Mercurial > repos > marcel > caddsuite_linux_x86_64

annotate CADDSuite/data/bond_lengths/BondOrder.xml @ 3:ff6df146c0d5

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Uploaded
author marcel
date Sun, 26 Jun 2011 13:53:57 -0400
parents bac3c274238f
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 <?xml version="1.0" encoding="ISO-8859-1"?>
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2 <table>
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3 <!-- This file supplies improved penalty scores for different
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4 atom types in bond type perception based on the work of
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5
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6 Wang, J., Wang, W., Kollman P. A.; Case, D. A. "Automatic atom type and
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7 bond type perception in molecular mechanical calculations". Journal of
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8 Molecular Graphics and Modelling , 25, 2006, 247260
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9
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10 A penalty score of 0 means that the corresponding valence is optimal.
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11 Note that the first matching entry is taken as the final atom type.
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12
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13 Note that in the SMARTS strings we use atomic numbers rather than symbols (e.g. #8 instead of O).
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14 The reason is that wrongly assigned aromatic bonds in the input would lead to failure to identify the
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15 right rule!
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16 -->
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17 <!-- for charged H -->
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18 <entry id="0">
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19 <elementstring>H</elementstring>
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20 <smartstring>SMARTS([#1+])</smartstring>
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21 <penalty valence="0">0</penalty>
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22 </entry>
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23 <entry id="1">
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24 <elementstring>H</elementstring>
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25 <smartstring>SMARTS([#1])</smartstring>
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26 <penalty valence="1">0</penalty>
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27 </entry>
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28 <entry id="2">
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29 <elementstring>F</elementstring>
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30 <smartstring>SMARTS(F)</smartstring>
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31 <penalty valence="0">64</penalty>
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32 <penalty valence="1">0</penalty>
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33 <penalty valence="2">64</penalty>
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34 </entry>
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35 <entry id="4">
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36 <elementstring>Br</elementstring>
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37 <smartstring>SMARTS(Br)</smartstring>
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38 <penalty valence="0">64</penalty>
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39 <penalty valence="1">0</penalty>
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40 <penalty valence="2">64</penalty>
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41 </entry>
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42 <entry id="5">
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43 <elementstring>I</elementstring>
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44 <smartstring>SMARTS(I)</smartstring>
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45 <penalty valence="0">64</penalty>
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46 <penalty valence="1">0</penalty>
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47 <penalty valence="2">64</penalty>
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48 </entry>
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49 <entry id="6"> <!-- SMARTS([CD1]~[ND2]) AND element(C)</smartstring> -->
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50 <elementstring>C</elementstring>
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51 <smartstring>SMARTS([$([#6D1](~[#7D2]))])</smartstring>
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52 <penalty valence="3">0</penalty>
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54 <penalty valence="5">32</penalty>
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55 </entry>
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56 <entry id="7">
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57 <elementstring>C</elementstring>
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58 <smartstring>SMARTS([#6D1])</smartstring>
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59 <penalty valence="3">1</penalty>
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61 <penalty valence="5">32</penalty>
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62 </entry>
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63 <entry id="9">
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64 <elementstring>C</elementstring>
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65 <smartstring>SMARTS([#6])</smartstring>
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66 <penalty valence="2">64</penalty>
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67 <penalty valence="3">32</penalty>
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68 <penalty valence="4">0</penalty>
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69 <penalty valence="5">32</penalty>
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70 <penalty valence="6">64</penalty>
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71 </entry>
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72 <entry id="10">
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73 <elementstring>Si</elementstring>
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74 <smartstring>SMARTS(Si)</smartstring>
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75 <penalty valence="4">0</penalty>
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76 </entry>
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77 <entry id="11">
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78 <elementstring>N</elementstring>
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79 <smartstring>SMARTS([$([#7D1](~[#7D2]))])</smartstring> <!--SMARTS([ND1]~[ND2]) AND SMARTS([ND1])</smartstring> -->
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80 <penalty valence="2">0</penalty>
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81 <penalty valence="3">0</penalty>
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82 </entry>
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83 <entry id="12">
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84 <elementstring>N</elementstring>
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85 <smartstring>SMARTS([#7D1])</smartstring>
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86 <penalty valence="2">3</penalty>
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87 <penalty valence="3">0</penalty>
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88 <penalty valence="4">32</penalty>
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89 </entry>
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90 <entry id="13">
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91 <elementstring>N</elementstring>
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92 <smartstring>SMARTS([$([#7D2](~[#7D1]))])</smartstring> <!--SMARTS([ND1]~[ND2]) AND SMARTS([ND2])</smartstring> -->
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93 <penalty valence="3">1</penalty>
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94 <penalty valence="4">0</penalty>
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95 </entry>
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96 <entry id="14">
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97 <elementstring>N</elementstring>
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98 <smartstring>SMARTS([#7D2])</smartstring>
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99 <penalty valence="2">4</penalty>
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100 <penalty valence="3">0</penalty>
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101 <penalty valence="4">2</penalty>
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102 </entry>
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103 <entry id="151"><!-- for charged N in O == N+ __ O- -->
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104 <elementstring>N</elementstring>
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105 <smartstring>SMARTS([$([#7D3](~[#8D1-,#16D1-])~[#8D1,#16D1])])</smartstring>
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106 <penalty valence="3">32</penalty>
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107 <penalty valence="4">0</penalty>
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108 <penalty valence="5">32</penalty>
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109 <penalty valence="6">64</penalty>
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110 </entry>
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111 <entry id="15">
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112 <elementstring>N</elementstring>
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113 <smartstring>SMARTS([$([#7D3](~[#8D1,#16D1])~[#8D1,#16D1])])</smartstring>
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114 <penalty valence="3">64</penalty>
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115 <penalty valence="4">32</penalty>
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116 <penalty valence="5">0</penalty>
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117 <penalty valence="6">32</penalty>
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118 </entry>
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119 <entry id="16">
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120 <elementstring>N</elementstring>
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121 <!-- <smartstring>SMARTS([$(*OD1)&amp;$(*aR)&amp;n]) OR SMARTS([$(*OD1);$(*R);N])</smartstring> -->
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122 <smartstring>SMARTS([$([#7D3](~[#8D1,#16D1])(~[!#8&amp;!#16,!D1])(~[!#8&amp;!#16,!D1]))])</smartstring>
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123 <penalty valence="3">1</penalty>
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124 <penalty valence="4">0</penalty>
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125 </entry>
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126 <entry id="17">
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127 <elementstring>N</elementstring>
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128 <smartstring>SMARTS([#7D3])</smartstring>
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129 <penalty valence="2">32</penalty>
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130 <penalty valence="3">0</penalty>
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131 <penalty valence="4">1</penalty>
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132 <penalty valence="5">2</penalty>
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133 </entry>
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134 <entry id="181"><!-- for charged N in N+ H_4 -->
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135 <elementstring>N</elementstring>
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136 <smartstring>SMARTS([#7D4+])</smartstring>
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137 <penalty valence="3">32</penalty>
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138 <penalty valence="4">0</penalty>
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139 </entry>
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140 <entry id="18">
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141 <elementstring>N</elementstring>
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142 <smartstring>SMARTS([#7D4])</smartstring>
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143 <penalty valence="2">64</penalty>
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144 <penalty valence="3">0</penalty>
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146 </entry>
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147 <entry id="182">
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148 <elementstring>N</elementstring>
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149 <smartstring>SMARTS([#7D5])</smartstring>
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150 <penalty valence="5">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
151 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
152 <entry id="191"><!-- for charged O- -->
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
153 <elementstring>O</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
154 <smartstring>SMARTS([#8D1-])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
155 <penalty valence="1">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
156 <penalty valence="2">32</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
157 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
158 <entry id="192">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
159 <elementstring>O</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
160 <smartstring>SMARTS([$([#8D1](~[#6D3]~[#8D1,#16D1]))])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
161 <penalty valence="1">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
162 <penalty valence="2">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
163 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
164 <entry id="19">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
165 <elementstring>O</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
166 <smartstring>SMARTS([#7D3](~[#8D1,#16D1])(~[!#8&amp;!#16,!D1])(~[!#8&amp;!#16,!D1])) AND element(O)</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
167 <penalty valence="1">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
168 <penalty valence="2">1</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
169 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
170 <entry id="20">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
171 <elementstring>O</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
172 <smartstring> SMARTS([#8D1])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
173 <penalty valence="1">1</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
174 <penalty valence="2">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
175 <penalty valence="3">64</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
176 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
177 <entry id="21">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
178 <elementstring>O</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
179 <smartstring>SMARTS([#8D2])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
180 <penalty valence="1">32</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
181 <penalty valence="2">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
182 <penalty valence="3">64</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
183 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
184 <entry id="211">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
185 <elementstring>O</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
186 <smartstring>SMARTS([#8D3])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
187 <penalty valence="3">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
188 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
189 <entry id="22">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
190 <elementstring>P</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
191 <smartstring>SMARTS(#15D1)</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
192 <penalty valence="2">2</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
193 <penalty valence="3">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
194 <penalty valence="4">32</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
195 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
196 <entry id="23">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
197 <elementstring>P</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
198 <smartstring>SMARTS(#15D2)</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
199 <penalty valence="2">4</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
200 <penalty valence="3">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
201 <penalty valence="4">2</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
202 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
203 <entry id="24">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
204 <elementstring>P</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
205 <smartstring>SMARTS(#15D3)</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
206 <penalty valence="2">32</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
207 <penalty valence="3">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
208 <penalty valence="4">1</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
209 <penalty valence="5">2</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
210 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
211 <entry id="251">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
212 <elementstring>P</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
213 <!-- Note: this is _SLOW_ -->
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
214 <smartstring>SMARTS([$([#15D4](~[#8D1,#16D1])(~[!#8&amp;!#16,!D1])(~[!#8&amp;!#16,!D1,#8D1-,#16D1-])(~[#8D1-,#16D1-]))])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
215 <penalty valence="5">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
216 <penalty valence="6">32</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
217 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
218 <entry id="25">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
219 <elementstring>P</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
220 <!-- Note: this is _SLOW_ -->
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
221 <smartstring>SMARTS([$([#15D4](~[#8D1,#16D1])(~[!#8&amp;!#16,!D1])(~[!#8&amp;!#16,!D1])(~[#8D1,#16D1]))])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
222 <penalty valence="5">32</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
223 <penalty valence="6">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
224 <penalty valence="7">32</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
225 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
226 <entry id="26">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
227 <elementstring>P</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
228 <smartstring>SMARTS([$([#15D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&amp;!#16,!D1]))])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
229 <penalty valence="6">32</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
230 <penalty valence="7">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
231 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
232 <entry id="27">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
233 <elementstring>P</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
234 <!-- This rule should be the last PD4 rule because it should only match when the other rules fail! -->
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
235 <smartstring>SMARTS(#15D4)</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
236 <penalty valence="3">64</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
237 <penalty valence="4">1</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
238 <penalty valence="5">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
239 <penalty valence="6">32</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
240 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
241 <entry id="28">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
242 <elementstring>S</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
243 <smartstring>SMARTS([#7D3](~[#16D1])(~[!#8&amp;!#16,!D1])(~[!#8&amp;!#16,!D1])) AND element(S)</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
244 <penalty valence="1">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
245 <penalty valence="2">1</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
246 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
247 <entry id="291">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
248 <elementstring>S</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
249 <smartstring>SMARTS([$([#16D1](~[#6D3]~[#8D1,#16D1]))])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
250 <penalty valence="1">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
251 <penalty valence="2">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
252 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
253 <entry id="29">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
254 <elementstring>S</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
255 <smartstring>SMARTS([#16D1])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
256 <penalty valence="1">2</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
257 <penalty valence="2">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
258 <penalty valence="3">64</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
259 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
260 <entry id="30">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
261 <elementstring>S</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
262 <smartstring>SMARTS([#16D2])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
263 <penalty valence="1">2</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
264 <penalty valence="2">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
265 <penalty valence="3">64</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
266 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
267 <entry id="31">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
268 <elementstring>S</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
269 <smartstring>SMARTS([#16D3])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
270 <penalty valence="3">1</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
271 <penalty valence="4">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
272 <penalty valence="5">2</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
273 <penalty valence="6">2</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
274 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
275 <entry id="32">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
276 <elementstring>S</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
277 <smartstring> SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&amp;!#16,!D1])(~[!#8&amp;!#16,!D1]))])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
278 <penalty valence="6">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
279 <penalty valence="7">32</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
280 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
281 <entry id="331"><!--for a charged O in SO_4 -->
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
282 <elementstring>S</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
283 <smartstring>SMARTS([$([#16D4](~[#8D1-,#16D1-])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&amp;!#16,!D1]))])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
284 <penalty valence="6">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
285 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
286 <entry id="33">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
287 <elementstring>S</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
288 <smartstring>SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&amp;!#16,!D1]))])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
289 <penalty valence="6">32</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
290 <penalty valence="7">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
291 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
292 <entry id="34">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
293 <elementstring>S</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
294 <smartstring>SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1]))])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
295 <penalty valence="6">32</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
296 <penalty valence="7">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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297 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
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298 <entry id="35">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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299 <elementstring>S</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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300 <smartstring>SMARTS([#16D4])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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301 <penalty valence="4">4</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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302 <penalty valence="5">2</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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303 <penalty valence="6">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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304 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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305 <entry id="36">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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306 <elementstring>S</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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307 <smartstring>SMARTS([#16D5])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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308 <penalty valence="5">2</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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309 <penalty valence="6">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
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310 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
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311 <!-- The following rules are added to cope with ions -->
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
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312 <entry id="40">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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313 <elementstring>Li</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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314 <smartstring>SMARTS([#3])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
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315 <penalty valence="0">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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316 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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317 <entry id="41">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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318 <elementstring>Na</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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319 <smartstring>SMARTS([#11])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
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320 <penalty valence="0">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
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321 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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322 <entry id="42">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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323 <elementstring>Mg</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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324 <smartstring>SMARTS([#12])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
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325 <penalty valence="0">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
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326 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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327 <entry id="43">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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328 <elementstring>K</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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329 <smartstring>SMARTS([#19])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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330 <penalty valence="0">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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331 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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332 <entry id="44">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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333 <elementstring>Ca</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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334 <smartstring>SMARTS([#20])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
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335 <penalty valence="0">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
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336 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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337 <entry id="45">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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338 <elementstring>Cu</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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339 <smartstring>SMARTS([#29])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
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340 <penalty valence="0">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
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341 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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342 <entry id="46">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
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343 <elementstring>Zn</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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344 <smartstring>SMARTS([#30])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
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345 <penalty valence="0">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
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346 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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347 <entry id="47">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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348 <elementstring>Fe</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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349 <smartstring>SMARTS([#26])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
350 <penalty valence="0">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
351 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
352 <entry id="48">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
353 <elementstring>Cl</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
354 <smartstring>SMARTS([#17-])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
355 <penalty valence="0">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
356 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
357 <entry id="49">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
358 <elementstring>Cl</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
359 <smartstring>SMARTS([#17])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
360 <penalty valence="0">64</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
361 <penalty valence="1">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
362 <penalty valence="2">64</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
363 <penalty valence="3">128</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
364 <penalty valence="4">128</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
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365 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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366 </table>