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<p><i><a href="../../index.html">Table of Contents</a></i></p>
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<th rowspan="2"
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align="left"
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bgcolor="#88bbee"><font color="#000000">Class: molecule</font>
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<th bgcolor="#88bbee"
width="90%"
align="right"><font color="#000000">../bkchem/molecule.py</font>
</th>
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<tr>
<td>
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rowspan="2"
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<font color="#000000">
<a name="Base Classes">Base Classes</a>
</font>
</th>
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valign="top"
align="left"
width="80%"
>
<font color="#000000"> </font>
</th>
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<tr>
<td>
container<br>
top_level<br>
id_enabled<br>
oasa.molecule<br>
with_paper<br>
</td></tr>
</table>
<table border="0" cellpadding="5" cellspacing="0" width="100%">
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<th bgcolor="#99ccff"
rowspan="2"
valign="top"
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<font color="#000000">
<a name="Methods">Methods</a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000"> </font>
</th>
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<tr>
<td>
<table border="0" cellspacing="2" cellpadding="2" width="100%">
<tr>
<td align="LEFT" valign="TOP">
<a href="#__init__">__init__</a><br>
<a href="#__iter__">__iter__</a><br>
<a href="#add_atom_to">add_atom_to</a><br>
<a href="#add_edge">add_edge</a><br>
<a href="#add_vertex">add_vertex</a><br>
<a href="#bbox">bbox</a><br>
<a href="#bond_between">bond_between</a><br>
<a href="#check_fragments">check_fragments</a><br>
<a href="#check_integrity">check_integrity</a><br>
<a href="#children_generator">children_generator</a><br>
<a href="#create_edge">create_edge</a><br>
<a href="#create_fragment">create_fragment</a><br>
<a href="#create_graph">create_graph</a><br>
<a href="#create_new_atom">create_new_atom</a><br>
<a href="#create_vertex">create_vertex</a><br>
<a href="#create_vertex_according_to_text">create_vertex_according_to_text</a><br>
<a href="#delete">delete</a><br>
</td>
<td align="LEFT" valign="TOP">
<a href="#delete_atom">delete_atom</a><br>
<a href="#delete_bond">delete_bond</a><br>
<a href="#delete_fragment">delete_fragment</a><br>
<a href="#delete_items">delete_items</a><br>
<a href="#draw">draw</a><br>
<a href="#eat_molecule">eat_molecule</a><br>
<a href="#expand_groups">expand_groups</a><br>
<a href="#find_least_crowded_place_around_atom">find_least_crowded_place_around_atom</a><br>
<a href="#find_place">find_place</a><br>
<a href="#flush_graph_to_file">flush_graph_to_file</a><br>
<a href="#gen_bonds_between">gen_bonds_between</a><br>
<a href="#get_angle">get_angle</a><br>
<a href="#get_formula_dict">get_formula_dict</a><br>
<a href="#get_fragment_by_id">get_fragment_by_id</a><br>
<a href="#get_fragments_with_edge">get_fragments_with_edge</a><br>
<a href="#get_fragments_with_vertex">get_fragments_with_vertex</a><br>
<a href="#get_geometry">get_geometry</a><br>
</td>
<td align="LEFT" valign="TOP">
<a href="#get_package">get_package</a><br>
<a href="#handle_overlap">handle_overlap</a><br>
<a href="#insert_atom">insert_atom</a><br>
<a href="#is_empty">is_empty</a><br>
<a href="#lift">lift</a><br>
<a href="#mark_template_atom">mark_template_atom</a><br>
<a href="#mark_template_bond">mark_template_bond</a><br>
<a href="#move">move</a><br>
<a href="#move_bonds_between_atoms">move_bonds_between_atoms</a><br>
<a href="#read_package">read_package</a><br>
<a href="#redraw">redraw</a><br>
<a href="#replace_vertices">replace_vertices</a><br>
<a href="#transform">transform</a><br>
</td>
</tr>
</table>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="__init__"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">__init__ </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
__init__ (
self,
paper=None,
package=None,
)
</pre></font>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="__iter__"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">__iter__ </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
__iter__ ( self )
</pre></font>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="add_atom_to"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">add_atom_to </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
add_atom_to (
self,
a1,
bond_to_use=None,
pos=None,
)
</pre></font>
<p>adds new atom bound to atom id with bond, the position of new atom can be specified in pos or is
decided calling find_place(), if x, y is specified and matches already existing atom it will be
used instead of creating new one</p>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="add_edge"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">add_edge </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
add_edge (
self,
v1,
v2,
e=None,
)
</pre></font>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="add_vertex"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">add_vertex </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
add_vertex ( self, v=None )
</pre></font>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="bbox"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">bbox </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
bbox ( self )
</pre></font>
<p>returns the bounding box of the object as a list of <a href="#refx1,y1,x2,y2">[x1,y1,x2,y2]</a></p>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="bond_between"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">bond_between </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
bond_between (
self,
a1,
a2,
)
</pre></font>
<p>returns id of bond between atoms a1 and a2</p>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="check_fragments"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">check_fragments </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
check_fragments ( self )
</pre></font>
<p>checks if all the fragments of this molecule are consistent and
removes and returns the ones that are not</p>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="check_integrity"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">check_integrity </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
check_integrity ( self )
</pre></font>
<p>after deleting atoms or bonds it is important to see if it's needed to divide molecule to fragments
and return them in form of list of new molecules</p>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="children_generator"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">children_generator </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
children_generator ( self )
</pre></font>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="create_edge"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">create_edge </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
create_edge ( self )
</pre></font>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="create_fragment"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">create_fragment </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
create_fragment (
self,
name,
edges,
vertices,
type="explicit",
strict=False,
)
</pre></font>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="create_graph"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">create_graph </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
create_graph ( self )
</pre></font>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="create_new_atom"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">create_new_atom </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
create_new_atom (
self,
x,
y,
name=None,
vertex_class=None,
)
</pre></font>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="create_vertex"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">create_vertex </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
create_vertex ( self, vertex_class=None )
</pre></font>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="create_vertex_according_to_text"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">create_vertex_according_to_text </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
create_vertex_according_to_text (
self,
old,
text,
interpret=1,
)
</pre></font>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="delete"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">delete </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
delete ( self )
</pre></font>
<p>deletes the molecule from canvas by calling delete for its children</p>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="delete_atom"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">delete_atom </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
delete_atom ( self, item )
</pre></font>
<p>remove links to atom from molecule records</p>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="delete_bond"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">delete_bond </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
delete_bond ( self, item )
</pre></font>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="delete_fragment"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">delete_fragment </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
delete_fragment ( self, f )
</pre></font>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="delete_items"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">delete_items </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
delete_items (
self,
items,
redraw=1,
delete_single_atom=1,
)
</pre></font>
<p>deletes items and also makes cleaning of orphan bonds and atoms</p>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="draw"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">draw </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
draw ( self, automatic="none" )
</pre></font>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="eat_molecule"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">eat_molecule </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
eat_molecule ( self, mol )
</pre></font>
<p>transfers everything from mol to self, now only calls feed_data</p>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="expand_groups"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">expand_groups </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
expand_groups ( self, atoms=[] )
</pre></font>
<p>expands all group atoms; optional atoms selects atoms to expand - all used if not present</p>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="find_least_crowded_place_around_atom"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">find_least_crowded_place_around_atom </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
find_least_crowded_place_around_atom (
self,
a,
range=10,
)
</pre></font>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="find_place"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">find_place </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
find_place (
self,
a,
distance,
added_order=1,
)
</pre></font>
<p>tries to find accurate place for next atom around atom <code>id</code>,
returns x,y and list of ids of <code>items</code> found there for overlap, those atoms are not bound to id</p>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="flush_graph_to_file"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">flush_graph_to_file </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
flush_graph_to_file ( self, name="/home/beda/oasa/oasa/mol.graph" )
</pre></font>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="gen_bonds_between"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">gen_bonds_between </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
gen_bonds_between (
self,
a1,
a2,
)
</pre></font>
<p>yields all bonds between atoms a1 and a2</p>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="get_angle"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">get_angle </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
get_angle (
self,
a1,
a2,
)
</pre></font>
<p>what is the angle between horizontal line through i1 and i1-i2 line</p>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="get_formula_dict"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">get_formula_dict </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
get_formula_dict ( self )
</pre></font>
<p>returns a formula dict as defined in the periodic_table.py::formula_dict</p>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="get_fragment_by_id"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">get_fragment_by_id </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
get_fragment_by_id ( self, id )
</pre></font>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="get_fragments_with_edge"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">get_fragments_with_edge </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
get_fragments_with_edge ( self, e )
</pre></font>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="get_fragments_with_vertex"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">get_fragments_with_vertex </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
get_fragments_with_vertex ( self, v )
</pre></font>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="get_geometry"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">get_geometry </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
get_geometry ( self )
</pre></font>
<p>returns a tuple of ((minx, miny, max, maxy), mean_bond_length)</p>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="get_package"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">get_package </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
get_package (
self,
doc,
items=None,
)
</pre></font>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="handle_overlap"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">handle_overlap </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
handle_overlap ( self )
</pre></font>
<p>deletes one of overlaping atoms and updates the bonds</p>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="insert_atom"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">insert_atom </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
insert_atom ( self, at )
</pre></font>
<p>inserts atom to molecule without any connections</p>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="is_empty"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">is_empty </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
is_empty ( self )
</pre></font>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="lift"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">lift </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
lift ( self )
</pre></font>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="mark_template_atom"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">mark_template_atom </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
mark_template_atom ( self, v )
</pre></font>
<table border="0" cellpadding="5" cellspacing="0" width="100%">
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="Exceptions">Exceptions</a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000"> </font>
</th>
</tr>
<tr>
<td>
ValueError, "submitted atom does not belong to this molecule"<br>
</td></tr>
</table>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="mark_template_bond"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">mark_template_bond </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
mark_template_bond ( self, b )
</pre></font>
<table border="0" cellpadding="5" cellspacing="0" width="100%">
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="Exceptions">Exceptions</a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000"> </font>
</th>
</tr>
<tr>
<td>
ValueError, "submitted bond does not belong to this molecule"<br>
</td></tr>
</table>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="move"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">move </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
move (
self,
dx,
dy,
)
</pre></font>
<p>moves the whole molecule</p>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="move_bonds_between_atoms"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">move_bonds_between_atoms </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
move_bonds_between_atoms (
self,
a1,
a2,
)
</pre></font>
<p>transfers all bonds from one atom to the other; both atoms must be in self</p>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="read_package"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">read_package </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
read_package ( self, package )
</pre></font>
<p>reads the dom element package and sets internal state according to it</p>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="redraw"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">redraw </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
redraw ( self, reposition_double=0 )
</pre></font>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="replace_vertices"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">replace_vertices </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
replace_vertices (
self,
old,
new,
)
</pre></font>
<p>replaces the vertex old with the vertex new</p>
<tr>
<th bgcolor="#99ccff"
rowspan="2"
valign="top"
align="left"
width="20%"
>
<font color="#000000">
<a name="transform"></a>
</font>
</th>
<th bgcolor="#99ccff"
valign="top"
align="left"
width="80%"
>
<font color="#000000">transform </font>
</th>
</tr>
<tr>
<td>
<font color="#000088"><pre>
transform ( self, tr )
</pre></font>
<p>applies given transformation to its children</p>
</td></tr>
</td></tr>
</table>
</td>
</tr>
</table>
<hr>
<p><i><a href="../../index.html">Table of Contents</a></i></p>
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