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# Source code for ase.io.xtd

    import xml.etree.ElementTree as ET
    from xml.dom import minidom

    import numpy as np

    from ase import Atoms
    from ase.io.xsd import SetChild, _write_xsd_html

    _image_header = ' ' * 74 + '0.0000\n!DATE     Jan 01 00:00:00 2000\n'
    _image_footer = 'end\nend\n'

    def _get_atom_str(an, xyz):
        s = f'{an:<5}'
        s += f'{xyz[0]:>15.9f}{xyz[1]:>15.9f}{xyz[2]:>15.9f}'
        s += ' XXXX 1      xx      '
        s += f'{an:<2}'
        s += '  0.000\n'
        return s

    def write_xtd(filename, images, connectivity=None, moviespeed=10):
        """Takes Atoms object, and write materials studio file
        atoms: Atoms object
        filename: path of the output file
        moviespeed: speed of animation. between 0 and 10

        note: material studio file cannot use a partial periodic system. If partial
        perodic system was inputted, full periodicity was assumed.
        """
        if moviespeed < 0 or moviespeed > 10:
            raise ValueError('moviespeed only between 0 and 10 allowed')

        if hasattr(images, 'get_positions'):
            images = [images]

        XSD, ATR = _write_xsd_html(images, connectivity)
        ATR.attrib['NumChildren'] = '2'
        natoms = len(images[0])

        bonds = []
        if connectivity is not None:
            for i in range(connectivity.shape[0]):
                for j in range(i + 1, connectivity.shape[0]):
                    if connectivity[i, j]:
                        bonds.append([i, j])

        # non-periodic system
        s = '!BIOSYM archive 3\n'
        if not images[0].pbc.all():
            # Write trajectory
            SetChild(ATR, 'Trajectory', dict(
                ID=str(natoms + 3 + len(bonds)),
                Increment='-1',
                End=str(len(images)),
                Type='arc',
                Speed=str(moviespeed),
                FrameClassType='Atom',
            ))

            # write frame information file
            s += 'PBC=OFF\n'
            for image in images:
                s += _image_header
                s += '\n'
                an = image.get_chemical_symbols()
                xyz = image.get_positions()
                for i in range(natoms):
                    s += _get_atom_str(an[i], xyz[i, :])
                s += _image_footer

        # periodic system
        else:
            SetChild(ATR, 'Trajectory', dict(
                ID=str(natoms + 9 + len(bonds)),
                Increment='-1',
                End=str(len(images)),
                Type='arc',
                Speed=str(moviespeed),
                FrameClassType='Atom',
            ))

            # write frame information file
            s += 'PBC=ON\n'
            for image in images:
                s += _image_header
                s += 'PBC'
                vec = image.cell.lengths()
                s += f'{vec[0]:>10.4f}{vec[1]:>10.4f}{vec[2]:>10.4f}'
                angles = image.cell.angles()
                s += '{:>10.4f}{:>10.4f}{:>10.4f}'.format(*angles)
                s += '\n'
                an = image.get_chemical_symbols()

                angrad = np.deg2rad(angles)
                cell = np.zeros((3, 3))
                cell[0, :] = [vec[0], 0, 0]
                cell[1, :] = (np.array([np.cos(angrad[2]), np.sin(angrad[2]), 0])
                              * vec[1])
                cell[2, 0] = vec[2] * np.cos(angrad[1])
                cell[2, 1] = ((vec[1] * vec[2] * np.cos(angrad[0])
                               - cell[1, 0] * cell[2, 0]) / cell[1, 1])
                cell[2, 2] = np.sqrt(vec[2]**2 - cell[2, 0]**2 - cell[2, 1]**2)
                xyz = np.dot(image.get_scaled_positions(), cell)
                for i in range(natoms):
                    s += _get_atom_str(an[i], xyz[i, :])
                s += _image_footer

        # print arc file
        if isinstance(filename, str):
            farcname = filename[:-3] + 'arc'
        else:
            farcname = filename.name[:-3] + 'arc'

        with open(farcname, 'w') as farc:
            farc.write(s)

        # check if file is an object or not.
        openandclose = False
        try:
            if isinstance(filename, str):
                fd = open(filename, 'w')
                openandclose = True
            else:  # Assume it's a 'file-like object'
                fd = filename

            # Return a pretty-printed XML string for the Element.
            rough_string = ET.tostring(XSD, 'utf-8')
            reparsed = minidom.parseString(rough_string)
            Document = reparsed.toprettyxml(indent='\t')

            # write
            fd.write(Document)
        finally:
            if openandclose:
                fd.close()

    def read_xtd(filename, index=-1):
        """Import xtd file (Materials Studio)

        Xtd files always come with arc file, and arc file
        contains all the relevant information to make atoms
        so only Arc file needs to be read
        """
        if isinstance(filename, str):
            arcfilename = filename[:-3] + 'arc'
        else:
            arcfilename = filename.name[:-3] + 'arc'

        # This trick with opening a totally different file is a gross violation of
        # common sense.
        with open(arcfilename) as fd:
            return read_arcfile(fd, index)

    def read_arcfile(fd, index):
        images = []

        # the first line is comment
        fd.readline()
        pbc = 'ON' in fd.readline()
        L = fd.readline()
        while L != '':
            if '!' not in L:  # flag for the start of an image
                L = fd.readline()
                continue
            if pbc:
                L = fd.readline()
                cell = [float(d) for d in L.split()[1:]]
            else:
                fd.readline()
            symbols = []
            coords = []
            while True:
                line = fd.readline()
                L = line.split()
                if not line or 'end' in L:
                    break
                symbols.append(L[0])
                coords.append([float(x) for x in L[1:4]])
            if pbc:
                image = Atoms(symbols, positions=coords, cell=cell, pbc=pbc)
            else:
                image = Atoms(symbols, positions=coords, pbc=pbc)
            images.append(image)
            L = fd.readline()

        if not index:
            return images
        else:
            return images[index]