def _write_pdb_to_stringio(self,
cys_cys_atomidx_set=None,
disulfide_conect=True,
noter=False,
**kwargs):
stringio_file = StringIO()
stringio_file_out = StringIO()
self.parm.write_pdb(stringio_file, **kwargs)
stringio_file.seek(0)
lines = stringio_file.readlines()
if noter:
for line in lines:
if line.startswith("TER"):
lines.remove(line)
# TODO: update ParmEd?
if disulfide_conect:
conect_record = [
'CONECT%5d%5d\n' % (idx0 + 1, idx1 + 1)
for (idx0, idx1) in cys_cys_atomidx_set
]
conect_str = ''.join(conect_record)
lines[-1] = conect_str + 'END\n'
if noter:
for line in lines:
if line.startswith("TER"):
lines.remove(line)
stringio_file_out.writelines(lines)
stringio_file_out.seek(0)
return stringio_file_out
def _html_(self):
r"""
HTML representation of a table.
Strings of html will be parsed for math inside dollar and
double-dollar signs. 2D graphics will be displayed in the
cells. Expressions will be latexed.
The ``align`` option for tables is ignored in HTML
output. Specifying ``header_column=True`` may not have any
visible effect in the Sage notebook, depending on the version
of the notebook.
OUTPUT:
A :class:`~sage.misc.html.HtmlFragment` instance.
EXAMPLES::
sage: T = table([[r'$\sin(x)$', '$x$', 'text'], [1,34342,3], [identity_matrix(2),5,6]])
sage: T._html_()
<div.../div>
sage: print(T._html_())
<div class="notruncate">
<table class="table_form">
<tbody>
<tr class ="row-a">
<td><script type="math/tex">\sin(x)</script></td>
<td><script type="math/tex">x</script></td>
<td>text</td>
</tr>
<tr class ="row-b">
<td><script type="math/tex">1</script></td>
<td><script type="math/tex">34342</script></td>
<td><script type="math/tex">3</script></td>
</tr>
<tr class ="row-a">
<td><script type="math/tex">\left(\begin{array}{rr}
1 & 0 \\
0 & 1
\end{array}\right)</script></td>
<td><script type="math/tex">5</script></td>
<td><script type="math/tex">6</script></td>
</tr>
</tbody>
</table>
</div>
Note that calling ``html(table(...))`` has the same effect as
calling ``table(...)._html_()``::
sage: T = table([["$x$", r"$\sin(x)$"]] + [(x,n(sin(x), digits=2)) for x in [0..3]], header_row=True, frame=True)
sage: T
+-----+-----------+
| $x$ | $\sin(x)$ |
+=====+===========+
| 0 | 0.00 |
+-----+-----------+
| 1 | 0.84 |
+-----+-----------+
| 2 | 0.91 |
+-----+-----------+
| 3 | 0.14 |
+-----+-----------+
sage: print(html(T))
<div class="notruncate">
<table border="1" class="table_form">
<tbody>
<tr>
<th><script type="math/tex">x</script></th>
<th><script type="math/tex">\sin(x)</script></th>
</tr>
<tr class ="row-a">
<td><script type="math/tex">0</script></td>
<td><script type="math/tex">0.00</script></td>
</tr>
<tr class ="row-b">
<td><script type="math/tex">1</script></td>
<td><script type="math/tex">0.84</script></td>
</tr>
<tr class ="row-a">
<td><script type="math/tex">2</script></td>
<td><script type="math/tex">0.91</script></td>
</tr>
<tr class ="row-b">
<td><script type="math/tex">3</script></td>
<td><script type="math/tex">0.14</script></td>
</tr>
</tbody>
</table>
</div>
"""
from itertools import cycle
rows = self._rows
header_row = self._options['header_row']
if self._options['frame']:
frame = 'border="1"'
else:
frame = ''
s = StringIO()
if rows:
s.writelines([
# If the table has < 100 rows, don't truncate the output in the notebook
'<div class="notruncate">\n'
if len(rows) <= 100 else '<div class="truncate">',
'<table {} class="table_form">\n'.format(frame),
'<tbody>\n',
])
# First row:
if header_row:
s.write('<tr>\n')
self._html_table_row(s, rows[0], header=header_row)
s.write('</tr>\n')
rows = rows[1:]
# Other rows:
for row_class, row in zip(cycle(["row-a", "row-b"]), rows):
s.write('<tr class ="{}">\n'.format(row_class))
self._html_table_row(s, row, header=False)
s.write('</tr>\n')
s.write('</tbody>\n</table>\n</div>')
from sage.misc.html import HtmlFragment
return HtmlFragment(s.getvalue())
def _html_(self):
r"""
HTML representation of a table.
Strings of html will be parsed for math inside dollar and
double-dollar signs. 2D graphics will be displayed in the
cells. Expressions will be latexed.
The ``align`` option for tables is ignored in HTML
output. Specifying ``header_column=True`` may not have any
visible effect in the Sage notebook, depending on the version
of the notebook.
OUTPUT:
A :class:`~sage.misc.html.HtmlFragment` instance.
EXAMPLES::
sage: T = table([[r'$\sin(x)$', '$x$', 'text'], [1,34342,3], [identity_matrix(2),5,6]])
sage: T._html_()
<div.../div>
sage: print(T._html_())
<div class="notruncate">
<table class="table_form">
<tbody>
<tr class ="row-a">
<td><script type="math/tex">\sin(x)</script></td>
<td><script type="math/tex">x</script></td>
<td>text</td>
</tr>
<tr class ="row-b">
<td><script type="math/tex">1</script></td>
<td><script type="math/tex">34342</script></td>
<td><script type="math/tex">3</script></td>
</tr>
<tr class ="row-a">
<td><script type="math/tex">\left(\begin{array}{rr}
1 & 0 \\
0 & 1
\end{array}\right)</script></td>
<td><script type="math/tex">5</script></td>
<td><script type="math/tex">6</script></td>
</tr>
</tbody>
</table>
</div>
Note that calling ``html(table(...))`` has the same effect as
calling ``table(...)._html_()``::
sage: T = table([["$x$", "$\sin(x)$"]] + [(x,n(sin(x), digits=2)) for x in [0..3]], header_row=True, frame=True)
sage: T
+-----+-----------+
| $x$ | $\sin(x)$ |
+=====+===========+
| 0 | 0.00 |
+-----+-----------+
| 1 | 0.84 |
+-----+-----------+
| 2 | 0.91 |
+-----+-----------+
| 3 | 0.14 |
+-----+-----------+
sage: print(html(T))
<div class="notruncate">
<table border="1" class="table_form">
<tbody>
<tr>
<th><script type="math/tex">x</script></th>
<th><script type="math/tex">\sin(x)</script></th>
</tr>
<tr class ="row-a">
<td><script type="math/tex">0</script></td>
<td><script type="math/tex">0.00</script></td>
</tr>
<tr class ="row-b">
<td><script type="math/tex">1</script></td>
<td><script type="math/tex">0.84</script></td>
</tr>
<tr class ="row-a">
<td><script type="math/tex">2</script></td>
<td><script type="math/tex">0.91</script></td>
</tr>
<tr class ="row-b">
<td><script type="math/tex">3</script></td>
<td><script type="math/tex">0.14</script></td>
</tr>
</tbody>
</table>
</div>
"""
import types
from itertools import cycle
rows = self._rows
header_row = self._options['header_row']
if self._options['frame']:
frame = 'border="1"'
else:
frame = ''
s = StringIO()
if rows:
s.writelines([
# If the table has < 100 rows, don't truncate the output in the notebook
'<div class="notruncate">\n' if len(rows) <= 100 else '<div class="truncate">' ,
'<table {} class="table_form">\n'.format(frame),
'<tbody>\n',
])
# First row:
if header_row:
s.write('<tr>\n')
self._html_table_row(s, rows[0], header=header_row)
s.write('</tr>\n')
rows = rows[1:]
# Other rows:
for row_class, row in zip(cycle(["row-a", "row-b"]), rows):
s.write('<tr class ="{}">\n'.format(row_class))
self._html_table_row(s, row, header=False)
s.write('</tr>\n')
s.write('</tbody>\n</table>\n</div>')
from sage.misc.html import HtmlFragment
return HtmlFragment(s.getvalue())
