays[key] = array[indices]
            sel.set_attributes(new_arrays)
        if len(self_indices) == 0:
            # remove old
            bpy.ops.batoms.delete(label=self.label)
            bpy.context.view_layer.objects.active = sel.obj
        else:
            remove_indices = list(set(range(len(self))) - set(self_indices))
            del self[remove_indices]
            bpy.context.view_layer.objects.active = self.obj

    def __iter__(self):
        batom = self.obj
        for i in range(len(self)):
            yield batom.matrix_world @ batom.data.vertices[i].co

    def __repr__(self) -> str:
        text = []
        text.append("label={0}, ".format(self.label))
        text.append("species=%s, " % (list(self.species.species)))
        text.append("cell={0}, ".format(self.cell))
        text.append("pbc={0}".format(self.pbc))
        # text.append('positions={0}'.format(self.positions))
        text = "".join(text)
        text = "Batoms(%s)" % text
        return text

    def replace(self, indices, species):
        """Replace species.
        Parameters:

        indices: list
            indices of atoms will be replaced.
        species: str
            atoms will be changed to this species.

        >>> h2o.replace([0], 'O_1')
        >>> h2o.replace([0], 'S')
        >>> h2o.replace(range(2), 'N')

        # TODO remove species which is completely replaced.
        """
        from batoms.utils import get_default_species_data

        # if kind exists, merger, otherwise build a new kind and add.
        bpy.context.view_layer.objects.active = self.obj
        if isinstance(species, str):
            ele = species.split("_")[0]
            species = [species, {"elements": {ele: {"occupancy": 1.0}}}]
            props = get_default_species_data(
                species[1]["elements"],
                radius_style=self.radius_style,
                color_style=self.color_style,
            )
            species[1].update(props)
            species[1]["elements"].update(props["elements"])
        if species[0] not in self.species:
            if len(species[0]) > 4:
                print(
                    "Warning: the name of the species: {}, should not be longer than four characters.".format(
                        species[0]
                    )
                )
                logger.warning(
                    "The name of the species: {}, should not be longer than four characters.".format(
                        species[0]
                    )
                )
            self.species[species[0]] = species[1]
            # add geometry node
            self.add_species_node(species[0], self.species.instancers[species[0]])
            #
        species_index = self.attributes["species_index"]
        species_array = self.attributes["species"]
        #
        species_index[indices] = string2Number(species[0])
        species_array[indices] = species[0]
        self.set_attributes({"species_index": species_index})
        self.set_attributes({"species": species_array})
        bpy.context.view_layer.objects.active = self.obj
        # print(mode)
        # print(self.species)
        # for sp in self.species:
        self.bond.settings.add_species(species[0])
        self.polyhedra.settings.add_species(species[0])

    def auto_build_species(self, tol=1e-5):
        """Auto build species based on equivalent_atoms.

        Args:
            tol (float, optional): _description_. Defaults to 1e-5.
        """
        from batoms.utils import get_equivalent_atoms

        equivalent_atoms = get_equivalent_atoms(self.as_ase(), tol)
        species = self.species
        species_array = self.get_attribute("species")
        icolor = 1
        for name, sp in species.items():
            n = 0
            atoms_sp = equivalent_atoms[sp.indices]
            unique_species = np.unique(atoms_sp)
            for usp in unique_species:
                indices = np.where(equivalent_atoms == usp)[0]
                if len(indices) > 0:
                    if n > 0:
                        name = "{}_{}".format(species_array[indices[0]], n)
                        self.replace(indices, name)
                        # self.species[name].color = jmol_colors[icolor]
                    n += 1
                    icolor += 1
            if n > 10:
                logger.critical("Name of species longer than 4 characters.")
            logger.info("{} kinds of species are found for {}".format(n, name))

    def add_atoms(self, arrays):
        """Used to add small number of atoms
        Todo: find a fast way.
        """
        from batoms.utils import local2global
        import bmesh

        # object_mode()
        n0 = len(self)
        positions = arrays.pop("positions")
        n1 = n0 + len(positions)
        # add positions
        positions = local2global(
            positions, np.array(self.obj.matrix_world), reversed=True
        )
        bm = bmesh.new()
        bm.from_mesh(self.obj.data)
        bm.verts.ensure_lookup_table()
        for pos in positions:
            bm.verts.new(pos)
        bm.to_mesh(self.obj.data)
        bm.clear()
        # add species
        self.species.add(list(set(arrays["species"])))
        self.set_attribute_with_indices("species", range(n0, n1), arrays["species"])
        if "species_index" not in arrays:
            species_index = [string2Number(sp) for sp in arrays["species"]]
            self.set_attribute_with_indices(
                "species_index", range(n0, n1), species_index
            )
        # add arrays
        if "show" not in arrays:
            show = np.ones(n1 - n0)
            self.set_attribute_with_indices("show", range(n0, n1), show)
        if "scale" not in arrays:
            scale = np.ones(n1 - n0)
            self.set_attribute_with_indices("scale", range(n0, n1), scale)
        # add bond setting
        bond_dicts = self.bond.settings.as_dict()
        species0 = self.species.keys()
        species1 = np.unique(arrays["species"])
        for sp1 in species1:
            for sp0 in species0:
                pair1 = (sp1, sp0)
                pair2 = (sp0, sp1)
                if pair1 not in bond_dicts and pair2 not in bond_dicts:
                    self.bond.settings.add(pair1)
                    sp3 = self.bond.settings.find(pair1)
                    sp4 = self.bond.settings.find(pair2)
                    if sp3:
                        self.bond.update_geometry_node_instancer(sp3.as_dict())
                    if sp4:
                        self.bond.update_geometry_node_instancer(sp4.as_dict())

    def get_cell(self):
        if self.label not in bpy.data.collections:
            return None
        bcell = bpy.data.collections["%s_cell" % self.label]
        cell = np.array(
            [bcell.matrix_world @ bcell.data.vertices[i].co for i in range(3)]
        )
        return cell

    def get_distances(self, i, indices, mic=False):
        """
        Return distances of atom No.i with a list of atoms.

        Use mic=True to use the Minimum Image Convention.

        >>> h2o.get_distances(0, 1)
        >>> h2o.get_distances(0, [1, 2])
        """
        from ase.geometry import get_distances

        positions = self.positions
        p1 = positions[i]
        p2 = positions[indices]
        cell = None
        pbc = None
        if mic:
            cell = self.cell
            pbc = self.pbc
        D, D_len = get_distances(p1, p2, cell=cell, pbc=pbc)
        D_len.shape = (-1,)
        return D_len

    def get_angle(self, i1, i2, i3, mic=False):
        """
        Get angle in degrees between the vectors i2->i1 and
        i2->i3.
        Use mic=True to use the Minimum Image Convention and calculate the
        angle across periodic boundaries.

        >>> h2o.get_angle(0, 1, 2)

        """
        from ase.geometry import get_angles

        positions = self.positions
        p1 = positions[i1]
        p2 = positions[i2]
        p3 = positions[i3]
        v12 = p1 - p2
        v32 = p3 - p2
        cell = None
        pbc = None
        if mic:
            cell = self.cell
            pbc = self.pbc
        return get_angles([v12], [v32], cell=cell, pbc=pbc)

    def get_dihedral(self, i1, i2, i3, i4, mic=False):
        """

        >>> h2o2.get_dihedral(0, 1, 2, 3)

        """
        from ase.geometry import get_dihedrals

        positions = self.positions
        p1 = positions[i1]
        p2 = positions[i2]
        p3 = positions[i3]
        p4 = positions[i4]
        v21 = p2 - p1
        v32 = p3 - p2
        v43 = p4 - p3
        cell = None
        pbc = None
        if mic:
            cell = self.cell
            pbc = self.pbc
        return get_dihedrals([v21], [v32], [v43], cell=cell, pbc=pbc)

    def get_center_of_mass(self, scaled=False):
        """Get the center of mass.

        If scaled=True the center of mass in scaled coordinates
        is returned.
        """
        return self.as_ase().get_center_of_mass(scaled=scaled)

    def get_center_of_geometry(self, coll=None):
        """ """
        vertices = self.get_all_vertices(coll=coll, cell=self.show_unit_cell)
        canvas = np.zeros([2, 3])
        canvas[0] = np.min(vertices, axis=0)
        canvas[1] = np.max(vertices, axis=0)
        center = np.mean(canvas, axis=0)
        return center

    @property
    def show(self):
        return self.get_show()

    @show.setter
    def show(self, state):
        self.set_show(state)

    def get_show(self):
        return self.attributes["show"]

    def set_show(self, show, only_atoms=False):
        #
        if not only_atoms:
            for obj in self.obj.children:
                obj.hide_render = not show
                obj.hide_set(not show)
        #
        if isinstance(show, (bool, int)):
            show = np.ones(len(self), dtype=bool) * show
        self.set_attributes({"show": show})
        # TODO: /home/xing/apps/beautiful-atoms/batoms/batoms.py:1269:
        # DeprecationWarning: In future, it will be an error for 'np.bool_'
        #  scalars to be interpreted as an index
        self.coll.batoms.show = show[0]

    @property
    def wrap(self):
        return self.get_wrap()

    @wrap.setter
    def wrap(self, state):
        self.set_wrap(state)

    def get_wrap(self):
        return list(self.coll.batoms.wrap)

    def set_wrap(self, wrap):
        """Use wrap node to wrap atoms."""
        wrap_node = self.gn_node_group.nodes[f"Wrap_{self.label}"]
        GroupInput = self.gn_node_group.nodes[0]
        self.update_gn_cell()
        if isinstance(wrap, bool):
            wrap = [wrap] * 3
        self.coll.batoms.wrap = list(wrap)
        wrap = np.array(wrap)
        to_sockets = []
        if not wrap.any():
            # switch off
            # reconnect to the group input geometry
            for link in wrap_node.outputs["Geometry"].links:
                to_sockets.append(link.to_socket)
                self.gn_node_group.links.remove(link)
            for socket in to_sockets:
                self.gn_node_group.links.new(GroupInput.outputs["Geometry"], socket)
        else:
            # switch on
            # reconnect to the wrap node
            for link in GroupInput.outputs["Geometry"].links:
                if link.to_node == wrap_node:
                    continue
                to_sockets.append(link.to_socket)
                self.gn_node_group.links.remove(link)
            for socket in to_sockets:
                self.gn_node_group.links.new(wrap_node.outputs["Geometry"], socket)
        wrap_node.node_tree.update_tag()
        # TODO: support selection

    def update_gn_cell(self):
        # update cell
        wrap_node = self.gn_node_group.nodes[f"Wrap_{self.label}"]
        nodes = wrap_node.node_tree.nodes
        cell = self.cell.array
        if np.isclose(np.linalg.det(self.cell.array), 0):
            cell = np.eye(3)
        icell = np.linalg.inv(cell)
        # set positions
        for i in range(3):
            tmp = get_node_by_name(
                nodes, "%s_VectorDot%s_%s" % (self.label, i, ""), "ShaderNodeVectorMath"
            )
            tmp.operation = "DOT_PRODUCT"
            tmp.inputs[1].default_value = cell[:, i]
            # icell
            tmp = get_node_by_name(
                nodes,
                "%s_VectorDot%s_%s" % (self.label, i, "scaled"),
                "ShaderNodeVectorMath",
            )
            tmp.operation = "DOT_PRODUCT"
            tmp.inputs[1].default_value = icell[:, i]

    def get_spacegroup_number(self, symprec=1e-5):
        """ """
        try:
            import spglib
        except ImportError:
            raise ImportError("spglib is not installed!")
        sg = spglib.get_spacegroup(
            (self.cell, self.get_scaled_positions(), self.arrays["numbers"]),
            symprec=symprec,
        )
        if sg is None:
            return None
        no = int(sg[sg.find("(") + 1 : sg.find(")")])  # noqa E203
        return no

    def find_primitive(
        self,
    ):
        """ """
        from ase import Atoms
        import spglib

        atoms = self.atoms
        lattice = atoms.cell
        points = atoms.get_scaled_positions()
        numbers = atoms.get_atomic_numbers()
        cell = (lattice, points, numbers)
        lattice, points, numbers = spglib.find_primitive(cell)
        atoms = Atoms(numbers=numbers, scaled_positions=points, cell=lattice)
        return atoms

    def get_all_vertices(self, coll=None, cell=True):
        """
        Get position of all vertices from all mesh in batoms.
        Used for plane boundary and calc_camera_data
        """
        positions = self.positions
        # isosurface, plane
        if coll is None:
            coll = self.coll
        for obj in coll.all_objects:
            if obj.type != "MESH":
                continue
            if obj.batoms.type == "INSTANCER" or obj.batoms.type == "VOLUME":
                continue
            if obj.hide_get():
                continue
            n = len(obj.data.vertices)
            vertices = np.empty(n * 3, dtype=np.float64)
            obj.data.vertices.foreach_get("co", vertices)
            vertices = vertices.reshape((n, 3))
            vertices = np.append(vertices, np.ones((n, 1)), axis=1)
            mat = np.array(obj.matrix_world)
            vertices = mat.dot(vertices.T).T
            # (natom, 4) back to (natom, 3)
            vertices = vertices[:, :3]
            positions = np.concatenate((positions, vertices), axis=0)
        return positions

    def get_canvas_box(self, direction=[0, 0, 1], padding=None, coll=None):
        """
        Calculate the canvas box from [0, 0, 1] and other direction.

        """
        from batoms.utils import get_canvas

        vertices = self.get_all_vertices(coll=coll, cell=self.show_unit_cell)
        canvas = get_canvas(vertices, direction=direction, padding=padding)
        width = canvas[1][0] - canvas[0][0]
        height = canvas[1][1] - canvas[0][1]
        depth = canvas[1][2] - canvas[0][2]
        return width, height, depth

    def lock_to_camera(self, obj):
        from batoms.utils.butils import lock_to

        for sp, instancer in self.species.instancers.items():
            lock_to(instancer, obj, location=False, rotation=True)

    @property
    def bonds(self):
        """bonds object."""
        deprecated('"bonds" will be deprecated in the furture, please use "bond".')
        return self.bond

    @property
    def bond(self):
        """bond object."""
        from batoms.bond.bond import Bond

        if self._bond is not None:
            return self._bond
        bond = Bond(self.label, batoms=self)
        self.bond = bond
        return bond

    @bond.setter
    def bond(self, bond):
        self._bond = bond

    @property
    def polyhedras(self):
        """polyhedras object."""
        deprecated(
            '"polyhedras" will be deprecated in the furture, please use "polyhedra".'
        )
        return self.polyhedra

    @property
    def polyhedra(self):
        """polyhedra object."""
        from batoms.polyhedra.polyhedra import Polyhedra, default_polyhedra_datas

        if self._polyhedra is not None:
            return self._polyhedra
        polyhedra = Polyhedra(
            self.label, polyhedra_datas=default_polyhedra_datas, batoms=self
        )
        self.polyhedra = polyhedra
        return polyhedra

    @polyhedra.setter
    def polyhedra(self, polyhedra):
        self._polyhedra = polyhedra

    @property
    def boundary(self):
        """boundary object."""
        from batoms.boundary import Boundary

        if self._boundary is not None:
            return self._boundary
        boundary = Boundary(self.label, batoms=self, location=self.location)
        self._boundary = boundary
        return boundary

    @boundary.setter
    def boundary(self, boundary):
        if isinstance(boundary, (int, float)):
            boundary = np.array([[-boundary, 1 + boundary]] * 3)
        elif len(boundary) == 3:
            if isinstance(boundary[0], (int, float)):
                boundary = np.array(
                    [
                        [-boundary[0], 1 + boundary[0]],
                        [-boundary[1], 1 + boundary[1]],
                        [-boundary[2], 1 + boundary[2]],
                    ]
                )
            elif len(boundary[0]) == 2:
                boundary = np.array(boundary)
        self.update_gn_cell()
        self.boundary[:] = boundary

    @property
    def isosurfaces(self):
        """isosurfaces object."""
        deprecated(
            '"isosurfaces" will be deprecated in the furture, please use "isosurface".'
        )
        return self.isosurface

    @property
    def ms(self):
        """ms object."""
        deprecated(
            '"ms" will be deprecated in the furture, please use "molecular_surface".'
        )
        return self.molecular_surface

    @property
    def render(self):
        """Render object."""
        from batoms.render.render import Render

        if self._render is not None:
            return self._render
        render = Render()
        self.render = render
        return render

    @render.setter
    def render(self, render):
        render.batoms = self
        self._render = render
        self.lock_to_camera(render.camera.obj)

    def get_image(
        self,
        viewport=None,
        engine=None,
        frame=1,
        animation=False,
        output=None,
        center=None,
        padding=None,
        canvas=None,
        gpu=False,
    ):
        """Rendering the model.

        Ask the attached render to rendering the model.

        frame: int
        animation: bool
        output: str
        center: array
        padding: float
        canvas: array of 3

        """
        if output is None:
            output = "%s.png" % self.label
        if self.render is None:
            raise RuntimeError("Batoms object has no render.")
        self.render.run_render = True
        if viewport is not None:
            self.render.viewport = viewport
        if engine is not None:
            self.render.engine = engine
        self.render.gpu = gpu
        image = self.render.run(
            self,
            frame=frame,
            animation=animation,
            output=output,
            center=center,
            padding=padding,
            canvas=canvas,
        )
        return image

    def draw(self, model_style=None):
        """
        Draw atoms, bond, polyhedra, .

        Parameters:

        model_style: str
        """
        if model_style is not None:
            self.model_style = model_style
        # self.draw_cell()
        self.draw_space_filling()
        self.draw_ball_and_stick()
        self.draw_polyhedra()
        self.draw_wireframe()

    def draw_space_filling(self):
        # mask = np.where(self.model_style_array == 0, True, False)
        # self.set_attribute_with_indices('scale', mask, self.scale)
        self.boundary.update()

    def draw_ball_and_stick(self):
        mask = np.where(self.model_style_array >= 1, True, False)
        if not mask.any():
            from batoms.bond.bond import default_bond_datas

            self.bond.set_arrays(default_bond_datas.copy())
            return
        # self.set_attribute_with_indices('scale', mask, self.scale)
        self.bond.hide = False
        self.boundary.hide = False
        self.bond.update()

    def draw_polyhedra(self):
        mask = np.where(self.model_style_array == 2, True, False)
        if not mask.any():
            from batoms.polyhedra.polyhedra import default_polyhedra_datas

            self.polyhedra.set_arrays(default_polyhedra_datas)
            return
        self.polyhedra.update()
        self.set_attribute_with_indices("show", mask, True)
        if self.polyhedra_style == 0:
            # self.set_attribute_with_indices('scale', mask, self.scale)
            self.boundary.hide = False
            self.bond.hide = False
            self.bond.search_bond.hide = False
            # self.bond.update()
        if self.polyhedra_style == 1:
            # only hide bond
            # self.set_attribute_with_indices('scale', mask, self.scale)
            self.bond.hide = True
            # show atoms
            if self.bond._search_bond is not None:
                self.bond.search_bond.hide = False
            self.boundary.hide = False
        elif self.polyhedra_style == 2:
            # hide bond and atoms, except center atoms
            for b in self.bond.settings:
                if b.polyhedra:
                    mask1 = np.where(
                        self.attributes["species"] == b.species1, True, False
                    )
                    self.set_attribute_with_indices("scale", mask1, self.scale)
                    mask[mask1] = False
            scale = 0
            # self.set_attribute_with_indices('scale', mask, self.scale)
            # self.boundary.hide = True
            self.bond.hide = True
            self.bond.search_bond.hide = True
            # self.set_attribute_with_indices('show', mask, False)
        elif self.polyhedra_style == 3:
            # hide all bond and atoms
            scale = 0.0001
            self.set_attribute_with_indices("scale", mask, scale)
            self.boundary.hide = True
            self.bond.hide = True
            self.bond.search_bond.hide = True
            # self.set_attribute_with_indices('show', mask, False)

    def draw_wireframe(self):
        mask = np.where(self.model_style_array == 3, True, False)
        # self.set_attribute_with_indices('show', mask, 0)
        self.set_attribute_with_indices("scale", mask, self.scale)
        # self.update(mask)

    def as_ase(self, local=True, with_attribute=True):
        """
        local: bool
            if True, use the origin of uint cell as the origin
        """
        from ase import Atoms

        positions = self.positions
        trajectory = self.get_trajectory()["positions"]
        arrays = self.arrays
        if len(trajectory) == 0:
            trajectory = [positions]
        nframe = len(trajectory)
        images = []
        for f in range(nframe):
            positions = trajectory[f]
            if not local:
                positions += self.cell.origin
            atoms = Atoms(
                symbols=arrays["elements"],
                positions=positions,
                cell=self.cell,
                pbc=self.pbc,
            )
            if with_attribute:
                for name, array in arrays.items():
                    if name in ["elements", "positions", "numbers"]:
                        continue
                    atoms.set_array(name, np.array(array))
            images.append(atoms)
        if nframe == 1:
            return images[0]
        else:
            return images

    def as_pybel(self, export_bond=False):
        """Convert an Batoms object to an OBMol object.

        Returns:
            OBMOL: OBMOL
        """
        from openbabel import pybel
        from ase.data import atomic_numbers

        mol = pybel.ob.OBMol()
        arrays = self.arrays
        natom = len(self)
        for i in range(natom):
            a = mol.NewAtom()
            a.SetAtomicNum(atomic_numbers[arrays["elements"][i]])
            a.SetVector(
                arrays["positions"][i][0],
                arrays["positions"][i][1],
                arrays["positions"][i][2],
            )
        if export_bond:
            bond_arrays = self.bond.arrays
            nbond = len(bond_arrays)
            for i in range(nbond):
                mol.AddBond(
                    int(bond_arrays["atoms_index1"][i]) + 1,
                    int(bond_arrays["atoms_index2"][i]) + 1,
                    bond_arrays["order"][i],
                )
        else:
            mol.ConnectTheDots()
            mol.PerceiveBondOrders()
        mol = pybel.Molecule(mol)
        return mol

    def write(self, filename, local=True):
        """
        Save batoms to structure file.
        >>> h2o.write('h2o.xyz')
        """
        self.as_ase(local).write(filename)

    def transform(self, matrix=None):
        """
        Transformation matrix
        make sure np.linalg.det(P) > 0, otherwise,
        a error raised by ASE last column [5, 5, 0] to
        translate new atoms, thus not overlap with old one.

        """
        from ase.build.supercells import make_supercell

        if matrix is not None:
            rotation = np.array([matrix[0][:3], matrix[1][:3], matrix[2][:3]])
            translation = np.array([matrix[0][3], matrix[1][3], matrix[2][3]])
            atoms = self.as_ase()
            atoms = make_supercell(atoms, rotation)
            batoms = self.__class__(
                label="%s_transform" % self.label,
                from_ase=atoms,
                model_style=self.model_style,
            )
        else:
            return
        batoms.translate(translation)
        # self.hide = True
        return batoms

    @property
    def draw_text(self):
        """draw_text object.
        Shoud be a global variable.
        """
        from batoms.draw.draw_screen import DrawText

        dns = bpy.app.driver_namespace
        if self.label in dns:
            return dns[self.label]
        context = bpy.context
        dns[self.label] = DrawText(context, self.label)
        return dns[self.label]

    @property
    def show_label(self):
        return self.coll.batoms.show_label

    @show_label.setter
    def show_label(self, label="species"):
        self.coll.batoms.show_label = str(label)
        arrays = self.arrays
        positions = arrays["positions"]
        self.draw_text.remove_handle()
        if label is None or label == "":
            return
        if label.lower() == "index":
            n = len(positions)
            texts = [str(i) for i in range(n)]
        elif label.lower() in arrays:
            texts = arrays[label]
        else:
            raise Exception("%s does not have %s attribute" % (self.label, label))
        self.draw_text.add_handle(positions, texts)

    def optmize(self, forcefield="mmff94", steps=500):
        """_summary_

        Args:
            forcefield (str, optional): _description_. Defaults to "mmff94".
            steps (int, optional): _description_. Defaults to 500.
        """
        from openbabel import openbabel as ob

        # from batoms.utils import read_from_pybel
        mol = self.as_pybel()
        mol.localopt(forcefield, steps)
        positions = []
        for atom in ob.OBMolAtomIter(mol.OBMol):
            positions.append([atom.GetX(), atom.GetY(), atom.GetZ()])
        # species, positions, arrays, cell, pbc, info = read_from_pybel(mol)
        self.positions = positions

    def export_mesh(
        self,
        filename,
        with_cell=False,
        with_polyhedra=False,
        with_bond=False,
        with_boundary=False,
        with_search_bond=False,
    ):
        """_summary_
        ctmviewer

        Args:
            filename (_type_): _description_

        """
        self.realize_instances = True
        objs = [self.obj]
        if with_cell:
            self.cell.obj.select_set(True)
        if with_boundary:
            self.boundary.realize_instances = True
            objs.insert(0, self.boundary.obj)
        if with_search_bond:
            self.bond.search_bond.realize_instances = True
            objs.insert(0, self.bond.search_bond.obj)
        if with_polyhedra:
            self.polyhedra.realize_instances = True
            objs.insert(0, self.polyhedra.obj)
        for obj in objs:
            bpy.context.view_layer.objects.active = obj
            # remove shape key
            if obj.data.shape_keys is not None:
                bpy.ops.object.shape_key_remove(all=True)
            bpy.ops.object.modifier_apply(modifier=obj.modifiers[0].name)
            obj.select_set(True)
        if filename.endswith(".x3d"):
            bpy.ops.export_scene.x3d(filepath=filename, use_selection=True)
        #  obj is not supported in Blender 4.0
        elif filename.endswith(".obj") or filename.endswith(".mtl"):
            bpy.ops.export_scene.obj(filepath=filename, use_selection=True)
        elif filename.endswith(".fbx"):
            bpy.ops.export_scene.fbx(filepath=filename, use_selection=True)
        else:
            raise ("File format %s is not supported." % filename)

    @property
    def crystal_view(self):
        return self.get_crystal_view()

    @crystal_view.setter
    def crystal_view(self, state):
        self.set_crystal_view(state)

    def get_crystal_view(self):
        return self.coll.batoms.crystal_view

    def set_crystal_view(self, crystal_view):
        #
        self.coll.batoms.crystal_view = crystal_view
        if crystal_view:
            self.boundary = 0.01
            self.bond.show_search = True
            self.bond.update()
            self.polyhedra.update()
        else:
            self.boundary = 0
            self.bond.show_search = False
            self.bond.update()
            self.polyhedra.update()

    @property
    def segments(self):
        return self.get_segments()

    @segments.setter
    def segments(self, segments):
        self.set_segments(segments)

    def get_segments(self):
        return self.coll.batoms.segments[:]

    def set_segments(self, segments):
        if isinstance(segments, int):
            segments = [segments, segments]
            # raise Exception('Segments should be int!')
        species = self._species
        self.coll.batoms.segments = segments
        for name, sp in species.items():
            sp.data.segments = segments
            sp.update(sp.data.as_dict())

    def auto_assign_charge(self, force_field="mmff94"):
        """Estimates atomic partial charges using openbabel.

        MMFF94 Partial Charges are assigned using a four stage algorithm.

        Args:
            force_field (str, optional): force field. Defaults to "mmff94".
        """
        tstart = time()
        ob = self.as_pybel()
        charges = np.array(ob.calccharges(model=force_field))
        self.set_attributes({"charges": charges})
        logger.debug("time: {:1.3f}".format(time() - tstart))
        return charges

    def calc_electrostatic_potential(self, points):
        """Calc electrostatic potential on given points
            based on partial charges.

        Args:
            points (array): points

        Returns:
            array: potentials at given points
        """
        from ase.geometry import get_distances

        tstart = time()
        positions = self.positions
        charges = self.get_attribute("charges")
        # parameter
        eps = 8.854e-12  # Permittivity of free space (F.m-1)
        k = 1 / 4 / np.pi / eps
        # calculate distance
        D, D_len = get_distances(positions, points)
        # matrix
        pot_mat = k / D_len * charges[:, None]
        # sum over all charge (atoms)
        potentials = np.sum(pot_mat, axis=0)
        logger.debug("time: {:1.3f}".format(time() - tstart))
        return potentials

    def set_hide(self, state):
        self.obj.hide_render = state
        self.obj.hide_set(state)
        self.cell.hide = True
        self.bond.hide = True


def hook_plugins(cls, plugin_info):
    tstart = time()

    def create_getter(name, data):
        def plugin_getter(self):
            """plugin object."""
            import importlib

            _name = "_{}".format(name)
            if hasattr(self, _name):
                plugin = getattr(self, _name)
                logger.debug("has plugin: {}".format(name))
                return plugin
            else:
                logger.debug("Does not have plugin: {}".format(name))
                plugin_module = getattr(
                    importlib.import_module("batoms.plugins.{}".format(data[0])),
                    data[1],
                )
                plugin = plugin_module(self.label, batoms=self)
                setattr(self, _name, plugin)
                return plugin

        return plugin_getter

    def create_setter(name):
        def plugin_setter(self, plugin):
            """Get plugin
            Args:
                plugin (_type_): _description_
            """
            logger.debug("set plugin: {}".format(name))
            _name = "_{}".format(name)
            setattr(self, _name, plugin)

        return plugin_setter

    for name, data in plugin_info.items():
        logger.debug("Add plugin: {}".format(name))
        setattr(
            cls,
            name,
            property(
                fget=create_getter(name, data),
                fset=create_setter(name),
                doc="test",
            ),
        )

    logger.debug("Hook plugins: {:1.2f}".format(time() - tstart))


hook_plugins(Batoms, plugin_info)
