Mercurial > repos > marcel > caddsuite_linux_x86_64

annotate CADDSuite/data/bond_lengths/BondOrderGAFF.xml @ 0:bac3c274238f

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Migrated tool version 0.93 from old tool shed archive to new tool shed repository
author marcel
date Tue, 07 Jun 2011 16:43:30 -0400
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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 penalty scores for different
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4 atom types in bond type perception accoring to
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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 Rev 14.12.2007 Conversion was done by Anna Dehof
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18 -->
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19 <entry id="1">
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20 <elementstring>H</elementstring>
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21 <smartstring>SMARTS([#1])</smartstring>
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22 <penalty valence="0">64</penalty>
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23 <penalty valence="1">0</penalty>
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24 <penalty valence="2">64</penalty>
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25 </entry>
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26 <entry id="2">
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27 <elementstring>F</elementstring>
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28 <smartstring>SMARTS(F)</smartstring>
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29 <penalty valence="0">64</penalty>
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30 <penalty valence="1">0</penalty>
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31 <penalty valence="2">64</penalty>
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32 </entry>
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33 <entry id="3">
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34 <elementstring>Cl</elementstring>
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35 <smartstring>SMARTS(Cl)</smartstring>
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36 <penalty valence="0">64</penalty>
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37 <penalty valence="1">0</penalty>
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38 <penalty valence="2">64</penalty>
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39 </entry>
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40 <entry id="4">
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41 <elementstring>Br</elementstring>
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42 <smartstring>SMARTS(Br)</smartstring>
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43 <penalty valence="0">64</penalty>
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44 <penalty valence="1">0</penalty>
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45 <penalty valence="2">64</penalty>
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46 </entry>
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47 <entry id="5">
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48 <elementstring>I</elementstring>
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49 <smartstring>SMARTS(I)</smartstring>
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50 <penalty valence="0">64</penalty>
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51 <penalty valence="1">0</penalty>
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52 <penalty valence="2">64</penalty>
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53 </entry>
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54 <entry id="6">
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55 <elementstring>C</elementstring>
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56 <smartstring>SMARTS([$([#6D1](~[#7D2]))])</smartstring>
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57 <!--SMARTS([CD1]~[ND2]) AND element(C)</smartstring> -->
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58 <penalty valence="3">0</penalty>
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59 <penalty valence="4">1</penalty>
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60 <penalty valence="5">32</penalty>
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61 </entry>
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62 <entry id="7">
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63 <elementstring>C</elementstring>
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64 <smartstring>SMARTS([#6D1])</smartstring>
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65 <penalty valence="3">1</penalty>
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66 <penalty valence="4">0</penalty>
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67 <penalty valence="5">32</penalty>
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68 </entry>
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69 <entry id="8">
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70 <elementstring>C</elementstring>
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71 <smartstring>SMARTS([$([#6D3](~[#8D1,#16D1])(~[#8D1,#16D1]))])</smartstring>
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72 <penalty valence="4">32</penalty>
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73 <penalty valence="5">0</penalty>
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74 <penalty valence="6">32</penalty>
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75 </entry>
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76 <entry id="9">
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77 <elementstring>C</elementstring>
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78 <smartstring>SMARTS([#6])</smartstring>
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79 <penalty valence="2">64</penalty>
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81 <penalty valence="4">0</penalty>
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83 <penalty valence="6">64</penalty>
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84 </entry>
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85 <entry id="10">
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86 <elementstring>Si</elementstring>
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87 <smartstring>SMARTS([#14])</smartstring>
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88 <penalty valence="4">0</penalty>
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89 </entry>
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90 <entry id="11">
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91 <elementstring>N</elementstring>
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92 <smartstring>SMARTS([$([#7D1](~[#7D2]))])</smartstring>
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93 <penalty valence="2">0</penalty>
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94 <penalty valence="3">0</penalty>
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95 </entry>
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96 <entry id="12">
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97 <elementstring>N</elementstring>
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98 <smartstring>SMARTS([#7D1])</smartstring>
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99 <penalty valence="2">3</penalty>
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100 <penalty valence="3">0</penalty>
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101 <penalty valence="4">32</penalty>
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102 </entry>
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103 <entry id="13">
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104 <elementstring>N</elementstring>
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105 <smartstring>SMARTS([$([#7D2](~[#7D1]))])</smartstring>
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106 <penalty valence="3">1</penalty>
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107 <penalty valence="4">0</penalty>
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108 </entry>
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109 <entry id="14">
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110 <elementstring>N</elementstring>
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111 <smartstring>SMARTS([#7D2])</smartstring>
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112 <penalty valence="2">4</penalty>
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113 <penalty valence="3">0</penalty>
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114 <penalty valence="4">2</penalty>
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115 </entry>
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116 <entry id="15">
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117 <elementstring>N</elementstring>
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118 <smartstring>SMARTS([$([#7D3](~[#8D1,#16D1])~[#8D1,#16D1])])</smartstring>
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119 <penalty valence="3">64</penalty>
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120 <penalty valence="4">32</penalty>
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121 <penalty valence="5">0</penalty>
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122 <penalty valence="6">32</penalty>
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123 </entry>
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124 <entry id="16">
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125 <elementstring>N</elementstring>
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126 <!-- <smartstring>SMARTS([$(*OD1)&amp;$(*aR)&amp;n]) OR SMARTS([$(*OD1);$(*R);N])</smartstring> -->
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127 <smartstring>SMARTS([$([#7D3](~[#8D1,#16D1])(~[!#8&amp;!#16,!D1])(~[!#8&amp;!#16,!D1]))])</smartstring>
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128 <penalty valence="3">1</penalty>
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129 <penalty valence="4">0</penalty>
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130 </entry>
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131 <entry id="17">
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132 <elementstring>N</elementstring>
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133 <smartstring>SMARTS([#7D3])</smartstring>
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134 <penalty valence="2">32</penalty>
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137 <penalty valence="5">2</penalty>
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138 </entry>
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139 <entry id="18">
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140 <elementstring>N</elementstring>
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141 <smartstring>SMARTS([#7D4])</smartstring>
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142 <penalty valence="2">64</penalty>
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143 <penalty valence="3">0</penalty>
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145 </entry>
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146 <entry id="19">
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147 <elementstring>O</elementstring>
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148 <smartstring>SMARTS([#7D3](~[#8D1,#16D1])(~[!#8&amp;!#16,!D1])(~[!#8&amp;!#16,!D1])) AND element(O)</smartstring>
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149 <penalty valence="1">0</penalty>
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150 <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
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="20">
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">1</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">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
157 <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
158 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
159 <entry id="21">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
160 <elementstring>O</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
161 <smartstring>SMARTS([#8D2])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
162 <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
163 <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
164 <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
165 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
166 <entry id="22">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
167 <elementstring>P</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
168 <smartstring>SMARTS(#15D1)</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
169 <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
170 <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
171 <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
172 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
173 <entry id="23">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
174 <elementstring>P</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
175 <smartstring>SMARTS(#15D2)</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
176 <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
177 <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
178 <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
179 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
180 <entry id="24">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
181 <elementstring>P</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
182 <smartstring>SMARTS(#15D3)</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
183 <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
184 <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
185 <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
186 <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
187 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
188 <entry id="25">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
189 <elementstring>P</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
190 <!-- Note: this is _SLOW_ -->
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
191 <smartstring>SMARTS([$([#15D4](~[#8D1,#16D1])(~[!#8&amp;!#16,!D1])(~[!#8&amp;!#16,!D1])(~[#8D1,#16D1]))])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
192 <penalty valence="5">32</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
193 <penalty valence="6">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
194 <penalty valence="7">32</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
195 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
196 <entry id="26">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
197 <elementstring>P</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
198 <smartstring>SMARTS([$([#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
199 <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
200 <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
201 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
202 <entry id="27">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
203 <elementstring>P</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
204 <!-- 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
205 <smartstring>SMARTS(#15D4)</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
206 <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
207 <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
208 <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
209 <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
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="28">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
212 <elementstring>S</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
213 <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
214 <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
215 <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
216 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
217 <entry id="29">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
218 <elementstring>S</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
219 <smartstring>SMARTS([#16D1])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
220 <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
221 <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
222 <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
223 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
224 <entry id="30">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
225 <elementstring>S</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
226 <smartstring>SMARTS([#16D2])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
227 <!-- These are the penalties given in the GAFF - paper; unfortunately, the values implemented in antechamber are different!
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
228 <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
229 <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
230 <penalty valence="3">32</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
231 <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
232 <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
233 <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
234 <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
235 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
236 <entry id="31">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
237 <elementstring>S</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
238 <smartstring>SMARTS([#16D3])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
239 <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
240 <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
241 <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
242 <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
243 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
244 <entry id="32">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
245 <elementstring>S</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
246 <smartstring> SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&amp;!#16,!D1])(~[!#8&amp;!#16,!D1]))])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
247 <penalty valence="6">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
248 <penalty valence="7">32</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
249 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
250 <entry id="33">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
251 <elementstring>S</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
252 <smartstring>SMARTS([$([#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
253 <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
254 <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
255 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
256 <entry id="34">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
257 <elementstring>S</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
258 <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
259 <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
260 <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
261 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
262 <entry id="35">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
263 <elementstring>S</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
264 <smartstring>SMARTS([#16D4])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
265 <penalty valence="4">4</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
266 <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
267 <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
268 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
269 <!-- 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
marcel
parents:
diff changeset
270 <entry id="40">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
271 <elementstring>Li</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
272 <smartstring>SMARTS([#3])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
273 <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
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="41">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
276 <elementstring>Na</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
277 <smartstring>SMARTS([#11])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
278 <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
279 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
280 <entry id="42">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
281 <elementstring>Mg</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
282 <smartstring>SMARTS([#12])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
283 <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
284 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
285 <entry id="43">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
286 <elementstring>K</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
287 <smartstring>SMARTS([#19])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
288 <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
289 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
290 <entry id="44">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
291 <elementstring>Ca</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
292 <smartstring>SMARTS([#20])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
293 <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
294 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
295 <entry id="45">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
296 <elementstring>Cu</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
297 <smartstring>SMARTS([#29])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
298 <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
299 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
300 <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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301 <elementstring>Zn</elementstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
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302 <smartstring>SMARTS([#30])</smartstring>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
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303 <penalty valence="0">0</penalty>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
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304 </entry>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
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305
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
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306 </table>