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===============
Report Document
===============
FinalCif is able to render a nice looking report document as MS Word format from the information contained in the CIF.
For a complete report, you have to finish the CIF first.
It is also advisable to deposit the file before the report generation in order to have the CCDC number
listed in the report text.
.. figure:: pics/finalcif_report.png
A report document example.
With a multi-CIF opened, also a report document where the values of all data\_ blocks are together in one table
is written to [filename]-multitable.docx.
.. figure:: pics/multitable.png
A report document from a multi-CIF.
CCDC Number
-----------
There are two ways of introducing the CCDC number into the .cif file:
* Edit the 'CCDC Number' field in the top of FinalCif. The number will be saved in the key '_database_code_depnum_ccdc_archive'.
* Drag&Drop the deposition response email from the CCDC (`in EML format <https://www.loc.gov/preservation/digital/formats/fdd/fdd000388.shtml>`_) into the work folder and reload the .cif file.
Picture
-------
FinalCif can add a picture of your structure to the report document.
* Either by previously performing an html or local checkcif. Then it automatically adds a picture from the checkcif report, as in the example above.
* Or you can add any other picture with the "Picture for Tables" button.
* A third possibility is the 'Show Details' page where you can use the current structure view as picture
for the report:
.. figure:: pics/finalcif_details.png
:width: 600
The Details page.
Customizing the Report
----------------------
.. figure:: pics/report_options.png
:width: 600
Report options with two templates.
Do you have specific expectations regarding the appearance of the structure report?
With self-defined templates this is possible in FinalCif. You can find example templates
at https://github.com/dkratzert/FinalCif. It is easier to change them than to create them from scratch.
The templates are an ordinary MS Word document (more specific: Office Open XML, https://de.wikipedia.org/wiki/Office_Open_XML)
So you can use them with MS Word, Openoffice or Libre Office and other Office Open capable programs.
FinalCif uses the Jinja2 template language to exchange specific instructions in the templates with
precalculated information and direct values from the CIF file.
In the templates, you have two different types of information to add:
1. A variable, starting with {{ and ending with }}, for example: :code:`{{ a_variable }}`
This would insert the content of the variable 'a_variable' at this point in the document
during the report generation.
2. A block, starting with {% and ending with %}, for example:
.. code-block:: jinja
Foo bar {% if a_variable %} Put this text here {% endif %} Some other text.
This would put the text enclosed in the block into the document depending if either :code:`a_variable`
has a value or not.
The second possibility for blocks is to iterate over the values of a Python dictionary:
.. code-block:: jinja
{% for atom in atoms %}
{{ atom.label }}
{% enfor %}
Produces a list of all atom names in a CIF.
If you need a table, :code:`{%tr foo %}` is used to generate table rows.
Data Available for the Report
-----------------------------
.. code-block:: text
'cif' : Gives you access to the full CIF information, use it like
{{ cif._exptl_crystal_density_diffrn }} or the variables in the next table.
'atomic_coordinates' : The atomic coordinates as ('label', 'x', 'y', 'z', 'u_eq') for each atom.
'displacement_parameters': The atomic displacement parameters as ('label', 'U11', 'U22', 'U33',
'U23', 'U13', 'U12') for each atom.
'bonds' : The bonds with lengths as ('atoms', 'dist') for each atom pair.
'angles' : The bond angles as ('atoms', 'angle') for each atom triple.
'ba_symminfo' : The symmetry operations used to generate equivalent atoms in the angles list.
'torsions' : The torsion angles as ('atoms', 'angle') for each atom quartet.
'torsion_symminfo' : The symmetry operations used to generate equivalent atoms in the torsion angles list.
'hydrogen_bonds' : The hydrogen bonds (in case there are some defined with HTAB) as
('atoms', 'dist_dh', 'dist_ha', 'dist_da', 'angle_dha').
'hydrogen_symminfo' : The symmetry operations used to generate equivalent atoms in the hydrogen bonds list
'literature' : A list of citations to the above used programs, e.g. literature.integration.richtext.
The richtext attribute formats the citation. Available literature:
('integration', 'absorption', 'solution', 'refinement', 'ccdc', 'finalcif')
'options' : A dictionary with {'without_h': True/False, 'atoms_table': True/False,
'text': True/False, 'bonds_table': True/False},
'space_group' : The space group formatted as formula object.
'structure_figure' : A picture selected with the 'Picture for Report' button.
'crystallization_method': The value of '_exptl_crystal_recrystallization_method'
'sum_formula' : The formatted version of '_chemical_formula_sum' with subscript numbers.
'moiety_formula' : The formatted version of '_chemical_formula_moiety' with subscript numbers.
'itnum' : The space group number from the international tables.
'crystal_size' : The crystal size as X x Y x Z.
'crystal_colour' : The crystal colour.
'crystal_shape' : The crystal shape.
'radiation' : The radiation type used like MoK_alpha.
'wavelength' : The wavelength in nm.
'theta_range' : The theta range.
'diffr_type' : The measurement device type.
'diffr_device' : The measurement device.
'diffr_source' : The radiation source.
'monochromator' : The monochromator.
'detector' : The detector model.
'lowtemp_dev' : The low-temperature device.
'index_ranges' : The preformatted index ranges.
'indepentent_refl' : The number of independent reflections.
'r_int' : The R_int of the data.
'r_sigma' : The R_sigma of the data.
'completeness' : The completeness of the data.
'theta_full' : The resolution of the dataset in degree theta.
'data' : the value of '_refine_ls_number_reflns'.
'restraints' : The value of '_refine_ls_number_restraints'.
'parameters' : The value of '_refine_ls_number_parameters'.
'goof' : The value of '_refine_ls_goodness_of_fit_ref'.
'ls_R_factor_gt' : The value of '_refine_ls_R_factor_gt'.
'ls_wR_factor_gt' : The value of '_refine_ls_wR_factor_gt'.
'ls_R_factor_all' : The value of '_refine_ls_R_factor_all'.
'ls_wR_factor_ref' : The value of '_refine_ls_wR_factor_ref'.
'diff_dens_min' : The minimum residual density in e/A^3.
'diff_dens_max' : The maximum residual density in e/A^3.
'exti' : The extinction coefficient.
'flack_x' : The value of the flack X parameter.
'integration_progr' : The name of the integration program used.
'abstype' : The value of '_exptl_absorpt_correction_type'.
'abs_details' : The name of the absortion correction program used.
'solution_method' : The structure solution method used.
'solution_program' : The name of the structure solution program.
'refinement_prog' : The name of the refinement program.
'refinement_details' : The text of '_refine_special_details'.
**This information from the 'cif' variable can also be useful:**
The cif variable contains values from the CIF directly and thus negative values have a hyphen and
no real minus sign in front. The former values hav hyphens replaced with minus signs.
.. code-block:: text
'cif.res_file_data' : The SHELX .res file text.
'cif.is_centrosymm' : It true if the space group of the structure is centrosymmetric.
'cif.atoms' : The list of atoms with 'label', 'type', 'x', 'y', 'z', 'part',
'occ', 'u_eq'.
'cif.hydrogen_atoms_present' : Is true if hydrogen atoms are present in the structure.
'cif.disorder_present' : Is true if atoms in parts are present in the structure.
'cif.cell' : The unit cell as 'a', 'b', 'c', 'alpha', 'beta', 'gamma', 'volume'.
'cif.bonds' : The list of bonds as 'label1', 'label2', 'dist', 'symm'.
'angles' : The list of angles as 'label1', 'label2', 'label3', 'angle_val',
'symm1', 'symm2'.
'torsion_angles' : The list of torsion angles as 'label1', 'label2', 'label3', 'label4',
'torsang', 'symm1', 'symm2', 'symm3', 'symm4'.
'hydrogen_bonds' : The list of hydrogen atoms involved in HTAB listings as 'label_d',
'label_h', 'label_a', 'dist_dh', 'dist_ha', 'dist_da', 'angle_dha',
'symm'.
'test_res_checksum' : True if the checksum of the SHELX .res file fits to the file content.
'test_hkl_checksum' : True if the checksum of the SHELX .hkl file fits to the file content.
The above is not limited to the templates of FinalCif. It is also possible to insert template tags
into any other Word document and replace them with values from a CIF file. There are no limits to
the imagination.
Further information for programmers:
`https://docxtpl.readthedocs.io/en/latest/ <https://docxtpl.readthedocs.io/en/latest/>`_
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