def get_atomic_coordinates(self, cif: CifContainer):
for at in cif.atoms(without_h=False):
yield {'label': at.label,
'type' : at.type,
'x' : at.x.replace('-', minus_sign),
'y' : at.y.replace('-', minus_sign),
'z' : at.z.replace('-', minus_sign),
'part' : at.part.replace('-', minus_sign),
'occ' : at.occ.replace('-', minus_sign),
'u_eq' : at.u_eq.replace('-', minus_sign)}
def add_coords_table(document: Document, cif: CifContainer, table_num: int):
"""
Adds the table with the atom coordinates.
:param document: The current word document.
:param cif: the cif object from CifContainer.
:return: None
"""
atoms = list(cif.atoms())
table_num += 1
headline = "Table {}. Atomic coordinates and ".format(table_num)
h = document.add_heading(headline, 2)
h.add_run('U').font.italic = True
h.add_run('eq').font.subscript = True
h.add_run('{}[{}'.format(protected_space, angstrom))
h.add_run('2').font.superscript = True
h.add_run('] for {}'.format(cif.block.name))
coords_table = document.add_table(rows=len(atoms) + 1,
cols=5,
style='Table Grid')
# Atom x y z U(eq)
head_row = coords_table.rows[0]
head_row.cells[0].paragraphs[0].add_run('Atom').bold = True
px = head_row.cells[1].paragraphs[0]
ar = px.add_run('x')
ar.bold = True
ar.italic = True
py = head_row.cells[2].paragraphs[0]
ar = py.add_run('y')
ar.bold = True
ar.italic = True
pz = head_row.cells[3].paragraphs[0]
ar = pz.add_run('z')
ar.bold = True
ar.italic = True
pu = head_row.cells[4].paragraphs[0]
ar = pu.add_run('U')
ar.bold = True
ar.italic = True
ar2 = pu.add_run('eq')
ar2.bold = True
ar2.font.subscript = True
# having a list of column cells before is *much* faster!
col0_cells = coords_table.columns[0].cells
col1_cells = coords_table.columns[1].cells
col2_cells = coords_table.columns[2].cells
col3_cells = coords_table.columns[3].cells
col4_cells = coords_table.columns[4].cells
rowidx = 1
for at in atoms:
c0, c1, c2, c3, c4 = col0_cells[rowidx], col1_cells[rowidx], col2_cells[rowidx], \
col3_cells[rowidx], col4_cells[rowidx]
rowidx += 1
c0.text = at[0] # label
c1.text = (str(at[2])) # x
c2.text = (str(at[3])) # y
c3.text = (str(at[4])) # z
c4.text = (str(at[7])) # ueq
p = document.add_paragraph()
p.style = document.styles['tabunterschr']
p.add_run('U').font.italic = True
p.add_run('eq').font.subscript = True
p.add_run(' is defined as 1/3 of the trace of the orthogonalized ')
p.add_run('U').font.italic = True
ij = p.add_run('ij')
ij.font.subscript = True
ij.font.italic = True
p.add_run(' tensor.')
set_column_width(coords_table.columns[0], Cm(2.3))
set_column_width(coords_table.columns[1], Cm(2.8))
set_column_width(coords_table.columns[2], Cm(2.8))
set_column_width(coords_table.columns[3], Cm(2.8))
set_column_width(coords_table.columns[4], Cm(2.8))
document.add_paragraph()
return table_num