#!/usr/bin/env python
# coding: utf-8

# # Viewing ase structure using HTML

# In[2]:


from  ase.build import  molecule
from  IPython.display import HTML


# In[3]:


def atoms_to_html(atoms):
    'Return the html representation the atoms object as string'

    from tempfile import NamedTemporaryFile
    
    with NamedTemporaryFile('r+', suffix='.html') as ntf:
        atoms.write(ntf.name, format='html')
        ntf.seek(0)
        html = ntf.read()
    return html


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tbut = atoms_to_html(molecule('trans-butane'))
HTML(tbut)


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benzene = atoms_to_html(molecule('C6H6'))
HTML(benzene)


# # Periodic structure - AFI zeolite

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aficif ='''data_AFI
#**************************************************************************
#
# CIF taken from the IZA-SC Database of Zeolite Structures
# Ch. Baerlocher and L.B. McCusker
# Database of Zeolite Structures: http://www.iza-structure.org/databases/ 
#
# The atom coordinates and the cell parameters were optimized with DLS76
# assuming a pure SiO2 composition.
#
#**************************************************************************


_cell_length_a                  13.8270(0)
_cell_length_b                  13.8270(0)
_cell_length_c                   8.5800(0)
_cell_angle_alpha               90.0000(0)
_cell_angle_beta                90.0000(0)
_cell_angle_gamma              120.0000(0)

_symmetry_space_group_name_H-M     'P 6/m c c'
_symmetry_Int_Tables_number         192
_symmetry_cell_setting             hexagonal


loop_
_symmetry_equiv_pos_as_xyz
'+x,+y,+z'
'-y,+x-y,+z'
'-x+y,-x,+z'
'-x,-y,+z'
'+y,-x+y,+z'
'+x-y,+x,+z'
'-y,-x,1/2+z'
'-x+y,+y,1/2+z'
'+x,+x-y,1/2+z'
'+y,+x,1/2+z'
'+x-y,-y,1/2+z'
'-x,-x+y,1/2+z'
'-x,-y,-z'
'+y,-x+y,-z'
'+x-y,+x,-z'
'+x,+y,-z'
'-y,+x-y,-z'
'-x+y,-x,-z'
'+y,+x,1/2-z'
'+x-y,-y,1/2-z'
'-x,-x+y,1/2-z'
'-y,-x,1/2-z'
'-x+y,+y,1/2-z'
'+x,+x-y,1/2-z'

loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
    O1    O      0.4565    0.3333    0.0000
    O2    O      0.3693    0.3693    0.2500
    O3    O      0.4200    0.2100    0.2500
    O4    O      0.5798    0.4202    0.2500
    T1    Si     0.4565    0.3334    0.1874

'''


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def from_string(string, fmt=None):
    'Instantiate Atoms object from a string with specific format'

    import ase.io
    from tempfile import NamedTemporaryFile

    with NamedTemporaryFile('r+') as ntf:
        ntf.write(string)
        ntf.seek(0)
        atoms = ase.io.read(ntf, format=fmt)

    return atoms


# In[10]:


afi = from_string(aficif, fmt='cif')


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afi_html = atoms_to_html(afi)


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HTML(afi_html)


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get_ipython().run_line_magic('version_information', 'ase, jupyter')