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bgcolor="#88bbee"><font color="#000000">Class: inchi</font>
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<th bgcolor="#88bbee"
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align="right"><font color="#000000">../bkchem/oasa/oasa/inchi.py</font>
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<a name="Base Classes">Base Classes</a>
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plugin<br>
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<a name="Methods">Methods</a>
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<a href="#__init__">__init__</a><br>
<a href="#cleanup">cleanup</a><br>
<a href="#compensate_for_forced_charges">compensate_for_forced_charges</a><br>
<a href="#deal_with_da_bonds">deal_with_da_bonds</a><br>
<a href="#get_layer">get_layer</a><br>
<a href="#get_number_of_hydrogens_in_hydrogen_layer">get_number_of_hydrogens_in_hydrogen_layer</a><br>
<a href="#get_structure">get_structure</a><br>
<a href="#process_forced_charges">process_forced_charges</a><br>
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<a href="#read_charge_layer">read_charge_layer</a><br>
<a href="#read_connectivity_layer">read_connectivity_layer</a><br>
<a href="#read_hydrogen_layer">read_hydrogen_layer</a><br>
<a href="#read_inchi">read_inchi</a><br>
<a href="#read_p_layer">read_p_layer</a><br>
<a href="#read_sum_layer">read_sum_layer</a><br>
<a href="#set_structure">set_structure</a><br>
<a href="#split_layers">split_layers</a><br>
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<font color="#000000">__init__ </font>
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<font color="#000088"><pre>
__init__ ( self, structure=None )
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<a name="cleanup"></a>
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<font color="#000000">cleanup </font>
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<font color="#000088"><pre>
cleanup ( self )
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<a name="compensate_for_forced_charges"></a>
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<font color="#000000">compensate_for_forced_charges </font>
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<font color="#000088"><pre>
compensate_for_forced_charges ( self )
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<p>if there were foced charges and they the molecule should not have any charge,
we have to take care of it here</p>
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<a name="deal_with_da_bonds"></a>
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<font color="#000000">deal_with_da_bonds </font>
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<font color="#000088"><pre>
deal_with_da_bonds ( self )
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<p>deal with donor-acceptor bonds, this fixes mostly boron containing compounds</p>
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<font color="#000000">get_layer </font>
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get_layer ( self, prefix )
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<a name="get_number_of_hydrogens_in_hydrogen_layer"></a>
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<font color="#000000">get_number_of_hydrogens_in_hydrogen_layer </font>
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<font color="#000088"><pre>
get_number_of_hydrogens_in_hydrogen_layer ( self )
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<a name="Exceptions">Exceptions</a>
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oasa_not_implemented_error( "INChI", "multiple compound systems are not supported by the library" )<br>
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<font color="#000000">get_structure </font>
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<font color="#000088"><pre>
get_structure ( self )
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<a name="process_forced_charges"></a>
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<font color="#000000">process_forced_charges </font>
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<font color="#000088"><pre>
process_forced_charges ( self )
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<p>this marks the charges that are forced by the connectivity and thus helps
process zwitrions</p>
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<a name="read_charge_layer"></a>
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<font color="#000000">read_charge_layer </font>
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<font color="#000088"><pre>
read_charge_layer ( self )
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oasa_exceptions.oasa_inchi_error( "The molecular charge could not be allocated to any atom (%d)." % charge )<br>
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<a name="read_connectivity_layer"></a>
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<font color="#000000">read_connectivity_layer </font>
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<font color="#000088"><pre>
read_connectivity_layer ( self )
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ValueError, "unexpected character %s in the connectivity layer" % c<br>
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<font color="#000000">read_hydrogen_layer </font>
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<font color="#000088"><pre>
read_hydrogen_layer ( self, run=0 )
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<a name="read_inchi"></a>
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<font color="#000000">read_inchi </font>
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<font color="#000088"><pre>
read_inchi ( self, text )
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oasa_inchi_error( "Localization of bonds, charges or movable hydrogens failed" )<br>
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<font color="#000000">read_p_layer </font>
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<font color="#000088"><pre>
read_p_layer ( self )
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<font color="#000000">read_sum_layer </font>
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<font color="#000088"><pre>
read_sum_layer ( self )
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<a name="Exceptions">Exceptions</a>
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oasa_not_implemented_error( "INChI", "multiple compound systems are not supported by the library" )<br>
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<font color="#000000">set_structure </font>
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<font color="#000088"><pre>
set_structure ( self, structure )
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<font color="#000000">split_layers </font>
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<font color="#000088"><pre>
split_layers ( self, text )
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<a name="Exceptions">Exceptions</a>
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"no '%s' tag found in xml string" % name<br>
"no structures found in xml string %s" % text<br>
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