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bgcolor="#88bbee"><font color="#000000">Class: atom</font>
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<th bgcolor="#88bbee"
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align="right"><font color="#000000">../bkchem/atom.py</font>
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<a name="Base Classes">Base Classes</a>
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<font color="#000000"> </font>
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<td>
drawable_chem_vertex<br>
oasa.atom<br>
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<a name="Methods">Methods</a>
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<font color="#000000"> </font>
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<a href="#__init__">__init__</a><br>
<a href="#__str__">__str__</a><br>
<a href="#after_undo">after_undo</a><br>
<a href="#bbox">bbox</a><br>
<a href="#decide_pos">decide_pos</a><br>
<a href="#draw">draw</a><br>
<a href="#focus">focus</a><br>
<a href="#generate_marks_from_cheminfo">generate_marks_from_cheminfo</a><br>
<a href="#get_charge_from_marks">get_charge_from_marks</a><br>
<a href="#get_formula_dict">get_formula_dict</a><br>
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<a href="#get_package">get_package</a><br>
<a href="#read_package">read_package</a><br>
<a href="#select">select</a><br>
<a href="#set_name">set_name</a><br>
<a href="#set_valency_from_name">set_valency_from_name</a><br>
<a href="#split_element_and_charge">split_element_and_charge</a><br>
<a href="#unfocus">unfocus</a><br>
<a href="#unselect">unselect</a><br>
<a href="#update_after_valency_change">update_after_valency_change</a><br>
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<a name="__init__"></a>
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<font color="#000000">__init__ </font>
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<font color="#000088"><pre>
__init__ (
self,
standard=None,
xy=(),
package=None,
molecule=None,
)
</pre></font>
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<a name="__str__"></a>
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<font color="#000000">__str__ </font>
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<font color="#000088"><pre>
__str__ ( self )
</pre></font>
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<font color="#000000">
<a name="after_undo"></a>
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<font color="#000000">after_undo </font>
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<font color="#000088"><pre>
after_undo ( self )
</pre></font>
<p>this is run after undo</p>
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<a name="bbox"></a>
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<font color="#000000">bbox </font>
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<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>
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<font color="#000000">
<a name="decide_pos"></a>
</font>
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<font color="#000000">decide_pos </font>
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<font color="#000088"><pre>
decide_pos ( self )
</pre></font>
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<a name="draw"></a>
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<font color="#000000">draw </font>
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<font color="#000088"><pre>
draw ( self, redraw=False )
</pre></font>
<p>draws atom with respect to its properties</p>
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<a name="focus"></a>
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<font color="#000000">focus </font>
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<font color="#000088"><pre>
focus ( self )
</pre></font>
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<font color="#000000">
<a name="generate_marks_from_cheminfo"></a>
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<font color="#000000">generate_marks_from_cheminfo </font>
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<font color="#000088"><pre>
generate_marks_from_cheminfo ( self )
</pre></font>
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<font color="#000000">
<a name="get_charge_from_marks"></a>
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<font color="#000000">get_charge_from_marks </font>
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<font color="#000088"><pre>
get_charge_from_marks ( self )
</pre></font>
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<font color="#000000">
<a name="get_formula_dict"></a>
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<font color="#000000">get_formula_dict </font>
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<font color="#000088"><pre>
get_formula_dict ( self )
</pre></font>
<p>returns formula as dictionary that can
be passed to functions in periodic_table</p>
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<a name="get_package"></a>
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<font color="#000000">get_package </font>
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<font color="#000088"><pre>
get_package ( self, doc )
</pre></font>
<p>returns a DOM element describing the object in CDML,
doc is the parent document which is used for element creation
(the returned element is not inserted into the document)</p>
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<a name="read_package"></a>
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<font color="#000000">read_package </font>
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<font color="#000088"><pre>
read_package ( self, package )
</pre></font>
<p>reads the dom element package and sets internal state according to it</p>
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<a name="select"></a>
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<font color="#000000">select </font>
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<font color="#000088"><pre>
select ( self )
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<a name="set_name"></a>
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<font color="#000000">set_name </font>
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<font color="#000088"><pre>
set_name (
self,
name,
interpret=1,
check_valency=1,
occupied_valency=None,
)
</pre></font>
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<a name="set_valency_from_name"></a>
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<font color="#000000">set_valency_from_name </font>
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<font color="#000088"><pre>
set_valency_from_name ( self )
</pre></font>
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<font color="#000000">
<a name="split_element_and_charge"></a>
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<font color="#000000">split_element_and_charge </font>
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<font color="#000088"><pre>
split_element_and_charge ( self, txt )
</pre></font>
<p>returns tuple of (element, charge) or None if the text does not match this pattern</p>
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<a name="unfocus"></a>
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<font color="#000000">unfocus </font>
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<font color="#000088"><pre>
unfocus ( self )
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<a name="unselect"></a>
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<font color="#000000">unselect </font>
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<font color="#000088"><pre>
unselect ( self )
</pre></font>
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<font color="#000000">
<a name="update_after_valency_change"></a>
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<font color="#000000">update_after_valency_change </font>
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<font color="#000088"><pre>
update_after_valency_change ( self )
</pre></font>
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