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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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53 <penalty valence="4">1</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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60 <penalty valence="4">0</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)&$(*aR)&n]) OR SMARTS([$(*OD1);$(*R);N])</smartstring> -->
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122 <smartstring>SMARTS([$([#7D3](~[#8D1,#16D1])(~[!#8&!#16,!D1])(~[!#8&!#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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145 <penalty valence="4">64</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>
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151 </entry>
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152 <entry id="191"><!-- for charged O- -->
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153 <elementstring>O</elementstring>
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154 <smartstring>SMARTS([#8D1-])</smartstring>
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155 <penalty valence="1">0</penalty>
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156 <penalty valence="2">32</penalty>
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157 </entry>
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158 <entry id="192">
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159 <elementstring>O</elementstring>
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160 <smartstring>SMARTS([$([#8D1](~[#6D3]~[#8D1,#16D1]))])</smartstring>
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161 <penalty valence="1">0</penalty>
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162 <penalty valence="2">0</penalty>
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163 </entry>
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164 <entry id="19">
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165 <elementstring>O</elementstring>
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166 <smartstring>SMARTS([#7D3](~[#8D1,#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1])) AND element(O)</smartstring>
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167 <penalty valence="1">0</penalty>
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168 <penalty valence="2">1</penalty>
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169 </entry>
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170 <entry id="20">
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171 <elementstring>O</elementstring>
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172 <smartstring> SMARTS([#8D1])</smartstring>
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173 <penalty valence="1">1</penalty>
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174 <penalty valence="2">0</penalty>
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175 <penalty valence="3">64</penalty>
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176 </entry>
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177 <entry id="21">
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178 <elementstring>O</elementstring>
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179 <smartstring>SMARTS([#8D2])</smartstring>
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180 <penalty valence="1">32</penalty>
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181 <penalty valence="2">0</penalty>
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182 <penalty valence="3">64</penalty>
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183 </entry>
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184 <entry id="211">
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185 <elementstring>O</elementstring>
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186 <smartstring>SMARTS([#8D3])</smartstring>
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187 <penalty valence="3">0</penalty>
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188 </entry>
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189 <entry id="22">
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190 <elementstring>P</elementstring>
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191 <smartstring>SMARTS(#15D1)</smartstring>
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192 <penalty valence="2">2</penalty>
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193 <penalty valence="3">0</penalty>
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194 <penalty valence="4">32</penalty>
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195 </entry>
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196 <entry id="23">
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197 <elementstring>P</elementstring>
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198 <smartstring>SMARTS(#15D2)</smartstring>
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199 <penalty valence="2">4</penalty>
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200 <penalty valence="3">0</penalty>
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201 <penalty valence="4">2</penalty>
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202 </entry>
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203 <entry id="24">
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204 <elementstring>P</elementstring>
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205 <smartstring>SMARTS(#15D3)</smartstring>
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206 <penalty valence="2">32</penalty>
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207 <penalty valence="3">0</penalty>
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208 <penalty valence="4">1</penalty>
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209 <penalty valence="5">2</penalty>
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210 </entry>
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211 <entry id="251">
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212 <elementstring>P</elementstring>
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213 <!-- Note: this is _SLOW_ -->
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214 <smartstring>SMARTS([$([#15D4](~[#8D1,#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1,#8D1-,#16D1-])(~[#8D1-,#16D1-]))])</smartstring>
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215 <penalty valence="5">0</penalty>
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216 <penalty valence="6">32</penalty>
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217 </entry>
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218 <entry id="25">
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219 <elementstring>P</elementstring>
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220 <!-- Note: this is _SLOW_ -->
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221 <smartstring>SMARTS([$([#15D4](~[#8D1,#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1])(~[#8D1,#16D1]))])</smartstring>
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222 <penalty valence="5">32</penalty>
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223 <penalty valence="6">0</penalty>
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224 <penalty valence="7">32</penalty>
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225 </entry>
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226 <entry id="26">
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227 <elementstring>P</elementstring>
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228 <smartstring>SMARTS([$([#15D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&!#16,!D1]))])</smartstring>
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229 <penalty valence="6">32</penalty>
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230 <penalty valence="7">0</penalty>
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231 </entry>
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232 <entry id="27">
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233 <elementstring>P</elementstring>
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234 <!-- This rule should be the last PD4 rule because it should only match when the other rules fail! -->
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235 <smartstring>SMARTS(#15D4)</smartstring>
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236 <penalty valence="3">64</penalty>
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237 <penalty valence="4">1</penalty>
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238 <penalty valence="5">0</penalty>
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239 <penalty valence="6">32</penalty>
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240 </entry>
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241 <entry id="28">
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242 <elementstring>S</elementstring>
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243 <smartstring>SMARTS([#7D3](~[#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1])) AND element(S)</smartstring>
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244 <penalty valence="1">0</penalty>
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245 <penalty valence="2">1</penalty>
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246 </entry>
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247 <entry id="291">
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248 <elementstring>S</elementstring>
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249 <smartstring>SMARTS([$([#16D1](~[#6D3]~[#8D1,#16D1]))])</smartstring>
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250 <penalty valence="1">0</penalty>
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251 <penalty valence="2">0</penalty>
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252 </entry>
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253 <entry id="29">
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254 <elementstring>S</elementstring>
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255 <smartstring>SMARTS([#16D1])</smartstring>
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256 <penalty valence="1">2</penalty>
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257 <penalty valence="2">0</penalty>
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258 <penalty valence="3">64</penalty>
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259 </entry>
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260 <entry id="30">
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261 <elementstring>S</elementstring>
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262 <smartstring>SMARTS([#16D2])</smartstring>
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263 <penalty valence="1">2</penalty>
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264 <penalty valence="2">0</penalty>
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265 <penalty valence="3">64</penalty>
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266 </entry>
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267 <entry id="31">
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268 <elementstring>S</elementstring>
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269 <smartstring>SMARTS([#16D3])</smartstring>
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270 <penalty valence="3">1</penalty>
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271 <penalty valence="4">0</penalty>
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272 <penalty valence="5">2</penalty>
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273 <penalty valence="6">2</penalty>
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274 </entry>
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275 <entry id="32">
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276 <elementstring>S</elementstring>
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277 <smartstring> SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1]))])</smartstring>
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278 <penalty valence="6">0</penalty>
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279 <penalty valence="7">32</penalty>
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280 </entry>
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281 <entry id="331"><!--for a charged O in SO_4 -->
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282 <elementstring>S</elementstring>
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283 <smartstring>SMARTS([$([#16D4](~[#8D1-,#16D1-])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&!#16,!D1]))])</smartstring>
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284 <penalty valence="6">0</penalty>
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285 </entry>
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286 <entry id="33">
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287 <elementstring>S</elementstring>
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288 <smartstring>SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&!#16,!D1]))])</smartstring>
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289 <penalty valence="6">32</penalty>
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290 <penalty valence="7">0</penalty>
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291 </entry>
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292 <entry id="34">
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293 <elementstring>S</elementstring>
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294 <smartstring>SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1]))])</smartstring>
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295 <penalty valence="6">32</penalty>
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296 <penalty valence="7">0</penalty>
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297 </entry>
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298 <entry id="35">
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299 <elementstring>S</elementstring>
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300 <smartstring>SMARTS([#16D4])</smartstring>
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301 <penalty valence="4">4</penalty>
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302 <penalty valence="5">2</penalty>
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303 <penalty valence="6">0</penalty>
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304 </entry>
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305 <entry id="36">
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306 <elementstring>S</elementstring>
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307 <smartstring>SMARTS([#16D5])</smartstring>
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308 <penalty valence="5">2</penalty>
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309 <penalty valence="6">0</penalty>
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310 </entry>
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311 <!-- The following rules are added to cope with ions -->
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312 <entry id="40">
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313 <elementstring>Li</elementstring>
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314 <smartstring>SMARTS([#3])</smartstring>
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315 <penalty valence="0">0</penalty>
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316 </entry>
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317 <entry id="41">
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318 <elementstring>Na</elementstring>
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319 <smartstring>SMARTS([#11])</smartstring>
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320 <penalty valence="0">0</penalty>
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321 </entry>
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322 <entry id="42">
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323 <elementstring>Mg</elementstring>
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324 <smartstring>SMARTS([#12])</smartstring>
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325 <penalty valence="0">0</penalty>
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326 </entry>
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327 <entry id="43">
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328 <elementstring>K</elementstring>
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329 <smartstring>SMARTS([#19])</smartstring>
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330 <penalty valence="0">0</penalty>
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331 </entry>
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332 <entry id="44">
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333 <elementstring>Ca</elementstring>
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334 <smartstring>SMARTS([#20])</smartstring>
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335 <penalty valence="0">0</penalty>
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336 </entry>
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337 <entry id="45">
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338 <elementstring>Cu</elementstring>
|
|
|
339 <smartstring>SMARTS([#29])</smartstring>
|
|
|
340 <penalty valence="0">0</penalty>
|
|
|
341 </entry>
|
|
|
342 <entry id="46">
|
|
|
343 <elementstring>Zn</elementstring>
|
|
|
344 <smartstring>SMARTS([#30])</smartstring>
|
|
|
345 <penalty valence="0">0</penalty>
|
|
|
346 </entry>
|
|
|
347 <entry id="47">
|
|
|
348 <elementstring>Fe</elementstring>
|
|
|
349 <smartstring>SMARTS([#26])</smartstring>
|
|
|
350 <penalty valence="0">0</penalty>
|
|
|
351 </entry>
|
|
|
352 <entry id="48">
|
|
|
353 <elementstring>Cl</elementstring>
|
|
|
354 <smartstring>SMARTS([#17-])</smartstring>
|
|
|
355 <penalty valence="0">0</penalty>
|
|
|
356 </entry>
|
|
|
357 <entry id="49">
|
|
|
358 <elementstring>Cl</elementstring>
|
|
|
359 <smartstring>SMARTS([#17])</smartstring>
|
|
|
360 <penalty valence="0">64</penalty>
|
|
|
361 <penalty valence="1">0</penalty>
|
|
|
362 <penalty valence="2">64</penalty>
|
|
|
363 <penalty valence="3">128</penalty>
|
|
|
364 <penalty valence="4">128</penalty>
|
|
|
365 </entry>
|
|
|
366 </table>
|
